Counting Phylogenetic Networks with Few Reticulation Vertices: Galled and Reticulation-Visible Networks

We give exact and asymptotic counting results for the number of galled networks and reticulation-visible networks with few reticulation vertices. Our results are obtained with the component graph method, which was introduced by L. Zhang and his coauthors, and generating function techniques. For galled networks, we in addition use analytic combinatorics. Moreover, in an appendix, we consider maximally reticulated reticulation-visible networks and derive their number, too.

Enumeration, antimicrobial resistance and genomic characterization of extended-spectrum β-lactamases producing Escherichia coli from supermarket chicken meat in the United Arab Emirates

The occurrence and counts of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in retail chicken sold in the United Arab Emirates (UAE) were investigated in this study. Results indicated that 79.68 % of chicken carcasses (251/315) sampled from UAE supermarkets harbored ESBL-producing E. coli. About half (51.75 % [163/315]) of the tested samples had an ESBL-producing E. coli count range between ≥3 log₁₀ and < 5 log₁₀ CFU/g. The antimicrobial resistance profiles of a subset of 100 isolates showed high rates of non-susceptibility to clinically significant antibiotics, particularly ciprofloxacin (80 %) and cefepime (46 %). Moreover, 7 % of the isolates exhibited resistance to colistin, with PCR-based screening revealing the presence of the mcr-1 gene in all colistin-resistant isolates. Multiplex PCR screening identified bla_CTX-M and bla_TEM genes as the most frequently presented genes among the phenotypically confirmed ESBL-producing E. coli. Further whole-genome sequencing and bioinformatic analysis of 27 ESBL-producing E. coli isolates showed that the gene family bla_CTX group 1 was the most prevalent, notably CTX-M-55 (55.55 % [15/27]), followed by CTX-M-15 (22.22 % [6/27]). The most common sequence types (STs) were ST359 and ST1011, with three evident clusters identified based on phylogenomic analysis, aligned with isolates from specific production companies. Analysis of plasmid incompatibility types revealed IncFIB, IncFII, Incl2, and IncX1 as the most commonly featured plasmids. The findings of this study indicate a noticeable prevalence and high counts of ESBL-producing E. coli in chicken sampled from supermarkets in the UAE. The high rates of antimicrobial resistance to clinically important antibiotics highlight the potential public health risk associated with consuming chicken contaminated with ESBL-producing E. coli. Overall, this study emphasizes the importance of continued antimicrobial resistance monitoring in the UAE food chain and calls for further exposure risk assessment of the consumption of ESBL-producing E. coli via chicken meat.

Development of a selective medium for the enumeration of lactic acid bacteria and bifidobacteria in food products

This study was conducted to develop a selective medium for enumerating LAB and Bifidobacteria in food samples. Thirteen media were evaluated to determine their suitability for selectively enumerating LAB (17 bacilli and 7 cocci) and Bifidobacteria (12 strains) under aerobic and anaerobic conditions. When BL, BCP, and mMRS were supplemented with propionic acid (5 ml/l) and adjusted to pH 5, the growth of all indicator microorganisms was inhibited; however, these media also inhibited the growth of certain LAB and Bifidobacterial strains. Using propionic acid, the pH levels of BL, BCP, and mMRS were adjusted to pH 5.2, 6.0, and 6.0, respectively. These media inhibited the growth of all indicator microorganisms, whereas they did not inhibit any of the LAB and Bifidobacteria strains under anaerobic conditions. Overall, BLP (pH 5.8) lacking blood showed significantly higher bacterial counts compared with other media in food products. Further analyses indicated that BLP (pH 5.8) was the most suitable medium for enumerating LAB and Bifidobacteria in food.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-022-01202-z.

Meat extract casein peptone agar - A novel culture medium for the enumeration of Bacillus endospores in commercial products

Here we propose a novel culture medium, Meat Extract Casein Peptone (MECP) agar, to support the enumeration of Bacillus endospores in commercial products. The formulation is the result of screening eight different veterinary, pharmaceutical, and industrial grade peptones for the ability to support the formation of small, well-defined Bacillus colonies on solid culture medium. The impact of agar purity, agar formulation rate, and metal cation additives were examined in prototype medium batches prepared from preferred peptone inputs. A customized plate counting assay based on the resultant MECP agar formulation was compared with standardized pour-plate and spread-plate assays (ISO 4833) and flow cytometry for the ability to accurately enumerate five Bacillus-based biostimulants and biofertilizers. Estimations of Bacillus endospore concentration generated by the customized spread-plate assay were significantly higher than those produced by ISO 4833 pour-plate and spread-plate assays for four out of the five tested products and were in better agreement with flow cytometry values; however, flow cytometry values were numerically higher than values returned by both plating methods. Both flow cytometry and plating assays based on MECP or similar culture media represent potential candidates for standardization and validation through organizations such as ISO and AOAC International for the enumeration of Bacillus-based products.

Machine learning for enumeration of cell colony forming units

As one of the most widely used assays in biological research, an enumeration of the bacterial cell colonies is an important but time-consuming and labor-intensive process. To speed up the colony counting, a machine learning method is presented for counting the colony forming units (CFUs), which is referred to as CFUCounter. This cell-counting program processes digital images and segments bacterial colonies. The algorithm combines unsupervised machine learning, iterative adaptive thresholding, and local-minima-based watershed segmentation to enable an accurate and robust cell counting. Compared to a manual counting method, CFUCounter supports color-based CFU classification, allows plates containing heterologous colonies to be counted individually, and demonstrates overall performance (slope 0.996, SD 0.013, 95%CI: 0.97–1.02, p value < 1e-11, r = 0.999) indistinguishable from the gold standard of point-and-click counting. This CFUCounter application is open-source and easy to use as a unique addition to the arsenal of colony-counting tools.

Visual field asymmetries in numerosity processing

A small number of objects can be rapidly and accurately enumerated, whereas a larger number of objects can only be approximately enumerated. These subitizing and estimation abilities, respectively, are both spatial processes relying on extracting information across spatial locations. Nevertheless, whether and how these processes vary across visual field locations remains unknown. Here, we examined if enumeration displays asymmetries around the visual field. Experiment 1 tested small number (1–6) enumeration at cardinal and non-cardinal peripheral locations while manipulating the spacing among the objects. Experiment 2 examined enumeration at cardinal locations in more detail while minimising crowding. Both experiments demonstrated a Horizontal-Vertical Asymmetry (HVA) where performance was better along the horizontal axis relative to the vertical. Experiment 1 found that this effect was modulated by spacing with stronger asymmetry at closer spacing. Experiment 2 revealed further asymmetries: a Vertical Meridian Asymmetry (VMA) with better enumeration on the lower vertical meridian than on the upper and a Horizontal Meridian Asymmetry (HMA) with better enumeration along the left horizontal meridian than along the right. All three asymmetries were evident for both subitizing and estimation. HVA and VMA have been observed in a range of visual tasks, indicating that they might be inherited from early visual constraints. However, HMA is observed primarily in mid-level tasks, often involving attention. These results suggest that while enumeration processes can be argued to inherit low-level visual constraints, the findings are, parsimoniously, consistent with visual attention playing a role in both subitizing and estimation.

Counting and optimising maximum phylogenetic diversity sets

In conservation biology, phylogenetic diversity (PD) provides a way to quantify the impact of the current rapid extinction of species on the evolutionary ‘Tree of Life’. This approach recognises that extinction not only removes species but also the branches of the tree on which unique features shared by the extinct species arose. In this paper, we investigate three questions that are relevant to PD. The first asks how many sets of species of given size k preserve the maximum possible amount of PD in a given tree. The number of such maximum PD sets can be very large, even for moderate-sized phylogenies. We provide a combinatorial characterisation of maximum PD sets, focusing on the setting where the branch lengths are ultrametric (e.g. proportional to time). This leads to a polynomial-time algorithm for calculating the number of maximum PD sets of size k by applying a generating function; we also investigate the types of tree shapes that harbour the most (or fewest) maximum PD sets of size k. Our second question concerns optimising a linear function on the species (regarded as leaves of the phylogenetic tree) across all the maximum PD sets of a given size. Using the characterisation result from the first question, we show how this optimisation problem can be solved in polynomial time, even though the number of maximum PD sets can grow exponentially. Our third question considers a dual problem: If k species were to become extinct, then what is the largest possible loss of PD in the resulting tree? For this question, we describe a polynomial-time solution based on dynamical programming.

Efficiently sparse listing of classes of optimal cophylogeny reconciliations

Background

Cophylogeny reconciliation is a powerful method for analyzing host-parasite (or host-symbiont) co-evolution. It models co-evolution as an optimization problem where the set of all optimal solutions may represent different biological scenarios which thus need to be analyzed separately. Despite the significant research done in the area, few approaches have addressed the problem of helping the biologist deal with the often huge space of optimal solutions.

