Genomic Analysis of Multidrug-Resistant Escherichia coli Strains Isolated in Tamaulipas, Mexico

The global spread of antimicrobial resistance genes (ARGs) is a major public health concern. Mobile genetic elements (MGEs) are the main drivers of this spread by horizontal gene transfer (HGT). Escherichia coli is widespread in various environments and serves as an indicator for monitoring antimicrobial resistance (AMR). Therefore, the objective of this work was to evaluate the whole genome of multidrug-resistant E. coli strains isolated from human clinical, animal, and environmental sources. Four E. coli strains previously isolated from human urine (n = 2), retail meat (n = 1), and water from the Rio Grande River (n = 1) collected in northern Tamaulipas, Mexico, were analyzed. E. coli strains were evaluated for antimicrobial susceptibility, followed by whole genome sequencing and bioinformatic analysis. Several ARGs were detected, including blaCTX-M-15, blaOXA-1, blaTEM-1B, blaCMY-2, qnrB, catB3, sul2, and sul3. Additionally, plasmid replicons (IncFIA, IncFIB, IncFII, IncY, IncR, and Col) and intact prophages were also found. Insertion sequences (ISs) were structurally linked with resistance and virulence genes. Finally, these findings indicate that E. coli strains have a large repertoire of resistance determinants, highlighting a high pathogenic potential and the need to monitor them.

Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolated from Food-Producing Animals in Tamaulipas, Mexico

Extended-spectrum β-lactamase (ESBL)-producing E. coli has become an important global problem for the public health sector. This study aims to investigate the E. coli antimicrobial resistance profile among living food-producing animals in Tamaulipas, Mexico. A total of 200 fecal samples were collected from bovines, pigs, chickens and sheep. A total of 5.0% of the strains were phenotypically confirmed as ESBL producers. A high percentage of phenotypic antimicrobial resistance was observed against gentamicin (93.3%), tetracycline (86.6%) and streptomycin (83.3%). The gentamicin-resistant strains showed MDR, distributed among 27 resistance patterns to different antimicrobials. The antimicrobial resistance gene tet(A) was detected in 73.3% of isolates, aadA1 in 60.0% and sul2 in 43.3% of strains. The bla_CTX-M gene was found in 23.3% of strains. The virulence gene hlyA was detected in 43.3% of isolates; stx1 and stx2 were not detected in any strain. The phylotyping indicated that the isolates belonged to groups A (33.3%), B1 (16.6%), B2 (40.0%) and D (10.0%). These results show that food-producing animals might be a reservoir of ESBL-producing bacteria and may play a role in their spread.

Molecular and Antimicrobial Susceptibility Characterization of Escherichia coli Isolates from Bovine Slaughterhouse Process

Antimicrobials are routinely used in human and veterinary medicine. With repeated exposure, antimicrobials promote antibiotic resistance, which poses a threat to public health. In this study, we aimed to determine the susceptibility patterns, virulence factors, and phylogroups of E. coli isolates during the killing process in a bovine slaughterhouse. We analyzed 336 samples (from water, surfaces, carcasses, and feces), and 83.3% (280/336) were positive for E. coli. The most common phenotypic resistances that we detected were 50.7% (142/280) for tetracycline, 44.2% (124/280) for cephalothin, 34.6% (97/280) for streptomycin, and 36.7% (103/280) for ampicillin. A total of 82.4% of the isolates had resistance for at least one antimicrobial, and 37.5% presented multiresistance. We detected a total of 69 different phenotypic resistance patterns. We detected six other resistance-related genes, the most prevalent being tetA (22.5%) and strB (15.7%). The prevalence values of the virulence genes were 5.4% in hlyA, 1.4% in stx1, and 0.7% in stx2. The frequencies of the pathogenic strains (B2 and D) were 32.8% (92/280) and 67.1% (188/280) as commensals A and B1, respectively. E. coli isolates with pathogenic potential and multiresistance may represent an important source of dissemination and a risk to consumers.

