Cytokine biomarkers of exacerbations in sputum from Chronic Obstructive Pulmonary Disease patients: a prospective cohort study.

BACKGROUND: We determined the relationships between cytokine expression in sputum and clinical data to characterise and understand Chronic Obstructive Pulmonary Disease (COPD) exacerbations in COPD patients. METHODS: We measured 30 cytokines in 936 sputum samples, collected at stable state (ST) and exacerbation (EX) visits from 99 participants in the Acute Exacerbation and Respiratory InfectionS in COPD (AERIS) study (NCT01360398, www.clinicaltrials.gov). We determined their longitudinal expression and examined differential expression based on disease status or exacerbation type. RESULTS: Of the cytokines, 17 were suitable for analysis. As for disease states, in EX sputum samples, IL-17A, TNF-α, IL-1ß, and IL-10 were significantly increased compared to ST sputum samples, but a logistic mixed model could not predict disease state. As for exacerbation types, bacteria-associated exacerbations showed higher expression of IL-17A, TNF-α, IL-1ß, and IL-1α. IL-1α, IL-1ß, and TNF-α were identified as suitable biomarkers for bacteria-associated exacerbation. Bacteria-associated exacerbations also formed a cluster separate from other exacerbation types in principal component analysis. CONCLUSIONS: Measurement of cytokines in sputum from COPD patients could help identify bacteria-associated exacerbations based on increased concentrations of IL-1α, IL-1ß, or TNF-α. This finding may provide a point-of-care assessment to distinguish a bacterial exacerbation of COPD from other exacerbation types.

Direct contact and very rapid valgus distortion characterise the injury mechanism of anterior cruciate ligament ruptures in judo.

PURPOSE: To analyse anterior cruciate ligament (ACL) rupture (ACLR) injury mechanisms in competitive judo using systematic video analysis, focusing on contact situations and biomechanics. METHODS: Seventeen videos of judo competitions wherein athletes developed ACLRs were included and retrospectively evaluated by five analysts. In all videos, the moment of initial contact and the index frame were defined. The judo techniques leading to the injury; the occurrence of direct contact, indirect contact or noncontact mechanisms; the time interval between the initial contact and index frame; the positions of the hip, knee and foot in relation to the initial contact and index frame; and the balance status during the initial contact and index frame were recorded. RESULTS: Eleven (65%) of ACLRs in judo involved direct contact. The mean time interval between initial contact and index frame was 15 ± 22 ms. Thirteen (77%) athletes were not balanced at initial contact. In the index frame, the hip was abducted in all cases and in combination with internal rotation in 12 (71%) cases. From initial contact to index frame, hip flexion increased in all cases; at index frame, the knee joint was internally rotated relative to the trunk in 12 (71%) cases, and the knee flexion angles increased from the initial contact. In the index frame, the foot was externally rotated relative to the knee in 12 (71%) cases, and severe valgus development of the knee with valgus collapse was observed in 14 (82%) cases. CONCLUSIONS: A direct attack on the knee was the most common injury mechanism observed. Valgus distortion appears to be the most important component of the mechanism of injury. With this knowledge, 'modified defence reactions' for specific judo techniques can be developed to reduce the injury risk. LEVEL OF EVIDENCE: Level IV.

[Enthalpies: Evidence and theory applied to sterilization practice]. / Base de données Enthalpies : évidence et théorie appliquée à la pratique en stérilisation.

OBJECTIVES: In order to share their knowledge, sterilization unit managers publish the results of their work in journals or at scientific conferences. The aim of Enthalpies is to list all such work in a single database. The work presented describes the construction of this database and the assessment of its feasibility for the washing step. METHODS: The first step was to carry out a literature review. Only articles published over 10years (2013-2023) in connection with the ten-year washing stage were included. Then, each publication was categorized, coded, graded and summarized by a pharmacist-internal pair. All this data was collated in an Excel® spreadsheet, and from the data categorization a tree structure was created, enabling the interface between the user and the platform hosting Enthalpies to be understood. RESULTS: Eighty-one publications were identified. These were categorized into 6 themes and 27 sub-themes. A reading grid was drawn up for each publication. Genially®, an online platform, was chosen to host our database. CONCLUSION: Enthalpies was not designed to issue recommendations for best practice. However, by collating published scientific data, this tool can be used to assist decision-making. It represents an innovative solution for providing a literature review in the field of hospital sterilization.

