Miracle-dz/UniFAR-FTUs huggingface dataset:
Combined use of two supervised learning algorithms to model sea turtle behaviours from tri-axial acceleration data

ABSTRACT Accelerometers are becoming ever more important sensors in animal-attached technology, providing data that allow determination of body posture and movement and thereby helping to elucidate behaviour in animals that are difficult to observe. We sought to validate the identification of sea turtle behaviours from accelerometer signals by deploying tags on the carapace of a juvenile loggerhead (Caretta caretta), an adult hawksbill (Eretmochelys imbricata) and an adult green turtle (Chelonia mydas) at Aquarium La Rochelle, France. We recorded tri-axial acceleration at 50 Hz for each species for a full day while two fixed cameras recorded their behaviours. We identified behaviours from the acceleration data using two different supervised learning algorithms, Random Forest and Classification And Regression Tree (CART), treating the data from the adult animals as separate from the juvenile data. We achieved a global accuracy of 81.30% for the adult hawksbill and green turtle CART model and 71.63% for the juvenile loggerhead, identifying 10 and 12 different behaviours, respectively. Equivalent figures were 86.96% for the adult hawksbill and green turtle Random Forest model and 79.49% for the juvenile loggerhead, for the same behaviours. The use of Random Forest combined with CART algorithms allowed us to understand the decision rules implicated in behaviour discrimination, and thus remove or group together some ‘confused’ or under-represented behaviours in order to get the most accurate models. This study is the first to validate accelerometer data to identify turtle behaviours and the approach can now be tested on other captive sea turtle species. Summary: The development of 3D accelerometers allows us to acquire new information about sea turtle behaviour; validation of the sensor signal for turtle behaviours is important in helping conservation efforts.
Human Gut Microbiota Predicts Susceptibility to Vibrio cholerae Infection

Background Cholera is a public health problem worldwide, and the risk factors for infection are only partially understood. Methods We prospectively studied household contacts of patients with cholera to compare those who were infected to those who were not. We constructed predictive machine learning models of susceptibility, using baseline gut microbiota data. We identified bacterial taxa associated with susceptibility to Vibrio cholerae infection and tested these taxa for interactions with V. cholerae in vitro. Results We found that machine learning models based on gut microbiota, as well as models based on known clinical and epidemiological risk factors, predicted V. cholerae infection. A predictive gut microbiota of roughly 100 bacterial taxa discriminated between contacts who developed infection and those who did not. Susceptibility to cholera was associated with depleted levels of microbes from the phylum Bacteroidetes. By contrast, a microbe associated with cholera by our modeling framework, Paracoccus aminovorans, promoted the in vitro growth of V. cholerae. Gut microbiota structure, clinical outcome, and age were also linked. Conclusion These findings support the hypothesis that abnormal gut microbial communities are a host factor related to V. cholerae susceptibility.
Shifting plant species composition in response to climate change stabilizes grassland primary production

Significance Climate change is altering the structure and function of high-elevation ecosystems. Combining long-term observations with manipulative experiments is a powerful, yet rarely used way to test the sensitivity of such ecosystems to climatic change. Here, experimental evidence and meta-analysis confirm long-term observations that demonstrate climate warming and associated drying did not change net primary production, but did lead to a shift of allocation belowground. This observed shift was caused by a change in community composition. Although alpine grassland productivity appears to be resistant to warming, deeper root systems in response to warming could alter the amount of soil organic carbon stored in the subsoil, indicating that rooting depth should be taken into account when predicting soil organic carbon stocks under warming. The structure and function of alpine grassland ecosystems, including their extensive soil carbon stocks, are largely shaped by temperature. The Tibetan Plateau in particular has experienced significant warming over the past 50 y, and this warming trend is projected to intensify in the future. Such climate change will likely alter plant species composition and net primary production (NPP). Here we combined 32 y of observations and monitoring with a manipulative experiment of temperature and precipitation to explore the effects of changing climate on plant community structure and ecosystem function. First, long-term climate warming from 1983 to 2014, which occurred without systematic changes in precipitation, led to higher grass abundance and lower sedge abundance, but did not affect aboveground NPP. Second, an experimental warming experiment conducted over 4 y had no effects on any aspect of NPP, whereas drought manipulation (reducing precipitation by 50%), shifted NPP allocation belowground without affecting total NPP. Third, both experimental warming and drought treatments, supported by a meta-analysis at nine sites across the plateau, increased grass abundance at the expense of biomass of sedges and forbs. This shift in functional group composition led to deeper root systems, which may have enabled plant communities to acquire more water and thus stabilize ecosystem primary production even with a changing climate. Overall, our study demonstrates that shifting plant species composition in response to climate change may have stabilized primary production in this high-elevation ecosystem, but it also caused a shift from aboveground to belowground productivity.
MiR-490-3p Functions As a Tumor Suppressor by Inhibiting Oncogene VDAC1 Expression in Colorectal Cancer