Prevalence of claudin 18.2 (CLDN18.2) and the association of biomarkers with clinical activity in patients with gastric or gastroesophageal adenocarcinoma (G/GEJa) treated with zolbetuximab

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Background: CLDN18.2, a targetable biomarker, is a tight junction protein normally confined to gastric mucosa of healthy tissue and often retained in G/GEJa. Zolbetuximab, a chimeric IgG1 monoclonal antibody, binds to CLDN18.2 and mediates cancer cell death via antibody-dependent cellular cytotoxicity (ADCC) and complement-dependent cytotoxicity (CDC). Phase 2 FAST study results showed prolonged survival with zolbetuximab+EOX (epirubicin, oxaliplatin, capecitabine) vs EOX in CLDN18.2-positive G/GEJa. In ILUSTRO Cohort 2, confirmed partial responses (PRs) and stable disease (SD) were previously reported in 63.2% and 10.5%, respectively, of patients (pts) treated with zolbetuximab+mFOLFOX6 (modified 5-FU, folinic acid, oxaliplatin). Here is an analysis of CLDN18.2 expression and exploratory biomarkers from 2 studies of zolbetuximab alone or with mFOLFOX6 in G/GEJa. Methods: Data are from phase 1 (NCT03528629) and phase 2 (NCT03505320, ILUSTRO Cohorts 1 and 2) studies. Pts with CLDN18.2-positive locally advanced/metastatic G/GEJa received zolbetuximab alone (phase 1 [ineligible for SOC], n = 18; phase 2 Cohort 1 [≥3rd-line], n = 30) or with mFOLFOX6 (phase 2 Cohort 2 [1st-line], n = 21). Archival (any time before treatment), baseline (during screening or ≤3 months before first study treatment), and on-treatment (Cycle 3) tumor samples were collected when possible. CLDN18.2 expression and immune cell populations were assessed by IHC. Blood samples collected longitudinally while on treatment (phase 2 study) were analyzed for ADCC activity (ex vivo cell-based assay), circulating tumor antigens, and circulating tumor DNA (ctDNA). Results: Of 416 screened pts in both studies, 26.2% (n = 109), 9.6% (n = 40), and 36.1% (n = 150) had tumors that were CLDN18.2-positive in 1%–49%, 50%–74%, and ≥75% of tumor cells ( = strong to moderate staining intensity), respectively; 28.1% (n = 117) were CLDN18.2-negative (0/1+). Analysis of pre- and on-treatment tissue samples (n = 8 matched pairs) with zolbetuximab alone showed an increased trend in immune cell infiltration, with CD8+ T cells and CD163+ cells showing the most consistent trend. A trend of increased on-treatment vs baseline ADCC activity was observed in PBMCs collected from pts treated with zolbetuximab alone and with mFOLFOX6. Rapid and deep decreases in circulating tumor antigens (in pts with elevated antigen levels) and ctDNA were observed with best overall responses of both PR and SD. Conclusions: CLDN18.2 is a high-prevalence biomarker in G/GEJa. Treatment with zolbetuximab is associated with tumor and peripheral biomarker changes related to its proposed mechanism of action. Clinical responses observed in pts treated with zolbetuximab and mFOLFOX6 are associated with correlative biomarkers of activity including rapid deep molecular responses (ctDNA). Clinical trial information: NCT03528629 .

Eco-friendly synthesis of ZnO-nanoparticles using Phoenix dactylifera L. polyphenols: physicochemical, microstructural, and functional assessment

Recently, nanoparticles (NPs) synthesis has evolved into a green nanotechnology field, requiring more eco-synthesis of nanoparticles due to the high costs of other chemical-physical methods. Among the most commonly used...

Evaluation of Retail Meat as a Source of ESBL Escherichia coli in Tamaulipas, Mexico

In recent decades, the appearance of a group of strains resistant to most β-lactam antibiotics, called extended-spectrum β-lactamases (ESBLs), has greatly impacted the public health sector. The present work aimed to identify the prevalence of ESBL-producing Escherichia coli strains in retail meat from northeast Tamaulipas. A total of 228 meat samples were obtained from 76 different stores. A prevalence of E. coli ESBL of 6.5% (15/228) was detected. All (15/15) of the ESBL strains were multiresistant. Altogether, 40% (6/15) of the strains showed the presence of class 1 integrons. The isolates identified with bla_CTX-M (20%) also showed co-resistance with the tet (A and B), str (A and B), and sul (2 and 3) genes. A total of 20% of the strains belonged to the B2 and D phylogroups, which are considered pathogenic groups. None of the ESBL-positive strains contained any of the virulence gene factors tested. The presence of ESBL-producing E. coli strains in meat indicates a potential risk to the consumer. Although most of these strains were classified as commensals, they were found to serve as reservoirs of multiresistance to antimicrobials and, therefore, are potential routes of dispersion of this resistance to other bacteria.