Human NCR3 gene variants rs2736191 and rs11575837 alter longitudinal risk for development of pediatric malaria episodes and severe malarial anemia.

BACKGROUND: Plasmodium falciparum malaria is a leading cause of pediatric morbidity and mortality in holoendemic transmission areas. Severe malarial anemia [SMA, hemoglobin (Hb) < 5.0 g/dL in children] is the most common clinical manifestation of severe malaria in such regions. Although innate immune response genes are known to influence the development of SMA, the role of natural killer (NK) cells in malaria pathogenesis remains largely undefined. As such, we examined the impact of genetic variation in the gene encoding a primary NK cell receptor, natural cytotoxicity-triggering receptor 3 (NCR3), on the occurrence of malaria and SMA episodes over time. METHODS: Susceptibility to malaria, SMA, and all-cause mortality was determined in carriers of NCR3 genetic variants (i.e., rs2736191:C > G and rs11575837:C > T) and their haplotypes. The prospective observational study was conducted over a 36 mos. follow-up period in a cohort of children (n = 1,515, aged 1.9-40 mos.) residing in a holoendemic P. falciparum transmission region, Siaya, Kenya. RESULTS: Poisson regression modeling, controlling for anemia-promoting covariates, revealed a significantly increased risk of malaria in carriers of the homozygous mutant allele genotype (TT) for rs11575837 after multiple test correction [Incidence rate ratio (IRR) = 1.540, 95% CI = 1.114-2.129, P = 0.009]. Increased risk of SMA was observed for rs2736191 in children who inherited the CG genotype (IRR = 1.269, 95% CI = 1.009-1.597, P = 0.041) and in the additive model (presence of 1 or 2 copies) (IRR = 1.198, 95% CI = 1.030-1.393, P = 0.019), but was not significant after multiple test correction. Modeling of the haplotypes revealed that the CC haplotype had a significant additive effect for protection against SMA (i.e., reduced risk for development of SMA) after multiple test correction (IRR = 0.823, 95% CI = 0.711-0.952, P = 0.009). Although increased susceptibility to SMA was present in carriers of the GC haplotype (IRR = 1.276, 95% CI = 1.030-1.581, P = 0.026) with an additive effect (IRR = 1.182, 95% CI = 1.018-1.372, P = 0.029), the results did not remain significant after multiple test correction. None of the NCR3 genotypes or haplotypes were associated with all-cause mortality. CONCLUSIONS: Variation in NCR3 alters susceptibility to malaria and SMA during the acquisition of naturally-acquired malarial immunity. These results highlight the importance of NK cells in the innate immune response to malaria.

Historical evaluation of the in vivo adventitious virus test and its potential for replacement with next generation sequencing (NGS).

The Consortium on Adventitious Agent Contamination in Biomanufacturing (CAACB) collected historical data from 20 biopharmaceutical industry members on their experience with the in vivo adventitious virus test, the in vitro virus test, and the use of next generation sequencing (NGS) for viral safety. Over the past 20 years, only three positive in vivo adventitious virus test results were reported, and all were also detected in another concurrent assay. In more than three cases, data collected as a part of this study also found that the in vivo adventitious virus test had given a negative result for a sample that was later found to contain virus. Additionally, the in vivo adventitious virus test had experienced at least 21 false positives and had to be repeated an additional 21 times all while using more than 84,000 animals. These data support the consideration and need for alternative broad spectrum viral detection tests that are faster, more sensitive, more accurate, more specific, and more humane. NGS is one technology that may meet this need. Eighty one percent of survey respondents are either already actively using or exploring the use of NGS for viral safety. The risks and challenges of replacing in vivo adventitious virus testing with NGS are discussed. It is proposed to update the overall virus safety program for new biopharmaceutical products by replacing in vivo adventitious virus testing approaches with modern methodologies, such as NGS, that maintain or even improve the final safety of the product.

Life history of oysters influences Vibrio parahaemolyticus accumulation in Pacific oysters (Crassostrea gigas).

