Miracle-dz/UniFAR-FTUs huggingface dataset:
Salmonella Typhimurium strain expressing OprF‐OprI protects mice against fatal infection by Pseudomonas aeruginosa

Pseudomonas aeruginosa poses a major threat to human health and to the mink industry. Thus, development of vaccines that elicit robust humoral and cellular immunity against P. aeruginosa is greatly needed. In this study, a recombinant attenuated Salmonella vaccine (RASV) that expresses the outer membrane proteins fusion OprF190–342‐OprI21–83 (F1I2) from P. aeruginosa was constructed and the potency of this vaccine candidate assessed by measuring F1I2‐specific humoral immune responses upon vaccination through s.c. or oral routes. S.C. administration achieved higher serum IgG titers and IgA titers in the intestine and induced stronger F1I2‐specific IgG and IgA titers in lung homogenate than did oral administration, which resulted in low IgG titers and no local IgA production. High titers of IFN‐γ, IL‐4, and T‐lymphocyte subsets induced a mixed Th1/Th2 response in mice immunized s.c. , indicating elicitation of cellular immunity. Importantly, when immunized mice were challenged with P. aeruginosa by the intranasal route 30 days after the initial immunization, s.c. vaccination achieved 77.78% protection, in contrast to 41.18% via oral administration and 66.67% via Escherichia coli‐expressed F1I2 (His‐F1I2) vaccination. These results indicate that s.c. vaccination provides a better protective response against P. aeruginosa infection than do oral administration and the His‐F1I2 vaccine.
Early‐shared Mycobacterium bovis bacillus Calmette–Guérin sub‐strains induce Th1 cytokine production in vivo

Interleukin‐12 is one of the cytokines that induce acquired immunity by progressing the differentiation of T cells. When antigens are presented by APCs, including macrophages and DCs, T cells are activated and produce the Th1 cytokines IL‐2 and IFN‐γ. We have previously reported greater IL‐12 production from macrophages infected with early‐shared BCG sub‐strains (ex. BCG‐Japan, ‐Sweden) than from those infected with late‐shared BCG (ex. BCG‐Pasteur and ‐Connaught) . In this study, we investigated the Th1 cytokine‐inducing activity of splenocytes co‐cultured with BCG‐infected DCs. Early‐shared BCG‐infected DCs produced IL‐12 and TNF‐α⋅ Furthermore, when they were co‐cultured with purified protein derivative‐stimulated DCs, the splenocytes of mice immunized with BCG‐Tokyo/Japan produced more Th1 cytokine than did those of mice immunized with BCG‐Connaught. In conclusion, early‐shared BCG sub‐strains more strongly induce Th1 cytokine production in vivo. This study provides basic information to inform the selection of candidates for primary vaccination.
A novel method for the contactless and continuous measurement of arterial blood pressure on a sleeping bed

Nighttime blood pressure (BP) is found to best predict the 5-year risk of cardiovascular death in comparison to daytime BP, BP measured over a 24-hour period and clinical BP. In view of this, a novel contactless system has been developed on a sleeping bed for the cuffless and continuous estimation of BP at night. Experiments were conducted on 11 subjects to evaluate the contactless system, particularly its performance compared to a contact system. The results of this study showed that the accuracy of the contactless system to estimate BP by a cuffless approach is comparable to that of the contact system when measured at the same posture. More studies have to be conducted in order to understand the difference of the cuffless BP estimation approach when measuring at supine and sitting postures.
Reflexões metodológicas para o estudo das práticas alimentares

Human nutrition is a very complex phenomenon as it invites at the same time the physiology, the psychology and the socio-cultural. That's also why food practice measures have caused the development of tools and methodologies within several disciplines. This article presents the approach of sociology and anthropology. It defines first of all the different dimensions of the social food space; from the eatable order to the process of social differentiation via the culinary, the consumption forms and the temporality. It analyses in detail the data types which can be used taking care in distinguishing the behavioural data that can be obtained either by observation or by declaration from the representation data. It presents the different collect tools and the ways of entry in the food phenomenon. These methodological tools built within a sociological theoretical framing are proposed to the researchers engaged in the study of the food facts so as to walk towards a pooling likely to result on a multi-field approach.
Cytotoxic T lymphocyte therapy with donor T cells prevents and treats adenovirus and Epstein-Barr virus infections after haploidentical and matched unrelated stem cell transplantation.