Colorectal cancer (CRC) is one of the most common cancers worldwide, usually with poor prognosis because many CRC patients are diagnosed at an advanced stage. Therefore, novel potential diagnostic and prognostic biomarkers are urgently needed. MicroRNAs have been reported to regulate a variety of biological processes, such as cell proliferation, differentiation and apoptosis. Accumulating studies have demonstrated that miR-490-3p could regulate the development and progression of multiple cancers, but its clinical significance and molecular mechanism in CRC are still elusive. Here, we try to further elucidate the regulatory mechanism of miR-490-3p in CRC. In the present study, miR-490-3p expression level observably down-regulated in CRC tissues and cell lines, and miR-490-3p expression in CRC tissues was significantly associated with TNM stage, histological grade, tumor size and overall survival (OS). In addition, we observed miR-490-3p expression was also decreased in CRC plasmas and could act as a promising diagnostic biomarker for screening CRC. Further studies in vitro demonstrated Voltage Dependent Anion Channel 1 (VDAC1) which highly expressed in CRC tissues and cell lines is a direct target of miR-490-3p, and miR-490-3p could markedly inhibit CRC cells proliferation, metastasis, invasion and anti-apoptosis through suppressing VDAC1/AMPK/mTOR pathway. These results indicated that miR-490-3p functions as a tumor suppressor in CRC, and may be a novel potential diagnostic and prognostic biomarker for CRC.
Seed Dormancy Involves a Transcriptional Program That Supports Early Plastid Functionality during Imbibition

Red rice fully dormant seeds do not germinate even under favorable germination conditions. In several species, including rice, seed dormancy can be removed by dry-afterripening (warm storage); thus, dormant and non-dormant seeds can be compared for the same genotype. A weedy (red) rice genotype with strong dormancy was used for mRNA expression profiling, by RNA-Seq, of dormant and non-dormant dehulled caryopses (here addressed as seeds) at two temperatures (30 °C and 10 °C) and two durations of incubation in water (8 h and 8 days). Aim of the study was to highlight the differences in the transcriptome of dormant and non-dormant imbibed seeds. Transcript data suggested important differences between these seeds (at least, as inferred by expression-based metabolism reconstruction): dry-afterripening seems to impose a respiratory impairment onto non-dormant seeds, thus glycolysis is deduced to be preferentially directed to alcoholic fermentation in non-dormant seeds but to alanine production in dormant ones; phosphoenolpyruvate carboxykinase, pyruvate phosphate dikinase and alanine aminotransferase pathways appear to have an important gluconeogenetic role associated with the restoration of plastid functions in the dormant seed following imbibition; correspondingly, co-expression analysis pointed out a commitment to guarantee plastid functionality in dormant seeds. At 8 h of imbibition, as inferred by gene expression, dormant seeds appear to preferentially use carbon and nitrogen resources for biosynthetic processes in the plastid, including starch and proanthocyanidins accumulation. Chromatin modification appears to be a possible mechanism involved in the transition from dormancy to germination. Non-dormant seeds show higher expression of genes related to cell wall modification, suggesting they prepare for acrospire/radicle elongation.
Economics- and policy-driven organic carbon input enhancement dominates soil organic carbon accumulation in Chinese croplands