Results

In this paper, we propose a new approach to tackle this problem. We introduce three different criteria under which two solutions may be considered biologically equivalent, and then we propose polynomial-delay algorithms that enumerate only one representative per equivalence class (without listing all the solutions).

Conclusions

Our results are of both theoretical and practical importance. Indeed, as shown by the experiments, we are able to significantly reduce the space of optimal solutions while still maintaining important biological information about the whole space.

Chlorinated paraffins - A historical consideration including remarks on their complexity

Chlorinated paraffins (CPs) are high production volume chemicals currently produced and used in higher quantities than any other medium-size polyhalogenated compound (class). In addition, the composition of industrial CP mixtures is highly complex and poorly understood. In this article, we searched in the literature for the beginning of the chlorination of alkanes and how this substance class developed from niche applications to unmatched quantities in various industrial applications. Also, an estimation was made on the theoretical variety of chloroparaffins and the possible complexity of industrial CP mixtures. These data may explain why little is known about CPs although the production volume throughout the industrial generation was virtually always higher than the one of PCBs and has continued to increase after the ban of the latter.

Challenging the "gold standard" of colony-forming units - Validation of a multiplex real-time PCR for quantification of viable Campylobacter spp. in meat rinses

Campylobacter jejuni is the leading bacterial food-borne pathogen in Europe. Despite the accepted limits of cultural detection of the fastidious bacterium, the "gold standard" in food microbiology is still the determination of colony-forming units (CFU). As an alternative, a live/dead differentiating qPCR has been established, using propidium monoazide (PMA) as DNA-intercalating crosslink agent for inactivating DNA from dead, membrane-compromised cells. The PMA treatment was combined with the addition of an internal sample process control (ISPC), i.e. a known number of dead C. sputorum cells to the samples. The ISPC enables i), monitoring the effective reduction of dead cell signal by the light-activated DNA-intercalating dye PMA, and ii), compensation for potential DNA losses during processing. Here, we optimized the method for routine application and performed a full validation of the method according to ISO 16140-2:2016(E) for the quantification of live thermophilic Campylobacter spp. in meat rinses against the classical enumeration method ISO 10272-2:2017. In order to render the method applicable and cost-effective for practical application, the ISPC was lyophilized to be distributable to routine laboratories. In addition, a triplex qPCR was established to simultaneously quantify thermophilic Campylobacter, the ISPC and an internal amplification control (IAC). Its performance was statistically similar to the two duplex qPCRs up to a contamination level of 4.7 log₁₀Campylobacter per ml of meat rinse. The limit of quantification (LOQ) of the alternative method was around 20 genomic equivalents per PCR reaction, i.e. 2.3 log₁₀ live Campylobacter per ml of sample. The alternative method passed a relative trueness study, confirming the robustness against different meat rinses, and displayed sufficient accuracy within the limits set in ISO 16140-2:2016(E). Finally, the method was validated in an interlaboratory ring trial, confirming that the alternative method was fit for purpose with a tendency of improved repeatability and reproducibility compared to the reference method for CFU determination. Campylobacter served as a model organism, challenging CFU as "gold standard" and could help in guidance to the general acceptance of live/dead differentiating qPCR methods for the detection of food-borne pathogens.

Evaluation of Sensitivity and Cost-Effectiveness of Molecular Methods for the Co-detection of Waterborne Pathogens in India

Waterborne microbial diseases are regarded as a major public health concern, particularly in nations with poor sanitation, a lack of social awareness, and problems linked with low socioeconomic status. Waterborne pathogen identification using traditional culture methods is time-consuming and labor-intensive. As a result, there is a growing demand for quick pathogen detection technologies. High sensitivity, specificity, and rapidity are all advantages of using molecular techniques like polymerase chain reaction (PCR) in such instances. In this study, we designed multiplex PCR and quantitative real-time PCR (qPCR) assays for the co-detection and enumeration of waterborne pathogens such as Aeromonas hydrophila, Pseudomonas aeruginosa, Salmonella enterica, Yersinia enterocolitica, Escherichia coli, Vibrio cholerae, and Shigella spp. Specific primers were selected against the virulence and species-specific genes of the seven target pathogens. For all seven target organisms, the detection limits for conventional culture methods were in the range of 10³-10⁴ cells/ml. While employing multiplex PCR method in this study, Pseudomonas aeruginosa and Shigella spp. have a detection sensitivity of 10¹ cells/ml, Vibrio cholerae and Aeromonas hydrophila have a detection sensitivity of 10² cells/ml, whereas Salmonella enterica, E. coli, and Yersinia enterocolitica have a detection sensitivity of only 10³ cells/ml. According to our cost-benefit analysis, these molecular technologies are less expensive, with unit analysis costs of ₹52 and ₹173 for qPCR and multiplex PCR, respectively. Furthermore, all of the target genes had a detection limit of 1 cell/ml in qPCR. Because of their speed, sensitivity, specificity, and cost-effectiveness, these multiplex and qPCR assays could be employed for successful co-detection of aquatic pathogens.

Finding the subitizing in groupitizing: Evidence for parallel subitizing of dots and groups in grouped arrays

‘Groupitizing’ refers to the observation that visually grouped arrays can be accurately enumerated much faster than can unstructured arrays. Previous research suggests that visual grouping allows participants to draw on arithmetic abilities and possibly use mental calculations to enumerate grouped arrays quickly and accurately. Here, we address how subitizing might be involved in finding the operands for mental calculations in grouped dot arrays. We investigated whether participants can use multiple subitizing processes to enumerate both the number of dots and the number of groups in a grouped array. We found that these multiple subitizing processes can take place within 150 ms and that dots and groups seem to be subitized in parallel and with equal priority. Implications for research on mechanisms of groupitizing are discussed.

Exploring adults' awareness of and suggestions for early childhood numerical activities

This study focuses on adults who are neither preschool teachers nor professional caregivers and investigates their beliefs regarding the importance of engaging young children with numerical activities. It also examines the types of numerical activities adults report having observed children engaging with, as well as the types of activities they propose as a way for promoting counting, enumerating, recognizing number symbols, and number composition and decomposition. Findings showed that participants believed to a great extent that engaging young children with numerical activities is important. Most reported that they had observed children engaging with at least some numerical activity. In general, participants relayed more activities and more detailed activities when suggesting activities for each competency, than they did when reporting observed activities. Findings also suggested a need to enhance adults' knowledge regarding the necessity to promote verbal counting, separate from object counting, as well as to increase adults' awareness of number composition and decomposition. For mathematics educators wishing to plan workshops for adults, this study offers a method for investigating adults' knowledge of early numerical activities, as well as a starting point with which to plan appropriate workshops.

Incubation temperature and culture medium formulation impact the accuracy of pour-plate techniques for the enumeration of industrial Bacillus assemblages

Aerobic plate counting assays based on the pour-plate technique are frequently used to enumerate microbial products; however, colony swarming and merging at the agar surface can reduce the accuracy of these assays. Some plating methods mitigate this risk through the inclusion of strategies including agar overlays; however, these interventions may be inadequate to mitigate swarming and merging of certain Bacillus colonies. In the present study, we assessed the accuracy of several pour-plate techniques for the enumeration of a mixed-species Bacillus assemblage. Tested modifications included a customized culture medium formulation, agar overlays, decreased incubation times and increased incubation temperature. Methods which produced countable plates were assessed for agreement with a Bacillus-specific plate counting assay and with total cell counts rendered by flow cytometry. While all tested pour-plate methods underestimated Bacillus endospore concentrations relative to flow cytometry and customized spread-plating, our results suggest that increasing incubation temperature and the inclusion of bile salts into culture medium formulations can improve the accuracy of pour-plate techniques when used to enumerate Bacillus assemblages by decreasing the incidence of spreading colonies. As Bacillus endospore preparations become more ubiquitous in the market, familiar enumeration methods such as the pour-plate technique may require methodological modifications to ensure that the cGMP compliance of Bacillus-based microbial products is assessed accurately.

Traditional Methods of Analysis for Listeria monocytogenes

Conventional methods for the detection of Listeria monocytogenes in foods and environmental samples rely on selective pre-enrichment, enrichment, and plating. This is followed by confirmation of suspected colonies by testing a limited number of biochemical markers.

A probabilistic approach for quantifying children's subitizing span

The development of enumeration skills over childhood is thought to reflect improvements in both subitizing (for small sets) and serial counting (for larger sets). However, investigations into the contribution of subitizing to advancing mathematics ability are limited by challenges in measuring subitizing capacity across developmental populations. Subitizing capacity in adults is traditionally assessed by calculating the bilinear inflection point for reaction times or accuracy across set sizes, but in children greater variability and dramatic improvements in counting ability introduce problems with this approach. This study demonstrates this limitation in a sample of elementary school children and proposes a novel probabilistic approach to measuring subitizing capacity. This metric captures well-established trends in the development of children's subitizing. Furthermore, the proposed metric predicts unique variance in symbolic arithmetic ability, corroborating previous research that suggests a foundational role for subitizing in the development of numerical cognition. Findings demonstrate the advantages of a probabilistic approach to determining subitizing capacity in young children and suggest that it may be practically and theoretically well-suited for investigating subitizing and its role in mathematics development.