Viral infection or reactivation remains a major cause of morbidity and mortality after allogeneic stem cell transplantation. We now show that infusions of single cytotoxic T lymphocyte (CTL) lines (5 x 10(6)-1.35 x 10(8) cells/m(2)) with specificity for 2 commonly detected viruses, Epstein-Barr virus (EBV) and adenovirus, can be safely administered to pediatric transplantation recipients receiving partially human leukocyte antigen-matched and haploidentical stem cell grafts (n = 13), without inducing graft-versus-host disease. The EBV-specific component of the CTLs expanded in vivo and persisted for more than 12 weeks, but the adenovirus-specific component only expanded in vivo in the presence of concomitant adenoviral infection. Nevertheless, adenovirus-specific T cells could be detected for at least 8 weeks in peripheral blood, even in CTL recipients without viral infection, provided the adenovirus-specific component of their circulating lymphocytes was first expanded by exposure to adenoviral antigens ex vivo. After infusion, none of these 13 high-risk recipients developed EBV-associated lymphoproliferative disease, while 2 of the subjects had resolution of their adenoviral disease. Hence, bispecific CTLs containing both EBV- and adenovirus-specific T cells can safely reconstitute an antigen responsive "memory" population of CTLs after human leukocyte antigen-mismatched stem cell transplantation and may provide antiviral activity. This trial was registered at www.clinicaltrials. gov as #NCT00590083.
Docking Ligands into Flexible and Solvated Macromolecules, 7. Impact of Protein Flexibility and Water Molecules on Docking-Based Virtual Screening Accuracy

The use of predictive computational methods in the drug discovery process is in a state of continual growth. Over the last two decades, an increasingly large number of docking tools have been developed to identify hits or optimize lead molecules through in-silico screening of chemical libraries to proteins. In recent years, the focus has been on implementing protein flexibility and water molecules. Our efforts led to the development of Fitted first reported in 2007 and further developed since then. In this study, we wished to evaluate the impact of protein flexibility and occurrence of water molecules on the accuracy of the Fitted docking program to discriminate active compounds from inactive compounds in virtual screening (VS) campaigns. For this purpose, a total of 171 proteins cocrystallized with small molecules representing 40 unique enzymes and receptors as well as sets of known ligands and decoys were selected from the Protein Data Bank (PDB) and the Directory of Useful Decoys (DUD), respectively. This study revealed that implementing displaceable crystallographic or computationally placed particle water molecules and protein flexibility can improve the enrichment in active compounds. In addition, an informed decision based on library diversity or research objectives (hit discovery vs lead optimization) on which implementation to use may lead to significant improvements.
What is the definition of sports-related concussion: a systematic review

Objectives Various definitions for concussion have been proposed, each having its strengths and weaknesses. We reviewed and compared current definitions and identified criteria necessary for an operational definition of sports-related concussion (SRC) in preparation of the 5th Concussion Consensus Conference (Berlin, Germany). We also assessed the role of biomechanical studies in informing an operational definition of SRC. Design This is a systematic literature review. Data sources Data sources include MEDLINE, Embase, Cumulative Index to Nursing and Allied Health Literature, Cochrane Central Register of Clinical Trials and SPORT Discus (accessed 14 September 2016). Eligibility criteria for selecting studies Eligibility criteria were studies reporting (clinical) criteria for diagnosing SRC and studies containing SRC impact data. Results Out of 1601 articles screened, 36 studies were included (2.2%), 14 reported on criteria for SRC definitions and 22 on biomechanical aspects of concussions. Six different operational definitions focusing on clinical findings and their dynamics were identified. Biomechanical studies were obtained almost exclusively on American football players. Angular and linear head accelerations linked to clinically confirmed concussions demonstrated considerable individual variation. Summary/conclusions SRC is a traumatic brain injury that is defined as a complex pathophysiological process affecting the brain, induced by biomechanical forces with several common features that help define its nature. Limitations identified include that the current criteria for diagnosing SRC are clinically oriented and that there is no gold/standard to assess their diagnostic properties. A future, more valid definition of SRC would better identify concussed players by demonstrating high predictive positive/negative values. Currently, the use of helmet-based systems to study the biomechanics of SRC is limited to few collision sports. New approaches need to be developed to provide objective markers for SRC.
Molecular cloning of IgZ heavy chain isotype in Catla catla and comparative expression profile of IgZ and IgM following pathogenic infection

