Miracle-dz/UniFAR-FTUs huggingface dataset:
The force–length–velocity potential of the human soleus muscle is related to the energetic cost of running

According to the force–length–velocity relationships, the muscle force potential is determined by the operating length and velocity, which affects the energetic cost of contraction. During running, the human soleus muscle produces mechanical work through active shortening and provides the majority of propulsion. The trade-off between work production and alterations of the force–length and force–velocity potentials (i.e. fraction of maximum force according to the force–length–velocity curves) might mediate the energetic cost of running. By mapping the operating length and velocity of the soleus fascicles onto the experimentally assessed force–length and force–velocity curves, we investigated the association between the energetic cost and the force–length–velocity potentials during running. The fascicles operated close to optimal length (0.90 ± 0.10 L0) with moderate velocity (0.118 ± 0.039 Vmax [maximum shortening velocity]) and, thus, with a force–length potential of 0.92 ± 0.07 and a force–velocity potential of 0.63 ± 0.09. The overall force–length–velocity potential was inversely related (r = −0.52, p = 0.02) to the energetic cost, mainly determined by a reduced shortening velocity. Lower shortening velocity was largely explained (p < 0.001, R2 = 0.928) by greater tendon gearing, shorter Achilles tendon lever arm, greater muscle belly gearing and smaller ankle angle velocity. Here, we provide the first experimental evidence that lower shortening velocities of the soleus muscle improve running economy.
External environment and internal state in relation to life-history behavioural profiles of adolescents in nine countries

The external environment has traditionally been considered as the primary driver of animal life history (LH). Recent research suggests that animals' internal state is also involved, especially in forming LH behavioural phenotypes. The present study investigated how these two factors interact in formulating LH in humans. Based on a longitudinal sample of 1223 adolescents in nine countries, the results show that harsh and unpredictable environments and adverse internal states in childhood are each uniquely associated with fast LH behavioural profiles consisting of aggression, impulsivity, and risk-taking in adolescence. The external environment and internal state each strengthened the LH association of the other, but overall the external environment was more predictive of LH than was the internal state. These findings suggest that individuals rely on a multitude and consistency of sensory information in more decisively calibrating LH and behavioural strategies.
Prevalence and risk factors of avian influenza H9N2 among backyard birds in Iran in 2015

Objective: To investigate the prevalence and the risk factors of H9N2 avian influenza among backyard birds in Iran between October and November 2015. Methods: In this study, a total of 15 500 blood samples and 2 884 cloacal swab samples of backyard birds were collected in villages of Iran between October and November 2015. Then, serum samples were examined with the hemagluttination inhibition test and cloacal swab samples were pooled together and examined by RT-PCR. The samples that had serological titer ≥ 4 (log2) and villages that had at least one seropositive sample were considered positive. Results: Out of 559 villages, 526 (94.10%) were seropositive for the infection. Among 15 500 serum samples, 7 468 (48.18%) samples were seropositive for the infection. The seroprevalence according to species was 54.02% among chickens, 17.59 % among ducks, 18.73% among turkeys, 84.21% among pigeons and 12.15% among ostriches, partridges and pheasants. Based on molecular test, 3.04% villages were positive. The seroprevalence in hot and humid area was less than that in cold and humid area (P<0.05). Conclusions: H9N2 avian influenza has high seroprevalence among backyard birds of Iran. Therefore, preventive measures such as biosecurity Practices and monitoring should be applied to reduce the prevalence.
Impact of obesity on disease activity and other health outcome measures in ankylosing spondylitis

Obesity is a rapidly increasing pandemic, with almost one-third of the world population being affected. It has its impact on various systems, of which musculoskeletal system is also majorly affected. Its impact on rheumatoid arthritis and psoriatic arthritis are already known, but its association with ankylosing spondylitis is debatable and very few studies are being conducted to support its impact. The below article is a review of the association and impact of obesity on the disease activity, factors involved in its pathogenesis, impact on others underlying diseases, and therapeutic affections. This article also urges the need for the physicians to treat obesity as a separate disease condition which requires treatment like any other disease to improve the quality of life of individuals and to limit the progress of other diseases.
Superior Treg-Expanding Properties of a Novel Dual-Acting Cytokine Fusion Protein