Vibrio parahaemolyticus infection in humans is associated with raw oyster consumption. Evaluation of V. parahaemolyticus presence in oysters is of most interest because of the economic and public health issues that it represents. To explore V. parahaemolyticus accumulation and depuration in adult Crassostrea gigas, we developed a GFP-tagged V. parahaemolyticus strain (IFVp201-gfp+ ), as well as a rapid and efficient quantification method in C. gigas oysters haemolymph by flow cytometry. Impact of the life history of C. gigas on accumulation and depuration of V. parahaemolyticus IFVp201 was subsequently investigated. We found that naive oysters, i.e. grown in controlled facilities with UV treated seawater, accumulated significantly more IFVp201 than environmental oysters, i.e. grown in intertidal environment. We hypothesized that environmental oysters could have been immune primed, thus could limit V. parahaemolyticus accumulation. Meanwhile, both naive and environmental oysters had similar depuration rates.

Yield of flow cytometry in addition to cytology for lymph node sampling in patients with incidental axillary adenopathy without a concurrent diagnosis of primary breast malignancy.

PURPOSE: Non-specific lymphadenopathy is increasingly being reported especially given the COVID-19 vaccination campaign and is a diagnostic dilemma especially in oncology patients. The purpose of this study was to evaluate the diagnostic accuracy and discordance rate between fine-needle aspiration (FNA) cytology and flow cytometry (FC) immunophenotyping in axillary FNA in patients with morphologically abnormal axillary lymph nodes on imaging and no concurrent diagnosis of primary breast malignancy. METHODS: This retrospective study included 222 patients who underwent screening or diagnostic axillary ultrasound that yielded suspicious lymphadenopathy without concurrent or recent prior diagnosis of breast cancer and who had subsequent image-guided axillary FNA and FC. Diagnostic accuracy, sensitivity, specificity, and positive and negative predictive value (PPV and NPV) were reported for FNA with cytology alone, and FC alone, and in combination. Discordance rate between FNA cytology and FC was assessed. Discordant cases were evaluated with histology or clinical and imaging follow-up. RESULTS: Diagnostic sensitivity, specificity, PPV, NPV, and diagnostic accuracy were 88%, 92%, 77%, 96%, and 91%, for FNA alone, 98%, 98%, 92%, 99%, and 98% for FC alone, and 100%, 92%, 79%, 100%, and 94% when combined. The overall discordance rate between FNA and FC was 7% (16/222). 7/16 (44%) patients with discordant results were diagnosed with lymphoma, while 9/16 (56%) patients with discordant results had benign findings. CONCLUSION: With a diagnostic accuracy of 91%, FNA with cytology is sufficient to screen patients with indeterminate and incidental lymphadenopathy. Flow cytometry could be initially deferred in patients with low pretest probability of lymphoma.

TIGA: target illumination GWAS analytics.

MOTIVATION: Genome-wide association studies can reveal important genotype-phenotype associations; however, data quality and interpretability issues must be addressed. For drug discovery scientists seeking to prioritize targets based on the available evidence, these issues go beyond the single study. RESULTS: Here, we describe rational ranking, filtering and interpretation of inferred gene-trait associations and data aggregation across studies by leveraging existing curation and harmonization efforts. Each gene-trait association is evaluated for confidence, with scores derived solely from aggregated statistics, linking a protein-coding gene and phenotype. We propose a method for assessing confidence in gene-trait associations from evidence aggregated across studies, including a bibliometric assessment of scientific consensus based on the iCite relative citation ratio, and meanRank scores, to aggregate multivariate evidence.This method, intended for drug target hypothesis generation, scoring and ranking, has been implemented as an analytical pipeline, available as open source, with public datasets of results, and a web application designed for usability by drug discovery scientists. AVAILABILITY AND IMPLEMENTATION: Web application, datasets and source code via https://unmtid-shinyapps.net/tiga/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Scale-Up to Pilot of a Non-Axenic Culture of Thraustochytrids Using Digestate from Methanization as Nitrogen Source.

The production of non-fish based docosahexaenoic acid (DHA) for feed and food has become a critical need in our global context of over-fishing. The industrial-scale production of DHA-rich Thraustochytrids could be an alternative, if costs turned out to be competitive. In order to reduce production costs, this study addresses the feasibility of the non-axenic (non-sterile) cultivation of Aurantiochytrium mangrovei on industrial substrates (as nitrogen and mineral sources and glucose syrup as carbon and energy sources), and its scale-up from laboratory (250 mL) to 500 L cultures. Pilot-scale reactors were airlift cylinders. Batch and fed-batch cultures were tested. Cultures over 38 to 62 h achieved a dry cell weight productivity of 3.3 to 5.5 g.L-1.day-1, and a substrate to biomass yield of up to 0.3. DHA productivity ranged from 10 to 0.18 mg.L-1.day-1. Biomass productivity appears linearly related to oxygen transfer rate. Bacterial contamination of cultures was low enough to avoid impacts on fatty acid composition of the biomass. A specific work on microbial risks assessment (in supplementary files) showed that the biomass can be securely used as feed. However, to date, there is a law void in EU legislation regarding the recycling of nitrogen from digestate from animal waste for microalgae biomass and its usage in animal feed. Overall, the proposed process appears similar to the industrial yeast production process (non-axenic heterotrophic process, dissolved oxygen supply limiting growth, similar cell size). Such similarity could help in further industrial developments.