Significance Soil organic carbon (C) stock in Chinese croplands increased by about 140 kg C ha−1 year−1 from 1980 to 2011. This soil organic C sequestration was largely due to drastic changes in management practices, such as fertilization, tillage, and residue treatments, induced by economic and policy incentives. Our analysis also indicates that excessive N inputs and inability to incorporate residue C into deeper soils will likely constrain the future C sequestration in Chinese croplands. These findings provide new insights into the causes and limitations of economics- and policy-driven soil C sequestration in China and offer some guidance for soil C management in many developing countries that are going through the similar economic and social transformations. China’s croplands have experienced drastic changes in management practices, such as fertilization, tillage, and residue treatments, since the 1980s. There is an ongoing debate about the impact of these changes on soil organic carbon (SOC) and its implications. Here we report results from an extensive study that provided direct evidence of cropland SOC sequestration in China. Based on the soil sampling locations recorded by the Second National Soil Survey of China in 1980, we collected 4,060 soil samples in 2011 from 58 counties that represent the typical cropping systems across China. Our results showed that across the country, the average SOC stock in the topsoil (0–20 cm) increased from 28.6 Mg C ha−1 in 1980 to 32.9 Mg C ha−1 in 2011, representing a net increase of 140 kg C ha−1 year−1. However, the SOC change differed among the major agricultural regions: SOC increased in all major agronomic regions except in Northeast China. The SOC sequestration was largely attributed to increased organic inputs driven by economics and policy: while higher root biomass resulting from enhanced crop productivity by chemical fertilizers predominated before 2000, higher residue inputs following the large-scale implementation of crop straw/stover return policy took over thereafter. The SOC change was negatively related to N inputs in East China, suggesting that the excessive N inputs, plus the shallowness of plow layers, may constrain the future C sequestration in Chinese croplands. Our results indicate that cropland SOC sequestration can be achieved through effectively manipulating economic and policy incentives to farmers.
Pseudomonas aeruginosa gshA Mutant Is Defective in Biofilm Formation, Swarming, and Pyocyanin Production

Pseudomonas aeruginosa is a ubiquitous bacterium that can cause severe opportunistic infections, including many hospital-acquired infections. It is also a major cause of infections in patients with cystic fibrosis. P. aeruginosa is intrinsically resistant to a number of drugs and is capable of forming biofilms that are difficult to eradicate with antibiotics. The number of drug-resistant strains is also increasing, making treatment of P. aeruginosa infections very difficult. Thus, there is an urgent need to understand how P. aeruginosa causes disease in order to find novel ways to treat infections. We show that the principal redox buffer, glutathione (GSH), is involved in intrinsic resistance to the fosfomycin and rifampin antibiotics. We further demonstrate that GSH plays a role in P. aeruginosa disease and infection, since a mutant lacking GSH has less biofilm formation, is less able to swarm, and produces less pyocyanin, a pigment associated with infection. ABSTRACT Pseudomonas aeruginosa is a ubiquitous Gram-negative bacterium that can cause severe opportunistic infections. The principal redox buffer employed by this organism is glutathione (GSH). To assess the role of GSH in the virulence of P. aeruginosa, a number of analyses were performed using a mutant strain deficient in gshA, which does not produce GSH. The mutant strain exhibited a growth delay in minimal medium compared to the wild-type strain. Furthermore, the gshA mutant was defective in biofilm and persister cell formation and in swimming and swarming motility and produced reduced levels of pyocyanin, a key virulence factor. Finally, the gshA mutant strain demonstrated increased sensitivity to methyl viologen (a redox cycling agent) as well as the thiol-reactive antibiotics fosfomycin and rifampin. Taken together, these data suggest a key role for GSH in the virulence of P. aeruginosa. IMPORTANCE Pseudomonas aeruginosa is a ubiquitous bacterium that can cause severe opportunistic infections, including many hospital-acquired infections. It is also a major cause of infections in patients with cystic fibrosis. P. aeruginosa is intrinsically resistant to a number of drugs and is capable of forming biofilms that are difficult to eradicate with antibiotics. The number of drug-resistant strains is also increasing, making treatment of P. aeruginosa infections very difficult. Thus, there is an urgent need to understand how P. aeruginosa causes disease in order to find novel ways to treat infections. We show that the principal redox buffer, glutathione (GSH), is involved in intrinsic resistance to the fosfomycin and rifampin antibiotics. We further demonstrate that GSH plays a role in P. aeruginosa disease and infection, since a mutant lacking GSH has less biofilm formation, is less able to swarm, and produces less pyocyanin, a pigment associated with infection.
Upper Columbia River Steelhead and Spring Chinook Salmon Population Structure and Biological Requirements