Autoimmune diseases are caused by uncontrolled endogenous immune responses against healthy cells. They may develop due to an impaired function of regulatory T cells (Tregs), which normally suppress self-specific effector immune cells. Interleukin 2 (IL-2) and tumor necrosis factor (TNF) have been identified as key players that promote expansion, function, and stability of Tregs. In vivo, both low-dose IL-2 therapy and TNF receptor 2 (TNFR2) agonism were shown to expand Tregs and alleviate autoimmunity. We here designed a novel dimeric dual-acting fusion cytokine, where mouse IL-2 is genetically linked to a TNFR2-selective single-chain TNF mutein (IL2-EHD2-sc-mTNFR2). IL2-EHD2-sc-mTNFR2 showed high affinity to TNFR2 and efficiently activated IL-2 and TNFR2-selective signaling pathways. Further, IL2-EHD2-sc-mTNFR2 promoted superior Treg expansion, with both the IL-2 and the TNFR2 agonist (sc-mTNFR2) component necessary for this biological response. Ultimately, we propose that IL2-EHD2-sc-mTNFR2 is a dual-acting cytokine that efficiently promotes Treg expansion and might have a superior therapeutic window than conventional IL-2-based drugs.
Lignocellulosic Biomass: Understanding Recalcitrance and Predicting Hydrolysis

Lignocellulosic biomass (LB) is an abundant and renewable resource from plants mainly composed of polysaccharides (cellulose and hemicelluloses) and an aromatic polymer (lignin). LB has a high potential as an alternative to fossil resources to produce second-generation biofuels and biosourced chemicals and materials without compromising global food security. One of the major limitations to LB valorisation is its recalcitrance to enzymatic hydrolysis caused by the heterogeneous multi-scale structure of plant cell walls. Factors affecting LB recalcitrance are strongly interconnected and difficult to dissociate. They can be divided into structural factors (cellulose specific surface area, cellulose crystallinity, degree of polymerization, pore size and volume) and chemical factors (composition and content in lignin, hemicelluloses, acetyl groups). Goal of this review is to propose an up-to-date survey of the relative impact of chemical and structural factors on biomass recalcitrance and of the most advanced techniques to evaluate these factors. Also, recent spectral and water-related measurements accurately predicting hydrolysis are presented. Overall, combination of relevant factors and specific measurements gathering simultaneously structural and chemical information should help to develop robust and efficient LB conversion processes into bioproducts.
Update on Fc-Mediated Antibody Functions Against HIV-1 Beyond Neutralization

Antibodies (Abs) are the major component of the humoral immune response and a key player in vaccination. The precise Ab-mediated inhibitory mechanisms leading to in vivo protection against HIV have not been elucidated. In addition to the desired viral capture and neutralizing Ab functions, complex Ab-dependent mechanisms that involve engaging immune effector cells to clear infected host cells, immune complexes, and opsonized virus have been proposed as being relevant. These inhibitory mechanisms involve Fc-mediated effector functions leading to Ab-dependent cellular cytotoxicity, phagocytosis, cell-mediated virus inhibition, aggregation, and complement inhibition. Indeed, the decreased risk of infection observed in the RV144 HIV-1 vaccine trial was correlated with the production of non-neutralizing inhibitory Abs, highlighting the role of Ab inhibitory functions besides neutralization. Moreover, Ab isotypes and subclasses recognizing specific HIV envelope epitopes as well as pecular Fc-receptor polymorphisms have been associated with disease progression. These findings further support the need to define which Fc-mediated Ab inhibitory functions leading to protection are critical for HIV vaccine design. Herein, based on our previous review Su & Moog Front Immunol 2014, we update the different inhibitory properties of HIV-specific Abs that may potentially contribute to HIV protection.
Contextual Cell Death in Adaptive Immunity: Selecting a Winning Response

Winning the game “Rock, Scissors, Paper” depends on what others do. There is no guarantee that one choice will always win. Does the adaptive immune system use the same intransitive logic to select winners? Here I propose that specialized receptor-ligand pairs, called clicks, initiate contextual cell death to select the best adaptive immune response to a particular challenge. The outcome depends heavily on the phenotypic plasticity of the immune system and upon cell assemblies built from different lineages. These assemblies are self-organizing and use clicks to determine the combination of cells best equipped to defeat a threat. The arrangement is highly adaptive and capable of rapid evolution. Opportunities exist to re-engineer click-based assemblies to produce novel therapeutics.
Identification of Modules With Similar Gene Regulation and Metabolic Functions Based on Co-expression Data

Biological systems respond to environmental perturbations and to a large diversity of compounds through gene interactions, and these genetic factors comprise complex networks. In particular, a wide variety of gene co-expression networks have been constructed in recent years thanks to the dramatic increase of experimental information obtained with techniques, such as microarrays and RNA sequencing. These networks allow the identification of groups of co-expressed genes that can function in the same process and, in turn, these networks may be related to biological functions of industrial, medical and academic interest. In this study, gene co-expression networks for 17 bacterial organisms from the COLOMBOS database were analyzed via weighted gene co-expression network analysis and clustered into modules of genes with similar expression patterns for each species. These networks were analyzed to determine relevant modules through a hypergeometric approach based on a set of transcription factors and enzymes for each genome. The richest modules were characterized using PFAM families and KEGG metabolic maps. Additionally, we conducted a Gene Ontology analysis for enrichment of biological functions. Finally, we identified modules that shared similarity through all the studied organisms by using comparative genomics.
Detailed Evaluation of Data Analysis Tools for Subtyping of Bacterial Isolates Based on Whole Genome Sequencing: Neisseria meningitidis as a Proof of Concept