Improving Knowledge and Attitudes About Child Trauma Among Parents and Staff in Head Start Programs

Background

Early childhood represents a sensitive developmental period when trauma-informed care may mitigate the effects of trauma on developmental and health outcomes. However, few interventions use a low-literacy scalable approach to improve child trauma knowledge and attitudes among parents and early childcare and education caregivers.

Methods

Representatives from 24 early head start (EHS) and head start (HS) agencies attended a 2 day online train-the trainer session and then delivered a child trauma and resilience training to staff at their sites, with the option to deliver a similar training to parents. Baseline and 3 month post-training surveys assessed participant knowledge and attitudes regarding childhood trauma and resilience. Paired T-tests and chi2 analyses assessed changes in responses over time.

Results

Thousand five hundred sixty seven staff from 24 agencies and 443 parents from 7 agencies completed baseline and follow up surveys. Over 55% of parents reported their child had experienced at least one adverse childhood experience. Staff and parents had high knowledge regarding causes of trauma at baseline. Both staff and parents, demonstrated significant improvements in identifying symptoms of child trauma. Staff also improved knowledge of resiliency and toxic stress. Parents reported more positive attitudes towards trauma-informed parenting practices.

Conclusion

This is the first training on childhood trauma among EHS/HS providers and parents using a low literacy train-the-trainer approach. Results suggest a potentially promising methodology with broad dissemination potential to prepare and train the one million plus teachers and caregivers in center-based settings and the parents and families who access them to recognize and respond to child trauma.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10995-022-03473-8.

Distribution of pathogenic vibrios and Vibrio spp. in the water column and sediment samples from the southern Gulf of Mexico

This study quantified the distribution of Vibrio spp. by qPCR and pathogenic vibrio species by metagenomics, during 2 oceanographic cruises-XIXIMI-04 and XIXIMI-05 -in the southern Gulf of Mexico (GoMex). A total of 708 samples from various levels of the water column and 22 sediment samples were analyzed, according to a designed net of sampling lines. Sampling was focused on reported water masses with distinctive characteristics, to detect the presence-absence of vibrios. The results indicated that the genus Vibrio was detected along the entire water column and in sediments. Pathogenic vibrios, such as V, campbellii, V. parahaemolyticus, V. vulnificus or V. cholerae were also detected in the water column and in sediments, in both oceanographic cruises. Thus, the ecological conditions of the GoMex permit the growth of Vibrio spp. in deep water environments of the GoMex, despite continuous oil input from natural and anthropogenic sources.

Genomic stability among O3:K6 V. parahaemolyticus pandemic strains isolated between 1996 to 2012 in American countries

BACKGROUND

The V. parahaemolyticus pandemic clone, results in the development of gastrointestinal illness in humans. Toxigenic strains of this species are frequently isolated from aquatic habitats and organisms such as mollusks and crustaceans. Reports on the isolation of the pandemic clone started in 1996, when a new O3:K6 clone was identified in Asia, that rapidly spread worldwide, becoming the predominant clone isolated from clinical cases. In this study whole genome sequencing was accomplished with an Illumina MiniSeq platform, upon six novel V. parahaemolyticus strains, that have been isolated in Mexico since 1998 and three representative genomes of strains that were isolated from reported outbreaks in other American countries, and were deposited in the GenBank. These nine genomes were compared against the reference sequence of the O3:K6 pandemic strain (RIMD 2210633), which was isolated in 1996, to determine sequence differences within American isolates and between years of isolation.

RESULTS

The results indicated that strains that were isolated at different times and from different countries, were highly genetically similar, among them as well as to the reference strain RIMD 2210633, indicating a high level of genetic stability among the strains from American countries between 1996 to 2012, without significant genetic changes relative to the reference strain RIMD 2210633, which was isolated in 1996 and was considered to be representative of a novel O3:K6 pandemic strain.

CONCLUSIONS

The genomes of V. parahaemolyticus strains isolated from clinical and environmental sources in Mexico and other American countries, presented common characteristics that have been reported for RIMD 2210633 O3:K6 pandemic strain. The major variations that were registered in this study corresponded to genes non associated to virulence factors, which could be the result of adaptations to different environmental conditions. Nevertheless, results do not show a clear pattern with the year or locality where the strains were isolated, which is an indication of a genomic stability of the studied strains.

FCSlib: an open-source tool for fluorescence fluctuation spectroscopy analysis for mobility, number and molecular brightness in R

SUMMARY

FCSlib is an open-source R tool for fluorescence fluctuation spectroscopy data analysis. It encompasses techniques such as Fluorescence Correlation Spectroscopy, Number and Brightness, Pair Correlation Function and Pair Correlation of Molecular Brightness.