Epidemiology of Injuries in Olympic Sports.

Injuries effect the performance of athletes. Severity of injuries is determined by time loss and sporting performance reduction. To treat injuries adequately, it is necessary to get an overview of varied injuries types in different sports disciplines. In a retrospective study 7.809 athletes from Germany, Switzerland and Austria competing in competitive or recreational levels of sports were included. Injury prevalence was highest in team sports (75%), followed by combat (64%), racquet (54%) and track and field (51%). Knee (28%) and shoulder (14%) were the most at risk joints. Time loss in sporting activity after injury was longest in the region of knee (26 weeks). Of all reported injuries, 48% were accompanied by a reduced level of performance. The highest injury prevalence occurred in the year 2016 (45%). More injuries occurred during training (58%) compared to competition (42%). Across Olympic disciplines, a large number of injuries occurred during training sessions. Injury frequency increased as the Olympic games drew closer. Knee and shoulder injuries were the most severe injuries with respect to time loss and reduction sporting performance.

Modified defense reaction reduces biomechanical and myoelectrical ACL injury risk factors in elite Judo.

In judo, an anterior cruciate ligament (ACL) injury is the most severe injury an athlete could experience. Most ACL ruptures occur when defending against an osoto-gari attack. This study aims to identify ACL risk factors during osoto-gari defence and implement a modified osoto-gari defence reaction, which is assumed to improve myoelectric patterns and ameliorate critical biomechanical risk factors for ACL injuries. Twenty-six elite judokas were enrolled in the cross-over trial (female: 6; male: 20). 3D kinematics and force dynamometrics were combined with electromyographical recordings to assess the effects of the common and the modified osoto-gari defence reaction. Compared to the common osoto-gari defence reaction (maximal knee flexion: 29 ± 12°; maximal valgus: 10 ± 5°; maximal valgus moment: 58 ± 17 Nm; peak internal rotation: 9 ± 5°), the modified osoto-gari defence reaction showed significantly reduced knee angles (31 ± 10° p < 0.05; 1 ± 0° p < 0.05; 31 ± 9 Nm p < 0.05; 3 ± 0° p < 0.05). The myoelectric activity of the hamstring increased (+5±% to +27±%, p < 0.05) in the modified compared to common defence reaction. The modified osoto-gari defence reaction reduced critical biomechanical risk factors and increased hamstring myoelectric activity. We recommend the implementation of the modified osoto-gari defence reaction in judo practice and seek to evaluate its long-term effectiveness in decreasing ACL injury incidences in elite judo.

Microbes support enhanced nitrogen requirements of coral holobionts in a high CO2 environment.

Ocean acidification is posing a threat to calcifying organisms due to the increased energy requirements of calcification under high CO2 conditions. The ability of scleractinian corals to cope with future ocean conditions will thus depend on their ability to fulfil their carbon requirement. However, the primary productivity of coral holobionts is limited by low nitrogen (N) availability in coral reef waters. Here, we employed CO2  seeps of Tutum Bay (Papua New Guinea) as a natural laboratory to understand how coral holobionts offset their increased energy requirements under high CO2 conditions. Our results demonstrate for the first time that under high pCO2 conditions, N assimilation pathways of Pocillopora damicornis are jointly modified. We found that diazotroph-derived N assimilation rates in the Symbiodiniaceae were significantly higher in comparison to an ambient CO2 control site, concomitant with a restructured diazotroph community and the specific prevalence of an alpha-proteobacterium. Further, corals at the high CO2  site also had increased feeding rates on picoplankton and in particular exhibited selective feeding on Synechococcus sp., known to be rich in N. Given the high abundance of picoplankton in oligotrophic waters at large, our results suggest that corals exhibiting flexible diazotrophic communities and capable of exploiting N-rich picoplankton sources to offset their increased N requirements may be able to cope better in a high pCO2 world.