Whole genome sequencing is increasingly recognized as the most informative approach for characterization of bacterial isolates. Success of the routine use of this technology in public health laboratories depends on the availability of well-characterized and verified data analysis methods. However, multiple subtyping workflows are now often being used for a single organism, and differences between them are not always well described. Moreover, methodologies for comparison of subtyping workflows, and assessment of their performance are only beginning to emerge. Current work focuses on the detailed comparison of WGS-based subtyping workflows and evaluation of their suitability for the organism and the research context in question. We evaluated the performance of pipelines used for subtyping of Neisseria meningitidis, including the currently widely applied cgMLST approach and different SNP-based methods. In addition, the impact of the use of different tools for detection and filtering of recombinant regions and of different reference genomes were tested. Our benchmarking analysis included both assessment of technical performance of the pipelines and functional comparison of the generated genetic distance matrices and phylogenetic trees. It was carried out using replicate sequencing datasets of high- and low-coverage, consisting mainly of isolates belonging to the clonal complex 269. We demonstrated that cgMLST and some of the SNP-based subtyping workflows showed very good performance characteristics and highly similar genetic distance matrices and phylogenetic trees with isolates belonging to the same clonal complex. However, only two of the tested workflows demonstrated reproducible results for a group of more closely related isolates. Additionally, results of the SNP-based subtyping workflows were to some level dependent on the reference genome used. Interestingly, the use of recombination-filtering software generally reduced the similarity between the gene-by-gene and SNP-based methodologies for subtyping of N. meningitidis. Our study, where N. meningitidis was taken as an example, clearly highlights the need for more benchmarking comparative studies to eventually contribute to a justified use of a specific WGS data analysis workflow within an international public health laboratory context.
Measuring Dynamics of Infant-Adult Synchrony Through Mocap

The temporal dynamics of parent-infant synchrony have been well documented. In recent years, the introduction of more accurate technologies for tracking movements has allowed the distinction of different morphological patterns of dyadic coordination. However, the potential of these technologies to explore infant-adult synchrony has not yet been explored. In the present study, we examined the temporal, spatial, and morphological synchrony patterns of infant-unknown adult pairs participating in a storytime session by a motion capture system (mocap). We find low but significant correlation levels of body synchrony between infants and unknown adults. This synchronized coactivity adopted two differentiated forms: mirror-like and anatomical. While the infants’ movements mirrored those of the adults with a lag (0.9 s), the adults’ reactions to the infants were anatomical with delay (0.4 s). This evidence could contribute novel insights to rethink synchrony and its measurement.
Automated Individualization of Size-Varying and Touching Neurons in Macaque Cerebral Microscopic Images

In biomedical research, cell analysis is important to assess physiological and pathophysiological information. Virtual microscopy offers the unique possibility to study the compositions of tissues at a cellular scale. However, images acquired at such high spatial resolution are massive, contain complex information, and are therefore difficult to analyze automatically. In this article, we address the problem of individualization of size-varying and touching neurons in optical microscopy two-dimensional (2-D) images. Our approach is based on a series of processing steps that incorporate increasingly more information. (1) After a step of segmentation of neuron class using a Random Forest classifier, a novel min-max filter is used to enhance neurons’ centroids and boundaries, enabling the use of region growing process based on a contour-based model to drive it to neuron boundary and achieve individualization of touching neurons. (2) Taking into account size-varying neurons, an adaptive multiscale procedure aiming at individualizing touching neurons is proposed. This protocol was evaluated in 17 major anatomical regions from three NeuN-stained macaque brain sections presenting diverse and comprehensive neuron densities. Qualitative and quantitative analyses demonstrate that the proposed method provides satisfactory results in most regions (e.g., caudate, cortex, subiculum, and putamen) and outperforms a baseline Watershed algorithm. Neuron counts obtained with our method show high correlation with an adapted stereology technique performed by two experts (respectively, 0.983 and 0.975 for the two experts). Neuron diameters obtained with our method ranged between 2 and 28.6 μm, matching values reported in the literature. Further works will aim to evaluate the impact of staining and interindividual variability on our protocol.
Work Limitation due to Low Back Pain among Tobacco Farmers in Southern Brazil.