AVAILABILITY AND IMPLEMENTATION

Source code available at https://cran.r-project.org/web/packages/FCSlib/ for Linux, Windows and macOS platforms. Sample data as well as a user's guide are available at https://github.com/FCSlib/FCSlib.

SUPPLEMENTARY INFORMATION

Supplementary data are available at Bioinformatics online.

Fishers' perception of the interaction between the South American sea lions and the Chinook salmon fishery in southern Chile

We studied how the South American sea lion (SASL, Otaria flavescens) interacts with the operation of an artisanal fishery of Chinook salmon, a non-native species in Chile, using a combination of biological and social approaches, including a valuation by fishers about this interaction. During austral summer of 2019, an observer onboard artisanal fishing boats characterized the attack behavior of SASLs to gillnet-captured Chinook salmon during 33 hauls and analyzed which factors may affect the intensity of attacks. To analyze the relationship between fishers and SASLs, a Likert scale about the perception and views about nature was applied. A total of 23 interviews—including 35 open and 16 closed questions—with fishers were conducted to describe how they perceived the interactions with SASLs. Interactions with SASLs were recorded in 35% of the fishing events and varied depending on both operational factors, such as the number of boats, as well as environmental factors, such as moon’s luminosity. Even though SASL interactions resulted in seven fish (~ 70 kg) damaged of a total catch of 2815 kg (2.5%) during the survey, boats with a damaged catch by SASL lost up to 11% of their revenue. This is consistent with 87% of the interviewed fishers who considered that the conflict with the SASL negatively impacts their activity and results in economic losses. A negative perception towards SASLs likely results from personal experience and revenue loss, even though impacts of SASL interactions at the scale of the entire fishery may be less important. While older fishers with less formal education have a productivist and instrumental focus, younger fishers with a more sustainable and conservationist view of fishing offer an opportunity to lead an improved local understanding of the relationship between salmon, SASLs, and humans.

Preliminary results of a network meta-analysis on the efficacy of long-acting injectable antipsychotics in schizophrenia

Introduction

Long-acting injectable antipsychotics (LAIs) are currently the most effective alternative for patients with schizophrenia who exhibit poor adherence. Although a recent meta-analysis reported similar efficacy between first and second-generation LAIs, these results were only based on 3 studies due to the limited number of head-to-head comparisons.

Objectives

Present the preliminary results of a network meta-analysis on the comparative efficacy of LAIs in schizophrenia.

Methods

Studies were obtained from a previous study, where we carried out a systematic search from until May 2019 in various databases. Included trials of adults with schizophrenia compared the efficacy of LAI vs LAI or placebo through the Positive and Negative Syndrome Scale (PANSS). Efficacy was evaluated through the mean differences (MD) from baseline to endpoint in the PANSS total scores. Network meta-analysis was performed in MetaInsight through direct and indirect comparisons using a Bayesian approach.

Results

from 12 studies are presented in Figures 1 and 2. All LAIs except zuclopenthixol were more effective than placebo. There were no significant differences between LAIs except for aripiprazole and risperidone, which were more efficacious than zuclopenthixol. The largest change occurred with aripiprazole LAI, but was not significantly higher than haloperidol.

Figure 1. Comparison of treatment pairs. Effect sizes are presented as MD and 95% confidence intervals (*p<0.05).

Figure 1. Overall change in symptoms

Conclusions

Preliminary results from a network meta-analysis also suggest that in the long-term haloperidol decanoate is equally effective in overall symptom changes compared to other LAIs. Further analyses are needed to obtain a better perspective on these drugs.

Disclosure

No significant relationships.

Cervical cancer, human papillomavirus (HPV), and HPV vaccination: exploring gendered perspectives, knowledge, attitudes, and cultural taboos among Mexican American adults