Immunoglobulins serve as a crucial arm of the adaptive immune system against detrimental pathogenic threats in teleosts. However, whether the novel Ig isotype IgZ is present in the Indian major carp, Catla catla, has not yet been elucidated. The present study reports the presence of IgZ ortholog in C. catla (CcIgZ) and further demonstrates its comparative tissue specific expression with IgM (CcIgM) in response to bacterial and parasitic stimulation. The putative 139 amino acid sequence of IgZ heavy chain cDNA of C. catla showed homology with IgZ constant domains of other teleosts. Phylogenetic analysis of the predicted IgZ transcript sequence clustered with previously identified IgZ heavy chain sequences of Cyprinidae family members. The inductive expression profiles of IgZ and IgM genes were evaluated in immunologically relevant tissues at 24, 48 and 72 hr post infection with Aeromonas hydrophila, Streptococcus uberis and Argulus sp. Both CcIgZ and CcIgM were expressed most strongly in the kidneys of healthy fish. Basal expression of CcIgM transcript was higher than that of CcIgZ in all the examined tissues. Stimulation with bacteria triggered significant increase of IgZ in the intestine (P < 0.001) and spleen (P < 0.01), whereas IgM was relatively up‐regulated in blood (P < 0.001) after stimulation with each of the three pathogens assessed. The study is the first to report identification of IgZ in C. catla. Further, it provides insights into the differential expression profiles of IgZ and IgM isotypes against various pathogenic infection in C. catla, which may facilitate better prophylaxis again such infections.
Acute:chronic training loads in tennis: which metrics should we monitor?

Recently, Pluim and Drew1 provided tips for managing loads to help reduce injury risk in tennis. A central premise was the importance for assessing the acute:chronic loads—a concept to understand that the rate of change towards high weekly loads is more problematic (ie, increases injury risk) than simply performing high loads. In general, activities performed by athletes can be viewed as stress (ie, external loads like running distances or the number of accelerations/decelerations performed) and strain (ie, internal loads like heart rate, blood lactate). Thus, metrics from several domains are necessary to comprehensively quantify training and competition loads; however, there is a paucity of literature describing these indicators for tennis across the developmental spectrum. This knowledge gap limits the ability to identify which key metrics should be targeted within a systematic monitoring plan and subsequently used to track the acute:chronic loads in tennis, thus enabling the development of strategies to reduce injury risk. To …
Genomic sequence and virulence evaluation of MN184A‐like porcine reproductive and respiratory syndrome virus in Japan