Phaedra Budy, U.S. Fish and Wildlife Service Craig Busack, Washington Dept. of Fish and Wildlife Don Chapman, Bioanalysts, Inc. Tom Cooney, National Marine Fisheries Service Tim Fisher, Beak Consultants, Inc. Jim Geiselman, Bonneville Power Administration Tracy Hillman, Bioanalysts, Inc. Joe Lukas, Grant County Public Utility District Chuck Peven, Chelan County Public Utility District Chris Toole, National Marine Fisheries Service Earl Weber, Columbia River Inter-Tribal Fish Commission Paul Wilson, Columbia Basin Fish and Wildlife Authority
Sporothrix schenckii sensu stricto and Sporothrix brasiliensis Are Differentially Recognized by Human Peripheral Blood Mononuclear Cells

Sporothrix schenckii sensu stricto and S. brasiliensis are usually associated to sporotrichosis, a subcutaneous mycosis worldwide distributed. Comparative analyses between these two species indicate they contain genetic and physiological differences that are likely to impact the interaction with host cells. Here, we study the composition of the cell wall from conidia, yeast-like cells and germlings of both species and found they contained the same sugar composition. The carbohydrate proportion in the S. schenckii sensu stricto wall was similar across the three cell morphologies, with exception in the chitin content, which was significantly different in the three morphologies. The cell wall from germlings showed lower rhamnose content and higher glucose levels than other cell morphologies. In S. brasiliensis, the wall sugars were constant in the three morphologies, but glucose was lower in yeast-like cells. In S. schenckii sensu stricto cells most of chitin and β1,3-glucan were underneath wall components, but in S. brasiliensis germlings, chitin was exposed at the cell surface, and β1,3-glucan was found in the outer part of the conidia wall. We also compared the ability of these cells to stimulate cytokine production by human peripheral blood mononuclear cells. The three S. schenckii sensu stricto morphologies stimulated increased levels of pro-inflammatory cytokines, when compared to S. brasiliensis cells; while the latter, with exception of conidia, stimulated higher IL-10 levels. Dectin-1 was a key receptor for cytokine production during stimulation with the three morphologies of S. schenckii sensu stricto, but dispensable for cytokine production stimulated by S. brasiliensis germlings. TLR2 and TLR4 were also involved in the sensing of Sporothrix cells, with a major role for the former during cytokine stimulation. Mannose receptor had a minor contribution during cytokine stimulation by S. schenckii sensu stricto yeast-like cells and germlings, but S. schenckii sensu stricto conidia and S. brasiliensis yeast-like cells stimulated pro-inflammatory cytokines via this receptor. In conclusion, S. brasiliensis and S. schenckii sensu stricto, have similar wall composition, which undergoes changes depending on the cell morphology. These differences in the cell wall composition, are likely to influence the contribution of immune receptors during cytokine stimulation by human monocytes.
Major limb-sparing treatment results following foot and ankle infection in patients with and without diabetes mellitus

Background: Little is known about the outcomes following major limb-sparing treatment (treatments avoiding below-knee amputation) in diabetic or non-diabetic patients with foot and ankle infection. This study was to compare patient-reported outcomes (PROs) and health-related quality of life (HrQoL) of diabetic and non-diabetic patients with foot and ankle infections in both pre-and post-treatment (major limb-sparing treatment) periods. Methods: This study included a total number of twenty-six patients who were divided as 15 patients with diabeticrelated foot and ankle infection and 11 patients who had foot and ankle infections without diabetes mellitus (DM). Baseline characteristics including site of infection, PROs via visual analogue scale foot and ankle (VASFA) score, and HrQoL via Short-Form (SF)-36 score were recorded in each patient. VASFA and SF-36 scores were compared between the two groups in both pre-and post-treatment periods. Results: Mean follow-up time was 11.1 months. There were significant improvements of the VASFA score and SF-36 score regarding the pre-and post-treatment periods (p 0.05). Conclusions: Regarding foot and ankle infection, the patients with and without DM could undergo the comparable results via patients’ PROs and HrQoL assessment following the major limb-sparing treatments.
Pro region engineering of nerve growth factor by deep mutational scanning enables a yeast platform for conformational epitope mapping of anti‐NGF monoclonal antibodies