Background: farming requires high physical effort and awkward postures, which are low back pain risk factors and restrain work. Low back pain, particularly chronic pain, causes a high number of sick leaves. Objective: to assess prevalence of work limitations due to chronic low back pain (CLBP), of low back pain in the last month (LBPLM) and of acute low back pain (ALBP), as well as the tasks farmers, owing to these injuries, are not able to cope with. Methods: cross-sectional study carried out in 2011 in a random sample of Brazilian tobacco farmers (2469) from São Lourenço do Sul/RS. Factors associated to limitation originated from LBPLM were evaluated via Poisson regression. Results: prevalence of work limitation due to CLBP, LBPLM and ALBP were respectively 37.6%, 14.4% and 7.8%. The tasks tobacco farmers most frequently had to give up were: carrying leaves, stacking firewood and harvesting bottom leaves. In the adjusted analysis, age, road tax expenses, difficulty in paying debts and minor psychiatric disorders were associated to work limitation due to LBPLM. ALBP individuals give up performing the same tasks as CLBP individuals, but CLBP individuals have higher work limitations.
Childhood-Onset Schizophrenia: A Systematic Overview of Its Genetic Heterogeneity From Classical Studies to the Genomic Era

Childhood-onset schizophrenia (COS), a very rare and severe chronic psychiatric condition, is defined by an onset of positive symptoms (delusions, hallucinations and disorganized speech or behavior) before the age of 13. COS is associated with other neurodevelopmental disorders such as autism spectrum disorder (ASD) and attention deficit and hyperactivity disorder. Copy number variations (CNVs) represent well documented neurodevelopmental disorder risk factors and, recently, de novo single nucleotide variations (SNVs) in genes involved in brain development have also been implicated in the complex genetic architecture of COS. Here, we aim to review the genetic changes (CNVs and SNVs) reported for COS, going from previous studies to the whole genome sequencing era. We carried out a systematic review search in PubMed using the keywords “childhood(early)-onset schizophrenia(psychosis)” and “genetic(s) or gene(s) or genomic(s)” without language and date limitations. The main inclusion criteria are COS (onset before 13 years old) and all changes/variations at the DNA level (CNVs or SNVs). Thirty-six studies out of 205 met the inclusion criteria. Cytogenetic abnormalities (n = 72, including 66 CNVs) were identified in 16 autosomes and 2 sex chromosomes (X, Y), some with a higher frequency and clinical significance than others (e.g., 2p16.3, 3q29, 15q13.3, 22q11.21 deletions; 2p25.3, 3p25.3 and 16p11.2 duplications). Thirty-one single nucleotide mutations in genes principally involved in brain development and/or function have been found in 12 autosomes and one sex chromosome (X). We also describe five SNVs in X-linked genes inherited from a healthy mother, arguing for the X-linked recessive inheritance hypothesis. Moreover, ATP1A3 (19q13.2) is the only gene carrying more than one SNV in more than one patient, making it a strong candidate for COS. Mutations were distributed in various chromosomes illustrating the genetic heterogeneity of COS. More than 90% of CNVs involved in COS are also involved in ASD, supporting the idea that there may be genetic overlap between these disorders. Different mutations associated with COS are probably still unknown, and pathogenesis might also be explained by the association of different genetic variations (two or more CNVs or CNVs and SNVs) as well as association with early acquired brain lesions such as infection, hypoxia, or early childhood trauma.
Immigration and HIV among Migrant Workers in Rural Southern Florida

We studied HIV seropositivity among a targeted sample of migrant workers who used drugs, primarily crack cocaine, and their sexual partners in rural southern Florida from 1993 to 1995. We enrolled men and women who were born in the United States (n = 369) or in other countries (n = 174). Overall, 11.2% of the sample were HIV positive, including 18% of Blacks from the United States, and about 8% of non-Hispanic whites from the United States, Blacks from the Caribbean, and persons from Central or South America. No Hispanics from the United States or the Caribbean, but 3.4% of Hispanics from Mexico, were HIV positive. In logistic regression analyses, race/ethnicity, gender, and age were most highly associated with HIV seropositivity. Immigration status, current drug use, and current sexual activity were not related to HIV seropositivity. HIV prevention programs must help reduce heterosexual transmission of HIV associated with drug use both locally and where migrants travel and work.
Zahora, a new monotypic genus from tribe Brassiceae (Brassicaceae) endemic to the Moroccan Sahara

Abstract Zahora ait-atta Lemmel & M.Koch, a new species from the Moroccan Sahara, is described and documented here and constitutes a monotypic new genus. The new taxon belongs to the tribe Brassiceae (Brassicaceae), and cytogenetic and phylogenetic analyses reveal that this diploid species has a remote status of Miocene origin in the northwestern Sahara Desert. We examined the morphological differences between morphologically related genera and provide photographs of the new species. The new genus may play a key role in future Brassica-Raphanus crop research since it is placed phylogenetically at the base of a generically highly diverse clade including Raphanus sativus, and it shows affinities to various Brassica species.