Background: Gendered perspectives may be particularly important in shaping norms and values around HPV and HPV vaccination, as previous research suggests that sexuality taboos (e.g. promiscuity) may contribute to low perceived risk among adolescent and young adult Hispanic females. However, research to date focuses primarily on Hispanic mothers, adolescent females, and women of HPV vaccine-eligible age. Hispanic father's perspectives are relatively unknown despite father's important role in shaping norms for their female children. Objective: To close this gap, this study examines gendered perspectives in knowledge, beliefs, and attitudes about HPV and HPV vaccination from Hispanic parents (mothers and fathers), women of vaccine-eligible age (18-26 years old), and women eligible for Pap Test screening (>26 years old) living in two counties along the Texas-Mexico border. Design: We conducted eight focus groups. Research staff transcribed audio recordings verbatim and uploaded them into Atlas(ti) 5.0 for analysis. The research team analyzed the data for content, meaning, patterns and themes using the constant comparison approach. Results: Perspectives were highly gendered. Women's (all groups combined) beliefs focused on misconceptions around how the HPV virus is contracted (e.g. toilet surfaces). Women also linked HPV-related sexual risk to adultery and indiscretion of male partners. Fathers (men) were more likely to link risk to female promiscuity. Fathers also worried that HPV vaccination might increase promiscuity. All groups believe that HPV vaccination is a way to protect Hispanic females in the face of beliefs around sexual behavior and risk of contracting HPV. Conclusion: Results suggest gendered differences in risk beliefs concerning HPV among Hispanics living along the Texas-Mexico border. Researchers can use these findings to address barriers to HPV vaccination, as well as to create culturally appropriate prevention messages that may help reduce disparities in HPV among Hispanic women.

Evaluation of smart gelatin matrices for the development of scaffolds via 3D bioprinting

Throughout history, different techniques have been used for the development of scaffolds for Tissue Engineering. Among them, three-dimensional (3D) printing for this application has been recently enhanced due to its ease in defining the structure of the material. In this sense, a novel potential alternative could be the development of a three-part device whose leading utility is to improve the introduction of the scaffold in a bioreactor. Thus, the device consists of a polycaprolactone support on which smart gelatin (GE) matrix, and finally, on top, a collagen (C) scaffold. This gelatin matrix is included to integrate the scaffold into the support, but once both are assembled, it must be removed, leaving only the support and the scaffold. Thus, in the present work, a small gelatin matrix has been evaluated. To this end, matrices with different gelatin percentages were studied, evaluating their mechanical and morphological properties at different temperatures (22 and 37 °C) to control their deposition and elimination. The results show the high application of this smart matrix for the development of scaffolds via 3D bioprinting for Tissue Engineering.

Statistical control of processes applied to geometric uncertainties for CTV expansion margins determination in prostate cancer patients treated with VMAT: a prospective study in 57 patients

PURPOSE

To study the control graphs applicability for the geometric uncertainties of VMAT treatments in prostate cancer patients, and their use to verify the hypothesis of the data obtained randomness, to apply the margins of Van Herk expression.

MATERIAL AND METHODS

During the first 5 days of treatment, and then once a week, a Kv CBCT was performed, compared with the simulation CT and adjusted the displacements, to determine the inter-fraction errors. Immediately after radiation therapy, another CBCT was performed (for intra-fraction errors). With these data, the X, R position control charts have been made. The patients, not maintained the deviations within the charts control limits, were called "anomalies". Then, we compared the deviations and margins calculated with the van Herk expression for all patients and for those without anomalies.

RESULTS

The margins determined show appreciable differences if there were calculated for the total set of patients or for the set of them without anomalies in the control charts. For the overall set of patients, the lateral, longitudinal, and vertical margins were 0.45 cm, 0.52 cm, 0.56 cm, while for the set of patients without anomalies were 0.29 cm, 0.35 cm, and 0.38 cm.

CONCLUSIONS

The use of control charts allows tracking geometric deviations both inter and intra-fraction, variability real-time control and to detect situations in which it can change for non-random reasons, and require immediate investigation. Maintaining geometric deviations in the control state decreases the margins needed to administer a high dose to CTV in a high percentage of cancer prostate patients.

Discount Rate Determination for Economic Evaluations in HTA in the Philippines

To inform the development of a reference case for economic evaluation, we explored various approaches to determine a base case discount rate and rate options for discounting benefits and costs.

We conducted literature review and expert consultations to list approaches to determine base case discount rates, noting the advantages and disadvantages of each approach. The same methods were used to identify whether different discount rates would be applied to costs and benefits. We computed a social rate of time preference using the Ramsey formula: rc = ρ+μg, where ρ = pure rate of time preference μ= elasticity of the marginal utility of consumption and g= growth rate in per capita income. We assumed ρ = 1%, μ = 1.4% consistent with international practice, but used actual g of the Philippines of 4.5%. We compared this with the official social discount rate and with rate most commonly used internationally. These options were presented to the Philippine Health Technology Assessment Council for decisionmaking.