Nerve growth factor (NGF) plays a central role in multiple chronic pain conditions. As such, anti‐NGF monoclonal antibodies (mAbs) that function by antagonizing NGF downstream signaling are leading drug candidates for non‐opioid pain relief. To evaluate anti‐canine NGF (cNGF) mAbs we sought a yeast surface display platform of cNGF. Both mature cNGF and pro‐cNGF displayed on the yeast surface but bound conformationally sensitive mAbs at most 2.5‐fold in mean fluorescence intensity above background, suggesting that cNGF was mostly misfolded. To improve the amount of folded, displayed cNGF, we used comprehensive mutagenesis, FACS, and deep sequencing to identify point mutants in the pro‐region of canine NGF that properly enhance the folded protein displayed on the yeast surface. Out of 1,737 tested single point mutants in the pro region, 49 increased the amount of NGF recognized by conformationally sensitive mAbs. These gain‐of‐function mutations cluster around residues A‐61–P‐26. Gain‐of‐function mutants were additive, and a construct containing three mutations increased amount of folded cNGF to 23‐fold above background. Using this new cNGF construct, fine conformational epitopes for tanezumab and three anti‐cNGF mAbs were evaluated. The epitope revealed by the yeast experiments largely overlapped with the tanezumab epitope previously determined by X‐ray crystallography. The other mAbs showed site‐specific differences with tanezumab. As the number of binding epitopes of functionally neutralizing anti‐NGF mAbs on NGF are limited, subtle differences in the individual interacting residues on NGF that bind each mAb contribute to the understanding of each antibody and variations in its neutralizing activity. These results demonstrate the potential of deep sequencing‐guided protein engineering to improve the production of folded surface‐displayed protein, and the resulting cNGF construct provides a platform to map conformational epitopes for other anti‐neurotrophin mAbs.
MRI by steering resonance through space

This work introduces a technique to excite MR signals locally and to steer this localized region over the object in a spatiotemporal manner. The purpose is to demonstrate the feasibility of MRI with multidimensional spatiotemporal‐encoding in a way that provides the ability to compensate extreme field inhomogeneity.
MicroRNA‐30d preserves pancreatic islet β‐cell function through negative regulation of the JNK signaling pathway via SOCS3 in mice with streptozotocin‐induced diabetes mellitus

The loss of pancreatic islet β‐cell function represents the classical feature in the pathogenesis of type 2 diabetes mellitus (T2DM). Previous evidence has highlighted the involvement of the activated JNK pathway in relation to islet β‐cell apoptosis. Hence, during the present study a streptozotocin‐induced DM mice model was established in a bid to ascertain as to whether microRNA‐30d (miR‐30d) plays a regulatory role in the JNK pathway in relation to islet β‐cell dysfunction. The collection and identification of the islet β cells from streptozotocin‐induced mice was performed. Islet β cells with elevated or suppressed levels of miR‐30 as well as knocked down SOCS3 were established in order to verify the regulatory mechanisms by which miR‐30d governs SOCS3 in vitro. We found miR‐30d was overexpressed among tissue samples obtained form streptozotocin‐induced mice and their islet β cells, as well as increasing miR‐30d expression when the JNK pathway was activated were found to promote islet β cell growth and cell cycle entry, and inhibit apoptosis. SOCS3, confirmed to be a miR‐30d target, was decreased in the islet β cells following the promotion of miR‐30d, while the JNK pathway was inhibited following SOCS3 knocdown. Furthermore, the effect of miR‐30d inhibition was lost in islet β cells when SOCS3 was knocked down. The data of the present study support the notion that miR‐30d‐mediated direct suppression of SOCS3 acts to protect pancreatic β‐cell functions through the JNK signaling pathway, emphasizing the potential of miR‐30d as a novel pharmacological target for treatment and intervention of DM.