Survival of a serotype 4b strain and a serotype 1/2a strain of Listeria monocytogenes, isolated from a stone fruit outbreak investigation, on whole stone fruit at 4 °C

In the summer of 2014, a multistate outbreak of listeriosis associated with contaminated stone fruit (peach and nectarine) was reported. A serotype 4b variant Listeria monocytogenes (Lm) strain of singleton Sequence Type (ST) 382 was isolated from clinical samples and stone fruit associated with the outbreak. A serotype 1/2b Lm strain of ST5, Clonal Complex 5 was isolated only from outbreak-associated stone fruit, not from clinical samples. Here we investigated the fate of the serotype 4b and 1/2b strains, at two inoculation levels (high level at 3.7 logCFU/fruit and low level at 2.7 logCFU/fruit), on the surfaces of white peach, yellow peach and yellow nectarine stored at 4 °C for 26 days. After rinsing the fruits, we determined the Lm levels in the rinsates and on the peels. We enumerated Lm using a direct plating method and compared two chromogenic agars. The Lm populations rapidly declined in the first 3 days and then declined more slowly until Day 19/21. The maximum decline was 1.6 logCFU/fruit on yellow peach inoculated with serotype 4b at high level. For fruits inoculated with high-level Lm, the lowest level of Lm (1.7 logCFU/fruit) was observed on for white peach inoculated with serotype 1/2b, and the highest level of Lm (2.6 logCFU/fruit) on Day 19/21 was observed on yellow peach inoculated with the serotype 1/2b strain. For fruits inoculated with low-level Lm, the lowest level of Lm (1.3 logCFU/fruit) was observed on yellow nectarine inoculated with either the serotype 4b or 1/2b strain, and the highest level of Lm (1.7 logCFU/fruit) on Day 19/21 was observed on yellow peach inoculated with ST382. The D-values ranged from 15 days to 28 days. Lm remained viable until the end of storage (Day 26), but the levels were not significantly different from those on Day 19/21. The types of stone fruit and Lm strain did not significantly affect the survival of Lm. These results demonstrate that contaminated stone fruit can carry a potential risk for causing listeriosis in susceptible populations. Comparison of direct plating results using two chromogenic agars showed that RAPID' L. mono and Agar Listeria Ottavani & Agosti performed equivalently for enumerating Lm on stone fruit. The fruit rinsing recovered 80% to 84% of Lm from fruit surfaces.

Subitizing object parts reveals a second stage of individuation

Humans can efficiently individuate a small number of objects. This subitizing ability is thought to be a consequence of limited attentional resources. However, how and what is selected during the individuation process remain outstanding questions. We investigated these in four experiments by examining if parts of objects are enumerated as efficiently as distinct objects in the presence and absence of distractor objects. We found that distractor presence reduced subitizing efficiency. Crucially, parts connected to multiple objects were enumerated less efficiently than independent objects or parts connected to a single object. These results argue against direct individuation of parts and show that objecthood plays a fundamental role in individuation. Objects are selected first and their components are selected in subsequent steps. This reveals that individuation operates sequentially over multiple levels.

Evaluation of a new culture medium for the enumeration and isolation of Streptococcus salivarius subsp. thermophilus from cheese

Enumeration and isolation of Streptococcus salivarius subsp. thermophilus from cheese is challenging, due to the relatively high number of species it may host. We describe medium SPY9.3 for the cultivation of S. salivarius subsp. thermophilus from cheese. The medium and related incubation conditions (SPY) was compared with 2 other protocols, M17 and ST: sensitivity was assessed by parallel cultivation of 55 strains of S. salivarius subsp. thermophilus, and selectivity by (i) parallel cultivation of 60 strains belonging to 20 different non-target species and sub-species and (ii) isolating bacteria from 3 raw-milk cheeses. Colony counts were similar on SPY9.3 and M17 (mean difference 0.07 log(cfu/mL), p > 0.001) and significantly higher on ST than on M17 and SPY9.3 (mean differences 0.42 and 0.48 log(cfu/mL), respectively, p < 0.001). SPY was more specific than ST and M17, with respectively 20%, 40%, and 50% of the investigated non-target species able to grow. S. salivarius subsp. thermophilus, Enterococcus spp., and Staphylococcus aureus were indistinguishable using all 3 protocols. Only SPY avoided growth of Lactobacillus delbrueckii subsp. lactis. Finally, ST and SPY displayed higher recoveries of S. salivarius subsp. thermophilus colonies from cheese than M17 (5.6, 5.5, and 3.0 adjusted log(cfu/mL), respectively) and the lowest proportion of non-specific isolates. The protocol described here and based on SPY9.3 presents a promising alternative to existing protocols for the enumeration and isolation of S salivarius subsp. thermophilus from cheese or other complex fermented products.

Does the standard search task predict performance in related tasks for Kanizsa-style illusory contours?

It is often assumed that results from standard visual search tasks will be replicated in related tasks but his idea is rarely tested. In a conceptual replication of Li, Cave, and Wolfe (2008), we investigated the attentional demands of Kanizsa-style illusory contours using orientation-based search, comparing performance for items defined by real- as compared to illusory contours. After confirming the initial findings in standard search, we tested the same manipulation in multiple-target search, Thornton and Gilden's (2007) hybrid standard/multiple-target search, and simple- and selective enumeration. The RT slope differences between real- and illusory contours did not replicate in Thornton and Gilden's task, though they did in multiple-target search and selective enumeration. In fact, absolute differences between real- and illusory contours in RT costs per distractor were 2 - 6 times larger than in standard search. To determine whether performance differences between real and illusory contours originated from shape-definition (necessary for distinguishing target shapes from distractors) or unit formation (grouping disconnected parts to define an item/unit), simple and selective enumeration were compared. The differences between real- and illusory-contours only emerged in selective enumeration (enumerating targets among distractors), which suggests the discrepancies between conditions originate from shape definition rather than unit formation processes. There was no evidence of subitizing in selective enumeration for illusory contour figures, but contrary to attention-based theories of enumeration, there was no subitizing for the real-contour controls either. This study contributes to research on illusory contours but it is especially important to the study of search and enumeration.

3M Petrifilm Lactic Acid Bacteria Count Plate Is a Reliable Tool for Enumerating Lactic Acid Bacteria in Bacon

ABSTRACT

This study aimed to evaluate the behavior of Petrifilm Lactic Acid Bacteria Count Plates (PLAB) as an alternative methodology to enumerate lactic acid bacteria (LAB) in bacon. Bacon samples (n = 40) were obtained from retail sale, 10-fold diluted with buffered peptone water (BPW, 0.2% [w/v]) and Letheen broth, and subjected to LAB enumeration according to four protocols: (i) de Man Rogosa Sharpe (MRS) agar, pH 5.7, 30°C; (ii) MRS, pH 5.7, 30°C, anaerobiosis; (iii) all-purpose Tween agar (APT), 25°C; and (iv) PLAB, 30°C. Colonies were enumerated at 24, 48, and 72 h, and the results expressed as log CFU per gram for comparison by analysis of variance and regression (P < 0.05). Furthermore, colonies were randomly selected and characterized as LAB (Gram staining and catalase). Mean LAB counts from MRS and PLAB did not present significant differences independently of incubation time or diluent (P > 0.05), whereas counts in APT with BPW after 24 h were significantly lower (P < 0.05). PLAB counts with BPW (24, 48, and 72 h) presented significant correlation with MRS (r ranging from 0.87 to 0.89; in anaerobiosis, r ranging from 0.94 to 0.95) and APT (r ranging from 0.84 to 0.86). With Letheen broth, PLAB (24, 48, and 72 h) presented significant correlation with MRS (r ranging from 0.92 to 0.94; in anaerobiosis, r ranging from 0.93 to 0.96) and APT (r ranging from 0.77 to 0.79). In total, 1,032 colonies (97%) from 1,063 colonies were characterized as LAB. Thus, PLAB can be considered as an alternative tool for enumerating LAB in bacon, with reliable results even after 24 h of incubation.

HIGHLIGHTS

CompRet: a comprehensive recommendation framework for chemical synthesis planning with algorithmic enumeration

In computer-assisted synthesis planning (CASP) programs, providing as many chemical synthetic routes as possible is essential for considering optimal and alternative routes in a chemical reaction network. As the majority of CASP programs have been designed to provide one or a few optimal routes, it is likely that the desired one will not be included. To avoid this, an exact algorithm that lists possible synthetic routes within the chemical reaction network is required, alongside a recommendation of synthetic routes that meet specified criteria based on the chemist’s objectives. Herein, we propose a chemical-reaction-network-based synthetic route recommendation framework called “CompRet” with a mathematically guaranteed enumeration algorithm. In a preliminary experiment, CompRet was shown to successfully provide alternative routes for a known antihistaminic drug, cetirizine. CompRet is expected to promote desirable enumeration-based chemical synthesis searches and aid the development of an interactive CASP framework for chemists.