A 13CO2 Enrichment Experiment to Study the Synthesis Pathways of Polyunsaturated Fatty Acids of the Haptophyte Tisochrysis lutea.

The production of polyunsaturated fatty acids (PUFA) in Tisochrysis lutea was studied using the gradual incorporation of a 13C-enriched isotopic marker, 13CO2, for 24 h during the exponential growth of the algae. The 13C enrichment of eleven fatty acids was followed to understand the synthetic pathways the most likely to form the essential polyunsaturated fatty acids 20:5n-3 (EPA) and 22:6n-3 (DHA) in T. lutea. The fatty acids 16:0, 18:1n-9 + 18:3n-3, 18:2n-6, and 22:5n-6 were the most enriched in 13C. On the contrary, 18:4n-3 and 18:5n-3 were the least enriched in 13C after long chain polyunsaturated fatty acids such as 20:5n-3 or 22:5n-3. The algae appeared to use different routes in parallel to form its polyunsaturated fatty acids. The use of the PKS pathway was hypothesized for polyunsaturated fatty acids with n-6 configuration (such as 22:5n-6) but might also exist for n-3 PUFA (especially 20:5n-3). With regard to the conventional n-3 PUFA pathway, Δ6 desaturation of 18:3n-3 appeared to be the most limiting step for T. lutea, "stopping" at the synthesis of 18:4n-3 and 18:5n-3. These two fatty acids were hypothesized to not undergo any further reaction of elongation and desaturation after being formed and were therefore considered "end-products". To circumvent this limiting synthetic route, Tisochrysis lutea seemed to have developed an alternative route via Δ8 desaturation to produce longer chain fatty acids such as 20:5n-3 and 22:5n-3. 22:6n-3 presented a lower enrichment and appeared to be produced by a combination of different pathways: the conventional n-3 PUFA pathway by desaturation of 22:5n-3, the alternative route of ω-3 desaturase using 22:5n-6 as precursor, and possibly the PKS pathway. In this study, PKS synthesis looked particularly effective for producing long chain polyunsaturated fatty acids. The rate of enrichment of these compounds hypothetically synthesized by PKS is remarkably fast, making undetectable the 13C incorporation into their precursors. Finally, we identified a protein cluster gathering PKS sequences of proteins that are hypothesized allowing n-3 PUFA synthesis.

Impact of a visual indicator on the noise level in an emergency medical dispatch centre - a pilot study.

BACKGROUND: Noise levels are monitored in call centres. A maximum of 52 to 55 dB(A) is recommended in order to prevent adverse events. We aimed at assessing the noise level and the impact of a visual noise indicator on the ambient noise level in a French Regional Emergency Medical Dispatch Centre (EMDC). METHODS: We conducted an observational study in the EMDC of the SAMU25 (University Hospital of Besancon). We measured the noise level using a SoundEarII® noise indicator (Dräger Medical SAS, France). The measurement took place in two phases on three consecutive days from 00:00 to 11:59 PM. At baseline, phase 1, the device recorded the average ambient noise for each minute without visual indication. Secondly, phase 2 included a sensor mounted with a light that would turn on green if noise was below 65 dB(A), orange if noise ever exceeded 65 and red if it exceeded 75 dB(A). RESULTS: In the presence of the visual noise indicator, the LAeq was significantly lower than in the absence of visual noise indicator (a mean difference of - 4.19 dB; P < 10-3). It was higher than 55 dB(A) in 84.9 and 43.9% of the time in phases 1 and 2, respectively. CONCLUSIONS: The noise levels were frequently higher than the standards, and sometimes close to recommended limits, requiring preventive measures. The noise indicator had a positive effect on the ambient noise level. This work will allow the implementation of effective prevention solutions and, based on future assessments, could improve operators' well-being and better care for patient.

Selection of Vibrio crassostreae relies on a plasmid expressing a type 6 secretion system cytotoxic for host immune cells.