Based on reviewed literature, 10 out of 22 countries used a 3.0% to 3.5% discount rate while 18 countries from the same pool applied equal discount rates for both costs and outcomes. The official social discount rate (SDR) prescribed by the Philippine National Economic Development Authority is 10% for all social investments. Upon input of the values, rc was calculated at 7%, which is above the international norm but below the official rate. Four discount rate options were identified: 3%, 3.5%, 7% and 10%.

Evidence suggested using a discount rate higher than 3% to 3.5% for low-to-middle income countries. A more conservative rate based on the Ramsey formula of 7% base case discount rate was selected in performing economic evaluations. Sensitivity analysis was set between 3% and 10% to allow benchmarking with international practice and with the official SDR, respectively. Given Philippines' early HTA implementation phase, it was agreed to subject these rates to regular review.

Key messages

Setting a discount rate in economic evaluations is a crucial process for HTA institutionalization. Discount rate determination heavily relies on decision context a country considers most relevant.

Clusters formation and fragmentation of nitromethane at 266 nm

We carry out experiments on the fragmentation of nitromethane by multiphoton absorption at the wavelength 266 nm. This was conducted in a reflectron (Jordan), modified in the laboratory. Due to the large number of fragments, special care has been taken into the calibration of the system, in the simultaneity between the laser pulse and the sample, and the associated electronics to ensure that produced fragment spectra arise from the interaction laser-sample. We emphasize the next aspects of the method:•

Simple design for introducing a gas sample at laser interaction region to facilitate the cluster formation

•

Astonishing number of fragments produced by multiphoton absorption.

Detection of Alcanivorax spp., Cycloclasticus spp., and Methanomicrobiales in water column and sediment samples in the Gulf of Mexico by qPCR

Water column and sediment samples were collected in the southern Gulf of Mexico (GoMex) during 3 oceanographic cruises: XIXIMI-04 (September 2015), XIXIMI-05 (June 2016), and XIXIMI-06 (August 2017). DNA that was extracted from the samples was analyzed by qPCR to detect and quantify bacterial groups that have been reported to metabolize alkanes (Alcanivorax) and aromatic hydrocarbons (Cycloclasticus) and are involved in methane production (Methanomicrobiales). The results were then analyzed with regard to the water masses that are currently detected in the GoMex. Generally, we observed a decrease in the proportion of Alcanivorax and a rise in those of Cycloclasticus and Methanomicrobiales in samples from the surface to deep waters and in sediment samples. Scatterplots of the results showed that the relative abundance of the 3 groups was higher primarily from the surface to 1000 m, but the levels of Cycloclasticus and Methanomicrobiales were high in certain water samples below 1000 m and in sediments. In conclusion, oil-degrading bacteria are distributed widely from the surface to deep waters and sediments throughout the southern GoMex, representing a potential inoculum of bacteria for various hydrocarbon fractions that are ready for proliferation and degradation in the event of an oil spill from the seafloor or along the water column.

Whole-genome comparison between reference sequences and oyster Vibrio vulnificus C-genotype strains

Whole-genome sequences of Vibrio vulnificus clinical genotype (C-genotype) from the CICESE Culture Collection, isolated from oysters, were compared with reference sequences of CMCP6 and YJ016 V. vulnificus C-genotype strains of clinical origin. The RAST web server estimated the whole genome to be ~4.8 Mb in CICESE strain 316 and ~4.7 Mb in CICESE strain 325. No plasmids were detected in the CICESE strains. Based on a phylogenetic tree that was constructed with the whole-genome results, we observed high similarity between the reference sequences and oyster C-genotype isolates and a sharp contrast with environmental genotype (E-genotype) reference sequences, indicating that the differences between the C- and E-genotypes do not necessarily correspond to their isolation origin. The CICESE strains share 3488 genes (63.2%) with the YJ016 strain and 3500 genes (63.9%) with the CMCP6 strain. A total of 237 pathogenicity associated genes were selected from reference clinical strains, where—92 genes were from CMCP6, 126 genes from YJ016, and 19 from MO6-24/O; the presence or absence of these genes was recorded for the CICESE strains. Of the 92 genes that were selected for CMCP6, 67 were present in both CICESE strains, as were as 86 of the 126 YJ016 genes and 13 of the 19 MO6-24/O genes. The detection of elements that are related to virulence in CICESE strains—such as the RTX gene cluster, vvhA and vvpE, the type IV pili cluster, the XII genomic island, and the viuB genes, suggests that environmental isolates with the C-genotype, have significant potential for infection.