The association between visual attention and arithmetic competence: The mediating role of enumeration

The current study aimed at clarifying the nature of relation between visual attention and arithmetic competence. A group of 301 Chinese second graders was assessed. Children's visual attention was measured using two versions of a visual search task, with efficient visual search (the similarity between the target and the distractors is low) tapping automatic, stimulus-driven visual attention and inefficient visual search (the similarity between the target and the distractors is high) tapping effortful, goal-directed visual attention. Children's arithmetic competence, enumeration skills (assessed in about half of the participants), and other domain-general cognitive abilities were also assessed. The results suggest that only inefficient visual search significantly predicted children's arithmetic competence, and such a relation was mediated through their enumeration skills. The findings highlight the role of fundamental cognitive capacities in mathematics learning and provide insights into potential interventions for improving children's arithmetic competence.

Cell Enumeration of Leptospira by Flow Cytometry

Rapid and reliable enumeration of Leptospira spp., the causative agent of leptospirosis, represents a technical challenge because leptospires are thin, highly motile, and slow-growing bacteria. The current gold standard for cell enumeration is the use of a Petroff-Hausser counting chamber and a dark-field microscope, but this method remains time-consuming and lacks reproducibility. New alternative techniques are then of great interest. Here we describe the protocol for counting leptospires by flow cytometry. This method is rapid, reproducible, sensitive, and hence suitable to become a new standard to enumerate Leptospira spp.

Enumeration of various Ayurvedic formulations listed in an ancient palm-leaf manuscript of Rayalaseema region in Andhra Pradesh state, India

ETHNOPHARMACOLOGICAL RELEVANCE

Ancient India relied on manuscripts written by scholars for storing, transferring and retrieving the information pertaining to culture, traditions, religion, geography and political issues. Similarly, Ayurveda, an ancient human health care management system in India and most of its information is available through palm-leaf manuscripts. Though each palm-leaf can persist for a fairly long time, it suffers gradual deterioration owing to physical, chemincal and biological factors, thus warranting digitiation. The palm-leaf manuscripts of Ayurveda are extensively studied for finding new drug or treatment methods to new-age diseases.

AIM OF THE STUDY

The present study concerns an unpublished ancient Telugu palm-leaf manuscript containing Ayurvedic medicine information enscripted on 33 palm-leaves. Since the palm-leaf manuscript is very old, the manual documentation, translation, digitization and analysis of it may shed light on hidden ayurvedic information that may be useful to the modern society.

MATERIALS AND METHODS

The palm-leaf manuscript with 33 folios were manually documented and digitized into a Telugu book followed by translation into English. The scientific names of historical diseases, plants, animals, metals and minerals were identified based on published sources.

RESULTS

A critical scrutiny of the palm-leaf manuscript revealed 120 formulations with 164 plants for 29 different kinds of diseases such as meha and prameha (urinary problems), eye diseases, skin diseases, respiratory diseases, fevers, digestive disorders, jaundice, tuberculosis, cancer and so on. Plant and animal products, metals and minerals mentioned in the said formulations were identified and listed.

CONCLUSION

Basing on our study, it is concluded that the said manuscript contains mono-or poly-herbo-mineral formulations for the treatment of various ailments.This information can be incorporated into and compared with available data bases to find out the effectiveness of the drug or formulation for any given diseases. Further validation of the formulations can be done by phytochemical and in vivo pharmacological assays.

How to think with models and targets: Hepatitis C elimination as a numbering performance

The field of public health is replete with mathematical models and numerical targets. In the case of disease eliminations, modelled projections and targets play a key role in evidencing elimination futures and in shaping actions in relation to these. Drawing on ideas within science and technology studies, we take hepatitis C elimination as a case for reflecting on how to think with mathematical models and numerical targets as 'performative actors' in evidence-making. We focus specifically on the emergence of 'treatment-as-prevention' as a means to trace the social and material effects that models and targets make, including beyond science. We also focus on how enumerations are made locally in their methods and events of production. We trace the work that models and targets do in relation to three analytical themes: governing; affecting; and enacting. This allows us to situate models and targets as technologies of governance in the constitution of health, which affect and are affected by their material relations, including in relation to matters-of-concern which extend beyond calculus. By emphasising models and targets as enactments, we draw attention to how these devices give life to new enumerated entities, which detach from their calculative origins and take flight in new ways. We make this analysis for two reasons: first, as a call to bring the social and enumeration sciences closer together to speculate on how we might think with models and targets differently and more carefully; and second, to encourage an approach to science which treats evidencing-making interventions, such as models and targets, as performative and political.

The role of attention in the enumeration of canonical patterns

We report novel findings from experiments on the enumeration of canonical patterns under attentional load. While previous studies have shown that the process of enumerating randomized arrangements can be disrupted by attentional load, the effect of attentional load on canonical patterns has been unexplored. To investigate this case, we adapted a spatial dual-task paradigm previously used to study attentional disruption during the enumeration of randomized arrangements. We begin by replicating previous findings for randomized arrangements, with enumeration error increasing with cluster numerosity and attentional load. For dice patterns, enumeration error also increased under attentional load. However, contrary to findings from studies on single-task enumeration of dice patterns, we observed conflation of patterns with similar outlines. In subsequent experiments, we manipulated the spatial location of the enumeration task, placing the dot cluster in the center. With centrally located, canonical patterns that remained in the same location across trials, enumeration accuracy was more consistent with results from single-task studies. We hypothesize that participants may be using shape cues to inform guessing during enumeration tasks when unable to both localize and fully attend to target patterns.

Individuation of object parts in aging

Research on enumeration with isolated objects has indicated that young and older adults can report up to three elements with similar efficiency (subitizing effect). Recent studies on subitizing in young adults have shown that individuation occurs over parts of an object as efficiently as over physically disconnected objects, suggesting that spatial separation is a sufficient requirement for efficient individuation. Do young and older adults share this sufficient requirement? In two experiments, we tested for the presence of subitizing in an enumeration task with a varying number of distinct objects and object parts. In Experiment 1, results indicated the presence of a bilinear function (with an inflection point between 3 and 4 elements, a proxy for subitizing) in the response speed of young and older adults, and in both stimulus conditions. In addition, the enumeration slope in older participants was steeper for object parts than for objects in the subitizing range, possibly due to perceptual degradation (e.g., in contour detection). The pattern found generalizes to other stimuli (Experiment 2), thus highlighting the robustness of the present findings. Overall, the results indicate that while some perceptual factors (such as contour detection or curvature polarity) may hamper subitizing speed of older individuals relative to young adults, the subitizing span remains at approximately three to four elements for multiple objects and object parts in both young and older adults. Thus, individuation of multiple objects and object parts is a mechanism relatively resistant to aging.

Enumeration strategy differences revealed by saccade-terminated eye tracking

Brain regions involved in saccadic eye movements partially overlap with a frontoparietal network implicated in encoding numerosities. Eye movement patterns may plausibly reflect strategic scanning behaviours to resolve the open-ended task of efficiently enumerating visual arrays. If so, these patterns may help explain individual differences in enumeration acuity in terms of well-understood visual attention mechanisms. Most enumeration eye-tracking paradigms, however, do not allow for direct manipulation of eye movement behaviours to test these claims. In the current study we terminated trials after a specified number of saccades to systematically probe the time course of enumeration strategies. Fifteen adults (11 naïve, 4 informed) enumerated random dot arrays under three conditions: (1) a novel saccade-terminated design where arrays were visible until one, two or four saccades had occurred; (2) a duration-terminated design where arrays were shown for 250, 500 or 1000 ms; and (3) a response-terminated design where arrays were visible until a response. Participants gave more accurate responses when enumerating saccade-terminated trials despite taking a similar time as in the duration-terminated trials. When participants were informed how trials would terminate, their saccade onset latencies shifted to match task demands. Rotating saccade vectors to align with salient image locations accounted for variability in the orientation of saccade trajectories. These findings (1) show a combination of stimulus-derived visual processing and task-based strategic demands account for enumeration eye movements patterns, (2) validate a novel saccade-contingent trial termination procedure for studying sequences of enumeration eye movements, and (3) highlight the need to include analyses of spatial and temporal eye movement patterns into models of visual enumeration strategies.

Estimating obstetric and gynecologic surgical rate: A benchmark of surgical capacity building in Ghana

OBJECTIVE

To estimate the annual rate of obstetric and gynecologic (ObGyn) operations performed in Ghana and establish a baseline for tracking the expansion of Ghana's surgical capacity.