In this study, a porcine reproductive and respiratory syndrome virus (PRRSV) that was isolated from a 9‐week‐old diseased pig on a farm in Japan with a high mortality rate during 2007–2008 was characterized. This unique isolate, designated as Jpn5‐37, did not have a high nucleotide identity in open reading frame 5 against any Japanese isolates. Among all available type 2 PRRSV complete genome sequences, Jpn5‐37 shared the highest nucleotide identity (93.6%) with virulent strain MN184A. The genomic characteristics of Jpn5‐37 were highly conserved with respect to the virulent MN184A, including a continuous eight amino acid deletion in the nonstructural protein 2 region. Moreover, virus distribution, viremia and the gross and microscopic characteristics of lesions were investigated in pigs 10 days post‐inoculation to elucidate the pathogenicity of the isolate. Intranasal inoculation was found to rapidly result in viremia and dissemination of the Jpn5‐37 isolate to several tissues in a similar manner to EDRD1; however, the amounts of Jpn5‐37 RNA in serum were significantly greater. Similarly, the quantities of Jpn5‐37 viral RNA in all organs tested tended to be higher than with EDRD1 infection. Mean rectal temperatures were significantly higher in the Jpn5‐37‐inoculated than in the control group at 4 and 6 days post infection (dpi) and in the EDRD1‐inoculated group at 6 and 8 dpi. These results suggest that the Jpn5‐37 strain replicates and is more efficiently distributed to the organs than is EDRD1 under the same conditions.
Bright spots, physical activity investments that work: JUMP-in: promoting physical activity and healthy nutrition at primary schools in Amsterdam

### Graphic programme card Regular physical activity (PA) is vital to children’s health. Therefore, to battle its decline among Amsterdam’s children, in 2002 the intervention Jump-in was developed.1 Jump-in is a primary school-based, preventive intervention focused on stimulating children’s healthy nutrition and PA, especially targeting schools where overweight prevalence is highest. Jump-in schools stimulate children to be physically active and discover different types of sports and to stimulate their structural …
Energy expenditure estimation using triaxial accelerometry and barometric pressure measurement

Energy expenditure (EE) is a parameter of great relevance in studies involving the assessment of physical activity. However, most reliable techniques for EE estimation are impractical for use in free-living environments, and those which are practically useful often poorly track EE when the subject is working to change their altitude, for example when ascending or descending stairs or slopes. The aim of this study is to evaluate the utility of adding barometric pressure related features, as a surrogate measure for altitude, to existing accelerometry related features to estimate the subject's EE. The EE estimation system described is based on a triaxial accelerometer (triax) and a barometric pressure sensor. The device is wireless, with Bluetooth connectivity for data retrieval, and is mounted at the subject's waist. Using a number of features extracted from the triax and barometric pressure signals, a linear model is trained for EE estimation. This EE estimation model is compared to its counterpart, which solely utilizes accelerometry signals. A protocol (comprising lying, sitting, standing, walking phases) was performed by 13 healthy volunteers (8 male and 5 female; age: 23.8 ± 3.7 years; weight: 70.5 ± 14.9 kg), whose instantaneous oxygen uptake was measured by means of an indirect calorimetry system. The model incorporating barometric pressure information estimated the oxygen uptake with the lowest mean square error of 4.5±1.7 (mlO2.min−1.kg−1)2, in comparison to 7.1±2.3 (mlO2.min−1.kg−1)2 using only accelerometry-based features.
Screening for Bacteriuria With a Test Paper for Glucose

A glucose-specific test paper which is sufficiently sensitive to react with the small amounts of glucose present in urine from normal persons in the fasting state can be used to discriminate between urine samples containing more than and those containing less than 1 to 1.5 mg of glucose per 100 ml of urine. This provides a screening method for significant bacteriuria in an apparently healthy population since urine samples, obtained under standardized conditions from subjects in the fasting state with such bacteriuria, contain either very little or no glucose.
Genetic characterization of an avian H4N6 influenza virus isolated from the Izumi plain, Japan

An influenza A virus of H4N6 subtype was isolated from the Izumi plain, Japan, in 2013. Genetic analyses revealed that two viral genes (M and NS gene segments) of this isolate were genetically distinct from those of the H4N6 virus isolated from the same place in 2012. Furthermore, three viral genes (PB2, PB1 and M gene segments) of this isolate share high similarity with those of the North American isolates of 2014. These results suggest a high frequency of genetic reassortment of avian influenza viruses in Asian waterfowl and intercontinental movements of avian influenza viruses via migratory waterfowl.
DOCKTITE - A Highly Versatile Step-by-Step Workflow for Covalent Docking and Virtual Screening in the Molecular Operating Environment