Improving network approaches to the study of complex social-ecological interdependencies

Achieving effective, sustainable environmental governance requires a better understanding of the causes and consequences of the complex patterns of interdependencies connecting people and ecosystems within and across scales. Network approaches for conceptualizing and analyzing these interdependencies offer one promising solution. Here, we present two advances we argue are needed to further this area of research: (i) a typology of causal assumptions explicating the causal aims of any given network-centric study of social-ecological interdependencies; (ii) unifying research design considerations that facilitate conceptualizing exactly what is interdependent, through what types of relationships, and in relation to what kinds of environmental problems. The latter builds on the appreciation that many environmental problems draw from a set of core challenges that re-occur across contexts. We demonstrate how these advances combine into a comparative heuristic that facilitates leveraging case-specific findings of social-ecological interdependencies to generalizable, yet context-sensitive, theories based on explicit assumptions of causal relationships.

Experimental Observation of Proton Bunch Modulation in a Plasma at Varying Plasma Densities

We give direct experimental evidence for the observation of the full transverse self-modulation of a long, relativistic proton bunch propagating through a dense plasma. The bunch exits the plasma with a periodic density modulation resulting from radial wakefield effects. We show that the modulation is seeded by a relativistic ionization front created using an intense laser pulse copropagating with the proton bunch. The modulation extends over the length of the proton bunch following the seed point. By varying the plasma density over one order of magnitude, we show that the modulation frequency scales with the expected dependence on the plasma density, i.e., it is equal to the plasma frequency, as expected from theory.

Experimental Observation of Plasma Wakefield Growth Driven by the Seeded Self-Modulation of a Proton Bunch

We measure the effects of transverse wakefields driven by a relativistic proton bunch in plasma with densities of 2.1×10^{14} and 7.7×10^{14}  electrons/cm^{3}. We show that these wakefields periodically defocus the proton bunch itself, consistently with the development of the seeded self-modulation process. We show that the defocusing increases both along the bunch and along the plasma by using time resolved and time-integrated measurements of the proton bunch transverse distribution. We evaluate the transverse wakefield amplitudes and show that they exceed their seed value (<15  MV/m) and reach over 300  MV/m. All these results confirm the development of the seeded self-modulation process, a necessary condition for external injection of low energy and acceleration of electrons to multi-GeV energy levels.

Development of a BiTE®-mediated CD8+ cytotoxic T-lymphocyte activity assay to assess immunomodulatory potential of drug candidates in Cynomolgus macaque

The immunotoxic potential of drug candidates is assessed through the examination of results from a variety of studies and endpoints. While the functional assessment of CD8⁺ cytotoxic T-lymphocytes (CTL) is well-characterized in the clinic, the lack of a robust macaque CTL functional assay has been an important hurdle in evaluating and accurately quantifying cell-mediated CD8⁺ T-cell effector responses in the nonclinical setting. This paper describes the development of an assay to measure CTL activity in peripheral blood mononuclear cells (PBMC) isolated from Cynomolgus macaques. A human EGFR/CD3 Bispecific T-cell Engager (BiTE^®) was used to mount a robust CD8⁺ T-cell response in the presence of target-expressing cells. Upon target engagement, degranulation of CD107a and production of interferon (IFN)-γ both reliably indicated a robust functional response in CD8⁺ T-cells. The BiTE^®-mediated stimulation method proved to be favorable when compared to other methods of stimulation in the absence of target cells. These studies demonstrated acceptable longitudinal variability of the functional assay and sensitivity to dexamethasone-mediated immunosuppression. Taken together, the results indicated an assay leveraging CD3-bispecific antibodies and target-expressing cells can provide a robust approach to the in vitro or ex vivo assessment of CTL function in Cynomolgus macaques. Because the impairment of CTL activity by immunomodulators is recognized to be an important contributor to decreased antiviral defense and increased carcinogenicity risk, we believe that this novel assay to be a valuable addition to the immunotoxicology assessment of therapeutic drug candidates.

Behaviour of the Contact Phase of Blood Coagulation in the Adult Respiratory Distress Syndrome (ARDS)

In order to assess the role of the kallikrein-kinin (K-K) system in the pathogenesis of the adult respiratory distress syndrome (ARDS) we have prospectively determined coagulation contact phase, blood gas and hemodynamic parameters in patients with ARDS at 0, 36 and 72 h from diagnosis.

