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.

Validation by interlaboratory trials of EN ISO 10272 - Microbiology of the food chain - Horizontal method for detection and enumeration of Campylobacter spp. - 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.