The formation of a covalent bond with the target is essential for a number of successful drugs, yet tools for covalent docking without significant restrictions regarding warhead or receptor classes are rare and limited in use. In this work we present DOCKTITE, a highly versatile workflow for covalent docking in the Molecular Operating Environment (MOE) combining automated warhead screening, nucleophilic side chain attachment, pharmacophore-based docking, and a novel consensus scoring approach. The comprehensive validation study includes pose predictions of 35 protein/ligand complexes which resulted in a mean RMSD of 1.74 Å and a prediction rate of 71.4% with an RMSD below 2 Å, a virtual screening with an area under the curve (AUC) for the receiver operating characteristics (ROC) of 0.81, and a significant correlation between predicted and experimental binding affinities (ρ = 0.806, R(2) = 0.649, p < 0.005).
So you want to understand subsequent injuries better? Start by understanding the minimum data collection and reporting requirements

In recent years, there has been increasing recognition of the importance of adequately describing multiple and subsequent injuries in sports injury datasets.1 2 Such information is needed to answer questions such as: Sports medicine professionals will often consider these questions when athletes present with certain injury profiles. When diagnosing injuries and determining suitable rehabilitation and recovery programmes, sports medicine professionals need to make links between the past, the present and the expected future injury outcomes. Suspecting links and decision making in relation to them should be evidence informed. Epidemiologists also ask similar questions at a broader level across populations or groups of athletes. Epidemiological answers to the above questions can provide important evidence to inform and underpin clinical decision making, but only when based on relevant and robust data. This editorial proposes a …
Interim positron emission tomography scans in diffuse large B-cell lymphoma: an independent expert nuclear medicine evaluation of the Eastern Cooperative Oncology Group E3404 study.

Positive interim positron emission tomography (PET) scans are thought to be associated with inferior outcomes in diffuse large B-cell lymphoma. In the E3404 diffuse large B-cell lymphoma study, PET scans at baseline and after 3 cycles of rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone were centrally reviewed by a single reader. To determine the reproducibility of interim PET interpretation, an expert panel of 3 external nuclear medicine physicians visually scored baseline and interim PET scans independently and were blinded to clinical information. The binary Eastern Cooperative Oncology Group (ECOG) study criteria were based on modifications of the Harmonization Criteria; the London criteria were also applied. Of 38 interim scans, agreement was complete in 68% and 71% by ECOG and London criteria, respectively. The range of PET(+) interim scans was 16% to 34% (P = not significant) by reviewer. Moderate consistency of reviews was observed: kappa statistic = 0.445 using ECOG criteria, and kappa statistic = 0.502 using London criteria. These data, showing only moderate reproducibility among nuclear medicine experts, indicate the need to standardize PET interpretation in research and practice. This trial was registered at www.clinicaltrials. gov as #NCT00274924 [corrected].
Spectral analysis of single-channel airflow and oxygen saturation recordings in obstructive sleep apnea detection

This study investigated the usefulness of the very low spectral content of single-channel airflow recordings to help in the diagnosis of the obstructive sleep apnea (OSA) syndrome. Additionally, we evaluated whether airflow frequency components in the 0.01 – 0.10 Hz band are linked with desaturations in blood oxygen saturation (SaO2) recordings due to apnea events. The relationship between changes in airflow and SaO2 was analyzed by means of the magnitude squared coherence (MSC) function. Power spectral density (PSD) was used to obtain the power spectrum of single airflow and SaO2 signals. Peak amplitude (PA) and relative power (PR) were used to parameterize the power spectrum in the very low frequency band. 148 subjects suspected of suffering from OSA were studied. Significant differences (p-value << 0.01) between OSA positive and OSA negative subjects were obtained from PSD and MSC features. We found a power increase in the very low frequency band of single-channel airflow linked with the periodic desaturations of OSA. Diagnostic sensitivity, specificity and accuracy of 84.0%, 85.4% and 84.5%, respectively, were reached with the peak amplitude of the airflow PSD. Thus, spectral features from the very low frequency components of single-channel airflow recordings could provide useful information to help in OSA diagnosis.