METHODS

Data were obtained for ObGyn operations performed in Ghana between 2014 and 2015 from a nationally representative sample of hospitals and scaled up for national estimates. Operations were classified as "essential" or "other" according to The World Bank's Disease Control Priorities Project. Data were used to calculate cesarean-to-total-operation ratio (CTR) and estimate the rate of cesarean deliveries based on the number of live births in 2014.

RESULTS

A total of 90 044 (95% uncertainty interval [UI] 69 461-110 628) ObGyn operations were performed nationally over the 1-year period, yielding an annual national ObGyn operation rate of 881/100 000 females aged 12 years and over (95% UI 679-1082). Eighty-seven percent were essential procedures, 80% of which were cesarean deliveries. District hospitals performed 71% of ObGyn operations. The national rate of cesarean deliveries was 7.2% and the CTR was 0.27.

CONCLUSION

The cesarean delivery rate of 7.2% suggests inadequate access to obstetric care. The CTR of 0.27 suggests inadequate overall surgical capacity. These measures, along with estimates of distribution of procedures by hospital level, provide useful baseline data to support surgical capacity building efforts in Ghana and similar countries.

Mapping and enumerating houses and households to support malaria control interventions on Bioko Island

BACKGROUND

Housing mapping and household enumeration are essential for the planning, implementation, targeting, and monitoring of malaria control interventions. In many malaria endemic countries, control efforts are hindered by incomplete or non-existent housing cartography and household enumeration. This paper describes the development of a comprehensive mapping and enumeration system to support the Bioko Island Malaria Control Project (BIMCP).

RESULTS

A highly detailed database was developed to include every housing unit on Bioko Island and uniquely enumerate the associated households residing in these houses. First, the island was divided into a virtual, geo-dereferenced grid of 1 × 1 km sequentially numbered map-areas, each of which was in turn subdivided into one hundred, 100 × 100 m sequentially numbered map-sectors. Second, high-resolution satellite imagery was used to sequentially and uniquely identify all housing units within each map-sector. Third, where satellite imagery was not available, global positioning systems (GPS) were used as the basis for uniquely identifying and mapping housing units in a sequential manner. A total of 97,048 housing units were mapped by 2018, 56% of which were concentrated in just 5.2% of Bioko Island's total mapped area. Of these housing units, 70.7% were occupied, thus representing uniquely identified households.

CONCLUSIONS

The housing unit mapping and household enumeration system developed for Bioko Island enabled the BIMCP to more effectively plan, implement, target, and monitor malaria control interventions. Since 2014, the BIMCP has used the unique household identifiers to monitor all household-level interventions, including indoor residual spraying, long-lasting insecticide-treated nets distribution, and annual malaria indicator surveys. The coding system used to create the unique housing unit and household identifiers is highly intuitive and allows quick location of any house within the grid without a GPS. Its flexibility has permitted the BIMCP to easily take into account the rapid and substantial changes in housing infrastructure. Importantly, by utilizing this coding system, an unprecedented quantity and diversity of detailed, geo-referenced demographic and health data have been assembled that have proved highly relevant for informing decision-making both for malaria control and potentially for the wider public health agenda on Bioko Island.

Visual search does not always predict performance in tasks that require finding targets among distractors: The case of line-ending illusory contours

The standard visual search task is integral to the study of selective attention and in search tasks target present slopes are the primary index of attentional demand. However, there are times when similarities in slopes may obscure important differences between conditions. To demonstrate this point, we used the case of line-ending illusory contours, building on a study by Li, Cave, and Wolfe (2008) where orientation-based search for figures defined by line-ending illusory contours was compared to that for the corresponding real-contour controls. Consistent with Li et al. (2008), we found search to be efficient for both illusory contour figures and the corresponding real-contour controls, with no significant differences between them. However, major differences between illusory contours and the real-contour controls emerged in selective enumeration, a task where participants enumerated targets in a display of distractors, with the number of targets and distractors manipulated. When looking at the distractor slopes, the increase in RT to enumerate a single target as a function of the number of distractors (a direct analogue to target present trials, with identical displays), we found distractor costs for illusory contour figures to be over 100 ms/distractor higher than for the corresponding real-contour controls. Furthermore, the discrepancies in RT slope between 1-3 and 6-8 targets associated with subitizing were only seen in the real-contour controls. These results show that similarities in RT slopes in search may mask important differences between conditions that emerge in other tasks.

Associations of processing level variables with Salmonella prevalence and concentration on broiler chicken carcasses and parts in Canada

A national baseline study was conducted between December 2012 and December 2013 to determine the pre-packaging prevalence and concentration of foodborne pathogens on broiler chicken carcasses and parts at processing; a survey was implemented simultaneously to collect data on the processing practices used to control these pathogens. Thirty federally-registered Canadian poultry processing establishments completed the questionnaire. A total of 2,732 samples of carcasses and parts (breast and thigh pieces) were collected over the study period from these establishments. For Salmonella, the overall proportion positive was 0.22 (95% CI 0.20, 0.23), and the mean concentration was 0.67 (95% CI 0.51, 0.83) MPN/mL of rinse fluid. Multivariable regression models with random intercepts for the establishment and the date of sampling were used to identify associations between Salmonella prevalence and concentration and processing practices. In the final logistic regression model for the prevalence outcome (positive or negative sample), there were three statistically significant variables: product type (carcass or part); chilling method (water or air); and chlorine use in the establishment (chlorine, cetylpyridinium chloride, or neither). The likelihood of testing positive for Salmonella was higher on parts than carcasses (OR 3.03, 95% CI 2.38, 3.86), and higher when cetylpyridinium chloride was used (OR 2.00, 95% CI 1.36, 2.95), or when other processing aids were used (OR 1.99, 95% CI 1.26, 3.15), than when chlorine was used. Water chilling was negatively associated with testing positive for Salmonella when compared with air chilling (OR 0.68, 95% CI 0.48, 0.96). In the final linear regression model for the concentration outcome (log₁₀ MPN/mL), there was one statistically significant variable chilling method, where water chilling was associated with a decrease in concentration (β -0.23, 95% CI -0.38, -0.08 log₁₀ MPN/mL). The intraclass correlation coefficients for establishment and date sampling were 0.02 and 0.23 in the linear regression model, and 0.01 and 0.34 in the logistic regression model, respectively. Further studies to explore the methods to reduce microbial contamination during the air chilling and cut-up and boning processes in broiler chicken establishments in Canada are recommended.

Environmental inactivation and irrigation-mediated regrowth of Escherichia coli O157:H7 on romaine lettuce when inoculated in a fecal slurry matrix

Field trials were conducted in July-August and October 2012 to quantify the inactivation rate of Escherichia coli O157:H7 when mixed with fecal slurry and applied to romaine lettuce leaves. Lettuce was grown under commercial conditions in Salinas Valley, California. One-half milliliter of rabbit, chicken, or pig fecal slurry, containing an average of 4.05 × 107 CFU E. coli O157:H7 (C0), was inoculated onto the upper (adaxial) surface of a lower leaf on 288 heads of lettuce per trial immediately following a 2.5 h irrigation event. To estimate the bacterial inactivation rate as a function of time, fecal matrix, irrigation and seasonal climate effects, sets of lettuce heads (n = 28) were sampled each day over 10 days and the concentration of E. coli O157:H7 (Ct) determined. E. coli O157:H7 was detected on 100% of heads during the 10-day duration, with concentrations ranging from ≤340 MPN/head (∼5-log reduction) to >3.45 × 1012 MPN/head (∼5-log growth). Relative to C0, on day 10 (Ct = 12) we observed an overall 2.6-log and 3.2-log mean reduction of E. coli O157:H7 in July and October, respectively. However, we observed relative maximum concentrations due to bacterial growth on day 6 (maximum Ct = 8) apparently stimulated by foliar irrigation on day 5. From this maximum there was a mean 5.3-log and 5.1-log reduction by day 10 (Ct = 12) for the July and October trials, respectively. This study provides insight into the inactivation and growth kinetics of E. coli O157:H7 on romaine lettuce leaves under natural field conditions. This study provides evidence that harvesting within 24 h post irrigation has the potential to increase the concentration of E. coli O157:H7 contamination, if present on heads of romaine lettuce; foliar irrigation can temporarily stimulate substantial regrowth of E. coli O157:H7.

Enumeration of CD34-positive Stem Cells Using the ADAMII Image-based Fluorescence Cell Counter

Background

It is very important to accurately enumerate CD34-positive (CD34+) cells for successful hematopoietic stem cell transplantation (HSCT). We evaluated the ability of the newly developed image based-immunofluorescence cell counter ADAMII (NanoEntek, Seoul, Korea) to enumerate CD34+ cells, which was improved through simultaneous CD45 analysis.