Pacific oyster mortality syndrome affects juveniles of Crassostrea gigas oysters and threatens the sustainability of commercial and natural stocks of this species. Vibrio crassostreae (V. crassostreae) has been repeatedly isolated from diseased animals, and the majority of the strains have been demonstrated to be virulent for oysters. In this study, we showed that oyster farms exhibited a high prevalence of a virulence plasmid carried by V. crassostreae, while oysters, at an adult stage, were reservoirs of this virulent population. The pathogenicity of V. crassostreae depends on a novel transcriptional regulator, which activates the bidirectional promoter of a type 6 secretion system (T6SS) genes cluster. Both the T6SS and a second chromosomal virulence factor, r5.7, are necessary for virulence but act independently to cause haemocyte (oyster immune cell) cytotoxicity. A phylogenetically closely related T6SS was identified in V. aestuarianus and V. tapetis, which infect adult oysters and clams respectively. We propose that haemocyte cytotoxicity is a lethality trait shared by a broad range of mollusc pathogens, and we speculate that T6SS was involved in parallel evolution of pathogen for molluscs.

Cyclooxygenase-2 haplotypes influence the longitudinal risk of malaria and severe malarial anemia in Kenyan children from a holoendemic transmission region.

Cyclooxygenase-2 [(COX-2) or prostaglandin endoperoxide H2 synthase-2 (PTGS-2)] induces the production of prostaglandins as part of the host-immune response to infections. Although a number of studies have demonstrated the effects of COX-2 promoter variants on autoimmune and inflammatory diseases, their role in malaria remains undefined. As such, we investigated the relationship between four COX-2 promoter variants (COX-2 -512 C > T, -608 T > C, -765 G > C, and -1195 A > G) and susceptibility to malaria and severe malarial anemia (SMA) upon enrollment and longitudinally over a 36-month follow-up period. All-cause mortality was also explored. The investigation was carried out in children (n = 1081, age; 2-70 months) residing in a holoendemic Plasmodium falciparum transmission region of western Kenya. At enrollment, genotypes/haplotypes (controlling for anemia-promoting covariates) did not reveal any strong effects on susceptibility to either malaria or SMA. Longitudinal analyses showed decreased malaria episodes in children who inherited the -608 CC mutant allele (RR = 0.746, P = 1.811 × 10-4) and -512C/-608T/-765G/-1195G (CTGG) haplotype (RR = 0.856, P = 0.011), and increased risk in TTCA haplotype carriers (RR = 1.115, P = 0.026). Over the follow-up period, inheritance of the rare TTCG haplotype was associated with enhanced susceptibility to both malaria (RR = 1.608, P = 0.016) and SMA (RR = 5.714, P = 0.004), while carriage of the rare TTGG haplotype increased the risk of malaria (RR = 1.755, P = 0.007), SMA (RR = 8.706, P = 3.97 × 10-4), and all-cause mortality (HR = 110.000, P = 0.001). Collectively, these results show that SNP variations in the COX-2 promoter, and their inherited combinations, are associated with the longitudinal risk of malaria, SMA, and all-cause mortality among children living in a high transmission area for P. falciparum.

LocalControl: An R Package for Comparative Safety and Effectiveness Research.

The LocalControl R package implements novel approaches to address biases and confounding when comparing treatments or exposures in observational studies of outcomes. While designed and appropriate for use in comparative safety and effectiveness research involving medicine and the life sciences, the package can be used in other situations involving outcomes with multiple confounders. LocalControl is an open-source tool for researchers whose aim is to generate high quality evidence using observational data. The package implements a family of methods for non-parametric bias correction when comparing treatments in observational studies, including survival analysis settings, where competing risks and/or censoring may be present. The approach extends to bias-corrected personalized predictions of treatment outcome differences, and analysis of heterogeneity of treatment effect-sizes across patient subgroups.

Side Differences Regarding the Limb Symmetry Index in Healthy Professional Athletes.

Side differences in the limb symmetry index during hop tests have been rarely investigated in uninjured athletes. Unknown differences can result in false interpretation of hop tests and affect return to sport decision. Hypothesis was that un-injured athletes in Judo and Taekwondo have side differences in hop test and that asymmetries can be predicted based on the athletes fighting display. Differences, risk relationships were analyzed using the chi-squared test and the odds ratio. A two-tailed p value of<0.05 was considered statistically significant. 115 athletes from the national teams were included (mean age 18.4 years; range 13-27 years). 93, 97.4 and 98.3% did not have symmetric hop distance for three hop tests. Up to a quarter did not reach a limb symmetry index of>90. Moreover, 57.4% (n=66) reached longer jumping distance with the standing leg. Ignoring such pre-existent side differences in evaluation of hop tests and not knowing which limb was dominant prior the injury, can lead to premature or delayed return to sports in the rehabilitation process. Therefore, it might be helpful to refer to individual jump lengths for each limb in case of injury by using hop tests in pre-season screening in professional athletes in Judo and Taekwondo.