Compared to normal values, significantly lower mean levels of factor XII (71.4 ± 9.8%, p <0.0005), prekallikrein (PPK) (52 ± 5.7%, p <0.0005), high molecular weight kininogen (HMWK) (73 ± 2%, p <0.0005) and α2-macroglobulin (α2-M) (51 ± 7.1%, p <0.0005) were found in ARDS patients.

The functional kallikrein inhibitory activity (KKI) and Cr esterase inhibitor antigenic (CIINH) were significantly higher in these patients (113.2 ± 5, p <0.005 and 124.7 ± 7.6, p <0.0005 respectively) compared with normal values during the entire study period.

The KKI/CIINH ratio decreased significantly in our ARDS patients at 0, 36 and 72 h (p <0.025; p <0.05 and p <0.005 respectively).

We found a significant correlation between PPK levels and oxigenation index (r = 0.69, p <0.001), PPK and the static thoracic compliance values (r = 0.64, p <0.001). There was also a significant correlation between PPK levels and Qs/Qt (r = -0.89, p <0.001). ARDS patients that survived presented a stability in the PPK values in successive tests. Nevertheless non-survivors showed a progressive decrease in PPK levels during the follow-up period.

Our results suggest that the plasma kallikrein system becomes activated during ARDS and that this activation might increase the lung vessels’ permeability. In addition, PPK levels are in our opinion a useful prognostic parameter in predicting the outcome of ARDS patients.

Consumer acceptability of beef from two sexes supplemented with essential oil mix

Essential oils are natural extracts from plants which can be included in cattle diets as an alternative to additives, such as ionophores, to improve the shelf life of meat. The aim of this study was to evaluate the sensory acceptability of meat from 57 crossbred (1/2 Angus–1/2 Nellore) animals of different sexes [heifers n = 30, and young bulls n = 27], finished in feedlot with isoenergetic and isonitrogenous diets, which differed in the level of supplementation (0.0, 3.5 or 7.0 g/animal/day) with a commercial mix of essential oils (Mixoil®) from seven plants: oregano, garlic, lemon, rosemary, thyme, eucalyptus and sweet orange. The Longissimus thoracis muscle, aged for 24 h, was evaluated by 120 consumers who scored tenderness acceptability, flavour acceptability and overall acceptability using a hedonic 9-point scale. The inclusion of essential oils affected tenderness acceptability and flavour acceptability (P ≤ 0.01), with a tendency (P < 0.10) for overall acceptability. Meat from heifers was more appreciated by consumers than that from young bulls in all attributes (P ≤ 0.001), however, different groups of consumers had different preferences. The inclusion of a mix of essential oils in beef diets was well accepted by consumers, and could improve the acceptability of meat from young bulls, when is added at a concentration of 3.5 g/animal/day during the last 4 months of fattening.

Experience in the treatment of osseous hydatidosis

Osseous hydatidosis is a very uncommon disease which often recurs after treatment. There is no well-established effective method of management. Radical excision may produce serious mutilation and often fails to control the disease. We have used oral mebendazole as adjuvant treatment in four patients. Two also underwent radical excision, one had received limited excision elsewhere and the other did not have operative treatment. The patients who underwent radical excision and the other who did not have an operation became and remain free of symptoms and are serologically negative.A combination of excision and treatment with mebendazole may have a role in the management of this complex disease.

Assessing the immunomodulatory potential of therapeutic agents in cynomolgus macaque cytotoxic T lymphocytes

The preclinical evaluation of therapeutic agents contributes to the understanding of associated risks and benefits. The non-human primate, and notably the cynomolgus macaque, is often a species of choice for such pharmacological and toxicological assessments. The degree of immunomodulation associated with these agents, intended or not, is a critical point to consider in that context. While there are tools to immunophenotype and enumerate effector T cells, the knowledge gap surrounding the functional characterization of cytotoxic T lymphocytes (CTL) persists. Here we present a multi-parametric cynomolgus macaque CTL functional assay. By using an EGFR expressing target cell line co-cultured with cynomolgus peripheral blood mononuclear cells (PBMC) and an EGFR Bispecific T Cell Engager (BiTE®), we were able to redirect lysis in a target-specific manner. In this assay we simultaneously monitored cytolytic potential (CD107a) and cytokine secretion (IFN-γ and TNF-α) of effector CTL against target cell growth. Overall our results demonstrate the ability to assess cynomolgus CTL function under known immunosuppressive agents, thereby enabling a multi-parametric approach of monitoring the impact of investigational drugs on an important component of the immune system.