Methods

We enumerated CD34+ cells with ADAMII using 19 peripheral blood (PB) and 91 leukapheresis samples from HSCT donors. Analytical performance, including precision and linearity, was analyzed, and sample stability during storage was evaluated. Viable CD34+ cell count (vCD34) and viable CD45+ cell count (vCD45) and the percentage of viable CD34+ cells among viable CD45+ cells (CD34/CD45) as measured by ADAMII were compared with the corresponding values from two flow cytometry assays, using regression analysis.

Results

ADAMII demonstrated acceptable precision, as CV values of vCD34 from six samples with different counts were all <10% (range: 3.49–9.51%). CV values of the vCD45 and CD34/45 ranged from 4.03% to 9.67% and from 2.48% to 10.07%, respectively. The linearity of vCD34 showed an excellent R² value (0.99) when analyzed using the intended count and flow cytometry data. The ADAMII and two flow cytometry-based assays generated very similar data for the PB and leukapheresis samples.

Conclusions

ADAMII demonstrated excellent performance for use as a routine clinical assay in terms of CD34+ cell enumeration from PB and leukapheresis samples. Moreover, it could be used as a point-of-care-test for determining mobilization time and predicting an adequate apheresis stem cell product.

Attractor Stability in Finite Asynchronous Biological System Models

We present mathematical techniques for exhaustive studies of long-term dynamics of asynchronous biological system models. Specifically, we extend the notion of [Formula: see text]-equivalence developed for graph dynamical systems to support systematic analysis of all possible attractor configurations that can be generated when varying the asynchronous update order (Macauley and Mortveit in Nonlinearity 22(2):421, 2009). We extend earlier work by Veliz-Cuba and Stigler (J Comput Biol 18(6):783-794, 2011), Goles et al. (Bull Math Biol 75(6):939-966, 2013), and others by comparing long-term dynamics up to topological conjugation: rather than comparing the exact states and their transitions on attractors, we only compare the attractor structures. In general, obtaining this information is computationally intractable. Here, we adapt and apply combinatorial theory for dynamical systems from Macauley and Mortveit (Proc Am Math Soc 136(12):4157-4165, 2008. https://doi.org/10.1090/S0002-9939-09-09884-0 ; 2009; Electron J Comb 18:197, 2011a; Discret Contin Dyn Syst 4(6):1533-1541, 2011b. https://doi.org/10.3934/dcdss.2011.4.1533 ; Theor Comput Sci 504:26-37, 2013. https://doi.org/10.1016/j.tcs.2012.09.015 ; in: Isokawa T, Imai K, Matsui N, Peper F, Umeo H (eds) Cellular automata and discrete complex systems, 2014. https://doi.org/10.1007/978-3-319-18812-6_6 ) to develop computational methods that greatly reduce this computational cost. We give a detailed algorithm and apply it to (i) the lac operon model for Escherichia coli proposed by Veliz-Cuba and Stigler (2011), and (ii) the regulatory network involved in the control of the cell cycle and cell differentiation in the Caenorhabditis elegans vulva precursor cells proposed by Weinstein et al. (BMC Bioinform 16(1):1, 2015). In both cases, we uncover all possible limit cycle structures for these networks under sequential updates. Specifically, for the lac operon model, rather than examining all [Formula: see text] sequential update orders, we demonstrate that it is sufficient to consider 344 representative update orders, and, more notably, that these 344 representatives give rise to 4 distinct attractor structures. A similar analysis performed for the C. elegans model demonstrates that it has precisely 125 distinct attractor structures. We conclude with observations on the variety and distribution of the models' attractor structures and use the results to discuss their robustness.

Attractor Stability in Finite Asynchronous Biological System Models

We present mathematical techniques for exhaustive studies of long-term dynamics of asynchronous biological system models. Specifically, we extend the notion of [Formula: see text]-equivalence developed for graph dynamical systems to support systematic analysis of all possible attractor configurations that can be generated when varying the asynchronous update order (Macauley and Mortveit in Nonlinearity 22(2):421, 2009). We extend earlier work by Veliz-Cuba and Stigler (J Comput Biol 18(6):783-794, 2011), Goles et al. (Bull Math Biol 75(6):939-966, 2013), and others by comparing long-term dynamics up to topological conjugation: rather than comparing the exact states and their transitions on attractors, we only compare the attractor structures. In general, obtaining this information is computationally intractable. Here, we adapt and apply combinatorial theory for dynamical systems from Macauley and Mortveit (Proc Am Math Soc 136(12):4157-4165, 2008. https://doi.org/10.1090/S0002-9939-09-09884-0 ; 2009; Electron J Comb 18:197, 2011a; Discret Contin Dyn Syst 4(6):1533-1541, 2011b. https://doi.org/10.3934/dcdss.2011.4.1533 ; Theor Comput Sci 504:26-37, 2013. https://doi.org/10.1016/j.tcs.2012.09.015 ; in: Isokawa T, Imai K, Matsui N, Peper F, Umeo H (eds) Cellular automata and discrete complex systems, 2014. https://doi.org/10.1007/978-3-319-18812-6_6 ) to develop computational methods that greatly reduce this computational cost. We give a detailed algorithm and apply it to (i) the lac operon model for Escherichia coli proposed by Veliz-Cuba and Stigler (2011), and (ii) the regulatory network involved in the control of the cell cycle and cell differentiation in the Caenorhabditis elegans vulva precursor cells proposed by Weinstein et al. (BMC Bioinform 16(1):1, 2015). In both cases, we uncover all possible limit cycle structures for these networks under sequential updates. Specifically, for the lac operon model, rather than examining all [Formula: see text] sequential update orders, we demonstrate that it is sufficient to consider 344 representative update orders, and, more notably, that these 344 representatives give rise to 4 distinct attractor structures. A similar analysis performed for the C. elegans model demonstrates that it has precisely 125 distinct attractor structures. We conclude with observations on the variety and distribution of the models' attractor structures and use the results to discuss their robustness.

Attractor Stability in Finite Asynchronous Biological System Models

We present mathematical techniques for exhaustive studies of long-term dynamics of asynchronous biological system models. Specifically, we extend the notion of [Formula: see text]-equivalence developed for graph dynamical systems to support systematic analysis of all possible attractor configurations that can be generated when varying the asynchronous update order (Macauley and Mortveit in Nonlinearity 22(2):421, 2009). We extend earlier work by Veliz-Cuba and Stigler (J Comput Biol 18(6):783-794, 2011), Goles et al. (Bull Math Biol 75(6):939-966, 2013), and others by comparing long-term dynamics up to topological conjugation: rather than comparing the exact states and their transitions on attractors, we only compare the attractor structures. In general, obtaining this information is computationally intractable. Here, we adapt and apply combinatorial theory for dynamical systems from Macauley and Mortveit (Proc Am Math Soc 136(12):4157-4165, 2008. https://doi.org/10.1090/S0002-9939-09-09884-0 ; 2009; Electron J Comb 18:197, 2011a; Discret Contin Dyn Syst 4(6):1533-1541, 2011b. https://doi.org/10.3934/dcdss.2011.4.1533 ; Theor Comput Sci 504:26-37, 2013. https://doi.org/10.1016/j.tcs.2012.09.015 ; in: Isokawa T, Imai K, Matsui N, Peper F, Umeo H (eds) Cellular automata and discrete complex systems, 2014. https://doi.org/10.1007/978-3-319-18812-6_6 ) to develop computational methods that greatly reduce this computational cost. We give a detailed algorithm and apply it to (i) the lac operon model for Escherichia coli proposed by Veliz-Cuba and Stigler (2011), and (ii) the regulatory network involved in the control of the cell cycle and cell differentiation in the Caenorhabditis elegans vulva precursor cells proposed by Weinstein et al. (BMC Bioinform 16(1):1, 2015). In both cases, we uncover all possible limit cycle structures for these networks under sequential updates. Specifically, for the lac operon model, rather than examining all [Formula: see text] sequential update orders, we demonstrate that it is sufficient to consider 344 representative update orders, and, more notably, that these 344 representatives give rise to 4 distinct attractor structures. A similar analysis performed for the C. elegans model demonstrates that it has precisely 125 distinct attractor structures. We conclude with observations on the variety and distribution of the models' attractor structures and use the results to discuss their robustness.