STRAIN: an R package for multi-locus sequence typing from whole genome sequencing data.

BACKGROUND: Multi-locus sequence typing (MLST) is a standard typing technique used to associate a sequence type (ST) to a bacterial isolate. When the output of whole genome sequencing (WGS) of a sample is available the ST can be assigned directly processing the read-set. Current approaches employ reads mapping (SRST2) against the MLST loci, k-mer distribution (stringMLST), selective assembly (GRAbB) or whole genome assembly (BIGSdb) followed by BLASTn sequence query. Here we present STRAIN (ST Reduced Assembly IdentificatioN), an R package that implements a hybrid strategy between assembly and mapping of the reads to assign the ST to an isolate starting from its read-sets. RESULTS: Analysis of 540 publicly accessible Illumina read sets showed STRAIN to be more accurate at correct allele assignment and new alleles identification compared to SRTS2, stringMLST and GRAbB. STRAIN assigned correctly 3666 out of 3780 alleles (capability to identify correct alleles 97%) and, when presented with samples containing new alleles, identified them in 3730 out of 3780 STs (capability to identify new alleles 98.7%) of the cases. On the same dataset the other tested tools achieved lower capability to identify correct alleles (from 28.5 to 96.9%) and lower capability to identify new alleles (from 1.1 to 97.1%). CONCLUSIONS: STRAIN is a new accurate method to assign the alleles and ST to an isolate by processing the raw reads output of WGS. STRAIN is also able to retrieve new allele sequences if present. Capability to identify correct and new STs/alleles, evaluated on a benchmark dataset, are higher than other existing methods. STRAIN is designed for single allele typing as well as MLST. Its implementation in R makes allele and ST assignment simple, direct and prompt to be integrated in wider pipeline of downstream bioinformatics analyses.

Genetic variation in interleukin-7 is associated with a reduced erythropoietic response in Kenyan children infected with Plasmodium falciparum.

BACKGROUND: Severe malarial anemia (SMA) is a leading cause of malaria-related morbidity and mortality in children. The genetic factors that influence development of SMA and inefficient erythropoiesis, a central pathogenic feature of SMA, are only partially understood. METHODS: We performed a pilot Genome-wide Association Study (GWAS) on children with Plasmodium falciparum. The GWAS was performed using the Illumina® Infinium® HD Super Assay in conjunction with Illumina's® Human Omni2.5-8v1 BeadChip (with > 2.45 M markers). Data were analyzed using single SNP logistic regression analysis with an additive model of inheritance controlling for covariates. Results from our pilot global genomics study identified that variation in interleukin (IL)-7 was associated with enhanced risk of SMA. To validate this finding, we investigated the relationship between genotypes and/or haplotypes of two single nucleotide polymorphisms (SNPs) in IL7 [72194 T/C and - 2440 A/G] and susceptibility to both SMA and inefficient erythropoiesis [i.e., reticulocyte production index (RPI) < 2.0 in anemic children (Hb < 11.0 g/dL). Children presenting with P. falciparum malaria (< 3 years, n = 883) were stratified into two groups: Uncomplicated malaria (UM, n = 718) and SMA (n = 165). RESULTS: Regression modeling, controlling for anemia-related confounders, revealed that carriage of the TC genotype at position 72194 T/C was associated with enhanced susceptibility to inefficient erythropoiesis (OR = 1.90; 95% CI 1.09-3.30; P = 0.02) as was homozygous CC (OR 5.14; 95% CI = 1.20-21.99; P = 0.03). Consistent with this finding, individuals with the CA (72194C/-2440A) haplotype had an increased risk of inefficient erythropoiesis (OR = 1.90; 95% CI = 1.10-3.30; P = 0.02), whereas TA haplotype carriers had marginal protection against inefficient erythropoiesis (OR = 0.24; 95% CI = 0.06-1.21; P = 0.05). These observations were supported by Cochran-Armitage trend test for inefficient erythropoiesis (CA > TA > CG; P < 0.01). Although none of the genotype and/or haplotypic variants were significantly associated with SMA, the direction of the risk profiles were consistent with the erythropoiesis results. CONCLUSION: Taken together, variation in IL7 is associated with erythropoietic responses in children with falciparum malaria, a central physiological feature contributing to development of SMA.