Attractor Stability in Finite Asynchronous Biological System Models

We present mathematical techniques for exhaustive studies of long-term dynamics of asynchronous biological system models. Specifically, we extend the notion of [Formula: see text]-equivalence developed for graph dynamical systems to support systematic analysis of all possible attractor configurations that can be generated when varying the asynchronous update order (Macauley and Mortveit in Nonlinearity 22(2):421, 2009). We extend earlier work by Veliz-Cuba and Stigler (J Comput Biol 18(6):783-794, 2011), Goles et al. (Bull Math Biol 75(6):939-966, 2013), and others by comparing long-term dynamics up to topological conjugation: rather than comparing the exact states and their transitions on attractors, we only compare the attractor structures. In general, obtaining this information is computationally intractable. Here, we adapt and apply combinatorial theory for dynamical systems from Macauley and Mortveit (Proc Am Math Soc 136(12):4157-4165, 2008. https://doi.org/10.1090/S0002-9939-09-09884-0 ; 2009; Electron J Comb 18:197, 2011a; Discret Contin Dyn Syst 4(6):1533-1541, 2011b. https://doi.org/10.3934/dcdss.2011.4.1533 ; Theor Comput Sci 504:26-37, 2013. https://doi.org/10.1016/j.tcs.2012.09.015 ; in: Isokawa T, Imai K, Matsui N, Peper F, Umeo H (eds) Cellular automata and discrete complex systems, 2014. https://doi.org/10.1007/978-3-319-18812-6_6 ) to develop computational methods that greatly reduce this computational cost. We give a detailed algorithm and apply it to (i) the lac operon model for Escherichia coli proposed by Veliz-Cuba and Stigler (2011), and (ii) the regulatory network involved in the control of the cell cycle and cell differentiation in the Caenorhabditis elegans vulva precursor cells proposed by Weinstein et al. (BMC Bioinform 16(1):1, 2015). In both cases, we uncover all possible limit cycle structures for these networks under sequential updates. Specifically, for the lac operon model, rather than examining all [Formula: see text] sequential update orders, we demonstrate that it is sufficient to consider 344 representative update orders, and, more notably, that these 344 representatives give rise to 4 distinct attractor structures. A similar analysis performed for the C. elegans model demonstrates that it has precisely 125 distinct attractor structures. We conclude with observations on the variety and distribution of the models' attractor structures and use the results to discuss their robustness.

The Isolation and Analysis of Circulating Tumor Cells

Circulating tumor cells (CTCs), with their close association with cancer metastasis, the most aggressive feature of solid tumors, represent an important aspect of "liquid biopsy," which provides minimally- or noninvasive approaches for cancer detection and disease status monitoring. CTC analysis has shown the potential clinical applications in several cancer types and has been approved by FDA for clinical use in advanced breast, prostate, and colorectal cancer prognosis. In this chapter, we describe a CTC isolation method using a cell size and deformability-based system, Parsortix, and the immunofluorescence staining method to detect CTCs with both epithelial and mesenchymal features. We also describe a repeated fluorescence in situ hybridization (FISH) approach to detect alterations of multiple genomic regions on the same CTCs after immunofluorescence analysis. This approach allows the study of CTCs as a biomarker for cancer detection, prognosis, and therapeutic response monitoring, as well as the study of the heterogeneity of CTCs and cancers.

Two's company, three's a crowd: Individuation is necessary for object recognition

Object recognition is essential for navigating the real world. Despite decades of research on this topic, the processing steps necessary for recognition remain unclear. In this study, we examined the necessity and role of individuation, the ability to select a small number of spatially distinct objects irrespective of their identity, in the recognition process. More specifically, we tested if the ability to rapidly individuate and enumerate a small number of objects (subitizing) can be impaired by crowding. Crowding is flanker-induced interference that specifically impedes the recognition process. We found that subitizing is impaired when objects are close to each other (Experiment 1), and if the target objects are surrounded by irrelevant but perceptually similar flankers (Experiments 2-4). This impairment cannot be attributed to confusion between targets and flankers, wherein flankers are inadvertently included in or targets are excluded from enumeration (Experiments 3-4). Importantly, the flanker induced interference was comparable in both subitizing and crowding tasks (Experiment 4), suggesting that individuation and identification share a common processing pathway. We conclude that individuation is an essential stage in the object recognition pipeline and argue for a cohesive proposal that both crowding and subitizing are due to limitations of selective attention.

Comparative performance of TCBS and TSA for the enumeration of trh+ Vibrio parahaemolyticus by direct colony hybridization

Vibrio parahaemolyticus is one of the important foodborne pathogens is of public health concern due to the emergence of pandemic strains causing disease outbreaks worldwide. We evaluated the DNA based colony hybridization technique for the detection and enumeration of total and pathogenic V. parahaemolyticus from the bivalve shellfish, clam using non-radioactive, enzyme-labeled probe targeting the tlh and trh genes, respectively. The digoxigenin (DIG) labeled probes designed in this study showed 100% specificity by dot blot assay. Colony hybridization using DIG probes was performed using both non-selective, trypticase soy agar (TSA) and the selective medium, thiosulfate citrate bile salts sucrose (TCBS) agar. Of 32 clam samples analyzed, 71.88% had>10,000 V. parahaemolyticus cells/g in TSA whereas it was 18.75% in case of TCBS. All the samples showed the presence of total V. parahaemolyticus in TSA and 97% in the case of TCBS. Interestingly, results of the trh⁺V. parahaemolyticus samples were quite high while using TCBS plates (62.5%) as compared to TSA (43.75%). However, the cell numbers obtained from TSA were higher than from TCBS. Several yellow colonies on TCBS turned out to be V. parahaemolyticus using colony hybridization, which was further confirmed by PCR and sucrose utilization test. Colony hybridization using DIG-labeled probe was found to be highly sensitive and could differentiate and enumerate pathogenic and non-pathogenic strains of V. parahaemolyticus. Since traditional methods are not only labor-intensive and time-consuming but also less sensitive, colony hybridization using DIG-labeled probes would be a useful alternative for the enumeration of V. parahaemolyticus in naturally contaminated seafood.

Efficacy of Propidium Monoazide on Quantitative Real-Time PCR-Based Enumeration of Staphylococcus aureus Live Cells Treated with Various Sanitizers

Propidium monoazide (PMA) has been used together with quantitative real-time PCR (qPCR) to enumerate live bacteria, while discriminating against the residual DNA of dead bacterial cells. Although the effectiveness of PMA at increasing the accuracy of enumeration of live bacteria treated with heat has been investigated in a number of studies, few studies have involved bacteria treated with sanitizers. In this study, dead Staphylococcus aureus cells were prepared by treatment with six kinds of sanitizers (ethanol, isopropyl alcohol, benzalkonium chloride, sodium hypochlorite, hydrogen peroxide, and nisin) and were mixed with a culture of live bacteria in different ratios. PMA-qPCR was able to accurately enumerate live bacteria with a <0.5 CFU/500 μL difference with that of plate counts for cultures treated with ethanol, isopropyl alcohol, and nisin. For ethanol and isopropyl alcohol treatments, live cells were accurately enumerated for live/dead cell ratios of 10/1 to 0.01/1, while live cells for the nisin treatment were accurately enumerated for live/dead cell ratios of 10/1 to 0.1/1. In contrast, PMA-qPCR was not able to accurately enumerate live cells in bacterial cultures treated with benzalkonium chloride and hydrogen peroxide. In addition, qPCR without PMA was able to enumerate live cells as consistently as plate counts with a bacterial culture treated with sodium hypochlorite. The results of this study show that the use of PMA for qPCR-based enumeration of live cells is not always recommended, and its effectiveness depends on the treatment used on the cells.

Prevalence and Concentration of Salmonella on Raw, Shelled Peanuts in the United States

Recalls and outbreaks associated with Salmonella contamination in peanut-containing products have been reported over the past several years. Very limited data existed on the prevalence and concentration of Salmonella on raw, shelled peanuts in the United States. An initial study was completed in 2012 to estimate the prevalence and concentration of Salmonella on Runner- and Virginia-type raw, shelled peanuts in the United States from the 2008 through 2011 crop years, which were proportionately sampled from each growing region based on 2007 production volume. That study was extended to include samples of Runner- and Virginia-type peanuts from 2013, 2014, and 2015 crop years proportionately sampled from each growing region on the basis of the 2008 through 2010 volumes. Of the total 2,506 raw, shelled peanut samples, 41 (1.63%) were positive for Salmonella by the VIDAS SLM assay. Salmonella serovars identified in this study included Agona, Anatum, Bardo, Braenderup, Cannstatt, Dessau, Gaminara, Litchfield, Hartford, Inverness, Mbandaka, Meleagridis, Muenchen, Newport, Pakistan, Rodepoort, Rubislaw, Tennessee, and Tornow. The concentration levels of Salmonella in positive samples, as determined by most probable number (MPN), ranged from <0.003 to 2.4 MPN/g. These data will be useful when designing and validating processes for the reduction or elimination of Salmonella in peanuts or peanut-containing products or both.

Spinal Enumeration by Morphologic Analysis of Spinal Variants: Comparison to Counting in a Cranial-To-Caudal Manner

Objective

To compare the spinal enumeration methods that establish the first lumbar vertebra in patients with spinal variants.

Materials and Methods

Of the 1446 consecutive patients who had undergone computed tomography of the spine from March 2012 to July 2016, 100 patients (62 men, 38 women; mean age, 47.9 years; age range, 19-88 years) with spinal variants were included. Two radiologists (readers 1 and 2) established the first lumbar vertebra through morphologic analysis of the thoracolumbar junction, and labeled the vertebra by counting in a cranial-to-caudal manner. Inter-observer agreement was established. Additionally, reader 1 detected the 20th vertebra under the assumption that there are 12 thoracic vertebra, and then classified it as a thoracic vertebra, lumbar vertebra, or thoracolumbar transitional vertebra (TLTV), on the basis of morphologic analysis.

Results

The first lumbar vertebra, as established by morphologic analysis, was labeled by each reader as the 21st segment in 65.0% of the patients, as the 20th segment in 31.0%, and as the 19th segment in 4.0%. Inter-observer agreement between the two readers in determining the first lumbar vertebra, based on morphologic analysis, was nearly perfect (κ value: 1.00). The 20th vertebra was morphologically classified as a TLTV in 60.0% of the patients, as the first lumbar segment in 31.0%, as the second lumbar segment in 4.0%, and as a thoracic segment in 5.0%.

Conclusion

The establishment of the first lumbar vertebra using morphologic characteristics of the thoracolumbar junction in patients with spinal variants was consistent with the morphologic traits of vertebral segmentation.

- Part 2: Colony-count technique

The validation in an interlaboratory study of the International Standards Organization standard method for the enumeration of Campylobacter in foods (ISO 10272-2) was performed after preparation of the revised Standard based on scientifically sound and validated methods of analysis. The matrices selected for testing in the collaborative trial were frozen spinach, minced meat, raw milk, chicken skin, and broiler caecal material. Each matrix was artificially inoculated with a different Campylobacter strain. Fifteen laboratories participated in the interlaboratory study. As a general indication of repeatability limit (r), the following overall values can be used when testing chicken skin samples: As a general indication of reproducibility limit (R), the following overall values can be used when testing chicken skin samples: The validation data for all matrices were incorporated in the newly published ISO standard EN ISO 10272-2:2017 - Microbiology of the food chain - Horizontal method for detection and enumeration of Campylobacter - Part 2: colony-count technique.

Longitudinal enumeration and cluster evaluation of circulating tumor cells improve prognostication for patients with newly diagnosed metastatic breast cancer in a prospective observational trial

Background

Circulating tumor cells (CTCs) carry independent prognostic information in patients with metastatic breast cancer (MBC) on different lines of therapy. Moreover, CTC clusters are suggested to add prognostic information to CTC enumeration alone but their significance is unknown in patients with newly diagnosed MBC. We aimed to evaluate whether longitudinal enumeration of circulating tumor cells (CTCs) and CTC clusters could improve prognostication and monitoring of patients with metastatic breast cancer (MBC) starting first-line therapy.

Methods

This prospective study included 156 women with newly diagnosed MBC. CTCs and CTC clusters were detected using CellSearch technology at baseline (BL) and after 1, 3, and 6 months of systemic therapy. The primary end point was progression-free survival (PFS) and the secondary end point overall survival (OS). Median follow-up time was 25 (7–69) months.

Results

There were 79 (52%) and 30 (20%) patients with ≥ 5 CTCs and ≥ 1 CTC cluster at baseline, respectively; both factors were significantly associated with impaired survival. Landmark analyses based on follow-up measurements revealed increasing prognostic hazard ratios for ≥ 5 CTCs and CTC clusters during treatment, predicting worse PFS and OS. Both factors added value to a prognostic model based on clinicopathological variables at all time points and ≥ 5 CTCs and presence of CTC clusters enhanced the model’s C-index to > 0.80 at 1, 3, and 6 months. Importantly, changes in CTCs during treatment were significantly correlated with survival and patients with a decline from ≥ 5 CTCs at BL to < 5 CTCs at 1 month had a similar odds ratio for progression to patients with < 5 CTCs at BL and 1 month. Stratification of patients based on CTC count and CTC clusters into four groups (0 CTCs, 1–4 CTCs, ≥ 5 CTCs, and ≥ 1 CTC + CTC clusters) demonstrated that patients with CTC clusters had significantly worse survival compared to patients without clusters.

Conclusions

Longitudinal evaluation of CTC and CTC clusters improves prognostication and monitoring in patients with MBC starting first-line systemic therapy. The prognostic value increases over time, suggesting that changes in CTC count are clinically relevant. The presence of CTC clusters adds significant prognostic value to CTC enumeration alone.

Trial registration

NCT01322893. Registered on 25 March 2011.

Electronic supplementary material

The online version of this article (10.1186/s13058-018-0976-0) contains supplementary material, which is available to authorized users.

Validation by an interlaboratory collaborative trial of EN ISO 21528 - microbiology of the food chain - horizontal methods for the detection and enumeration of Enterobacteriaceae

The methods for the detection and enumeration of Enterobacteriaceae, described in EN ISO 21528, parts 1 and 2, were validated by order of the European Commission under the mandate M/381. Fourteen laboratories from seven European countries participated in the collaborative trials, organized by The Netherlands Food and Consumer Product Safety Authority (Wageningen/Utrecht, The Netherlands). Five different matrices from different food categories were selected to be tested in the collaborative trials, in order to validate the method horizontally, according to ISO 16140. The matrices included meat, tiramisu, infant formula, liquid egg, smoked salmon (detection method only) and animal feed (enumeration method only). The raw meat and liquid egg were naturally contaminated and the other matrices were artificially contaminated with a cocktail of four different Enterobacteriaceae strains. The samples used in the trial were tested for homogeneity and stability before distribution. The method for detection of Enterobacteriaceae showed a specificity and sensitivity above 95% for all matrices. The method for the enumeration had a repeatability limit r of 0.37 (expressed as a difference between log₁₀-transformed test results) and a reproducibility limit R of 0.87 (expressed as a difference between log₁₀-transformed test results). The validation data were incorporated in the newly published ISO standards EN ISO 21528:2017- Microbiology of the food chain - Horizontal methods for the detection and enumeration of Enterobacteriaceae - Part 1: Detection method, and Part 2: Colony-count technique.

Pseudoneglect is maintained in aging but not in mild Alzheimer's disease: new insights from an enumeration task

Neurologically healthy young adults display a behavioral bias, called pseudoneglect, which favors the processing of stimuli appearing in the left visual field. Pseudoneglect arises from the right hemisphere dominance for visuospatial attention. Previous studies investigating the effects of normal aging on pseudoneglect in line bisection and greyscale tasks have produced divergent results. In addition, scarce systematic investigations of visual biases in dementia have been reported. The aim of the present study was to evaluate whether the leftward bias appearing during an enumeration task in young adults would be preserved in normal aging and at different stages of severity of Alzheimer's disease. In Experiment 1, young and older healthy adults showed a comparable pseudoneglect, performing better when targets appeared in the left visual field. In Experiment 2, the leftward bias was maintained in amnesic mild cognitive impairment patients (aMCI), but it vanished in mild Alzheimer's disease patients (AD). The maintenance of pseudoneglect in normal aging and in aMCI patients is consistent with compensatory phenomena involving the right fronto-parietal network, which allow maintaining the right hemisphere dominance. Conversely, the lack of pseudoneglect in the sample of AD patients likely results from a loss of the right hemisphere dominance, caused by the selective degeneration of the right fronto-parietal network. These results highlight the need of further systematic investigations of visuospatial biases along the continuum of normal and pathological aging, both for a better understanding of the changes characterizing cognitive aging and for improvements in the evaluation of neglect in Alzheimer's disease.

Capuchin monkeys (Cebus apella) treat small and large numbers of items similarly during a relative quantity judgment task

A key issue in understanding the evolutionary and developmental emergence of numerical cognition is to learn what mechanism(s) support perception and representation of quantitative information. Two such systems have been proposed, one for dealing with approximate representation of sets of items across an extended numerical range and another for highly precise representation of only small numbers of items. Evidence for the first system is abundant across species and in many tests with human adults and children, whereas the second system is primarily evident in research with children and in some tests with non-human animals. A recent paper (Choo & Franconeri, Psychonomic Bulletin & Review, 21, 93-99, 2014) with adult humans also reported "superprecise" representation of small sets of items in comparison to large sets of items, which would provide more support for the presence of a second system in human adults. We first presented capuchin monkeys with a test similar to that of Choo and Franconeri in which small or large sets with the same ratios had to be discriminated. We then presented the same monkeys with an expanded range of comparisons in the small number range (all comparisons of 1-9 items) and the large number range (all comparisons of 10-90 items in 10-item increments). Capuchin monkeys showed no increased precision for small over large sets in making these discriminations in either experiment. These data indicate a difference in the performance of monkeys to that of adult humans, and specifically that monkeys do not show improved discrimination performance for small sets relative to large sets when the relative numerical differences are held constant.