Miracle-dz/UniFAR-FTUs huggingface dataset:
Survival Rates in a Nonharvested Brown Hare Population

Survival in the brown hare (Lepus europaeus) is poorly documented because only life tables and other nonrobust methods have been used to estimate constant annual survival rates. We used recent developments in mark-recapture analysis to model survival patterns in a Danish hare population monitored from 1957 to 1970. Goodness-of-fit tests revealed that the Cormack-Jolly-Seber (CJS) model was an adequate starting point for adults, and age-dependence was considered in modeling survival of yearlings. We found no differences in annual survival rates (Φ) from 1957 to 1967 in adults, but males survived better than females (Φ males = 0.55, 95% CI = 0.50-0.61; Φ females = 0.50, 95% CI = 0.44-0.56). Yearling survival rates were time dependent and varied with winter severity, sex, and mass. Indeed, body mass strongly influenced the survival of yearling hares: larger animals (≥3 kg) had higher survival rates than smaller animals, in both males and females (Φ = 0.40-0.68 for heavy males and Φ = 0.20-0.44 for lighter males; Φ = 0.31-0.52 for heavy females and Φ = 0.22-0.40 for lighter females). These variations in survival rates were parallel between body mass classes over time (modeled as a function of winter temperature) within each sex.
Genetic interaction profiles of regulatory kinases differ between environmental conditions and cellular states

Cell growth and quiescence in eukaryotic cells is controlled by an evolutionarily conserved network of signaling pathways. Signal transduction networks operate to modulate a wide range of cellular processes and physiological properties when cells exit proliferative growth and initiate a quiescent state. How signaling networks function to respond to diverse signals that result in cell cycle exit and establishment of a quiescent state is poorly understood. Here, we studied the function of signaling pathways in quiescent cells using global genetic interaction mapping in the model eukaryotic cell, Saccharomyces cerevisiae (budding yeast). We performed pooled analysis of genotypes using molecular barcode sequencing (Bar‐seq) to test the role of ~4,000 gene deletion mutants and ~12,000 pairwise interactions between all non‐essential genes and the protein kinase genes TOR1, RIM15, and PHO85 in three different nutrient‐restricted conditions in both proliferative and quiescent cells. We detect up to 10‐fold more genetic interactions in quiescent cells than proliferative cells. We find that both individual gene effects and genetic interaction profiles vary depending on the specific pro‐quiescence signal. The master regulator of quiescence, RIM15, shows distinct genetic interaction profiles in response to different starvation signals. However, vacuole‐related functions show consistent genetic interactions with RIM15 in response to different starvation signals, suggesting that RIM15 integrates diverse signals to maintain protein homeostasis in quiescent cells. Our study expands genome‐wide genetic interaction profiling to additional conditions, and phenotypes, and highlights the conditional dependence of epistasis.
Relationship between the seed rain and the establishment of vegetation in two areas abandoned after peat harvesting

In this study the number and species composition of diaspores dispersing into two newly abandoned peat harvesting areas in Finland were investigated. In an area abandoned six years earlier a total of 2978 living seeds m−2, representing 18 species, was captured by using water-filled traps during two summers. In a one-year-old succession area the total number of living seeds m−2 was 2241, representing 16 plant species. The soil seed banks were found to be empty of viable seeds. In neither area there appeared to be any relation between number of dispersing seeds and of plant individuals of the same species in the pioneer vegetation. It is suggested that unfavourable conditions on the soil surface for seed germination and seedling growth of most dispersed species are majors factor in determining the structure of the established vegetation.
HECNet: a hierarchical approach to enzyme function classification using a Siamese Triplet Network

MOTIVATION Understanding an enzyme's function is one of the most crucial problem domains in computational biology. Enzymes are a key component in all organisms and many industrial processes as they help in fighting diseases and speed up essential chemical reactions. They have wide applications and therefore, the discovery of new enzymatic proteins can accelerate biological research and commercial productivity. Biological experiments, to determine an enzyme's function, are time-consuming and resource expensive. RESULTS In this study, we propose a novel computational approach to predict an enzyme's function up to the fourth level of the Enzyme Commission (EC) Number. Many studies have attempted to predict an enzyme's function. Yet, no approach has properly tackled the fourth and final level of the EC number. The fourth level holds great significance as it gives us the most specific information of how an enzyme performs its function. Our method uses innovative deep learning approaches along with an efficient hierarchical classification scheme to predict an enzyme's precise function. On a dataset of 11,353 enzymes and 402 classes, we achieved a hierarchical accuracy and Macro-F1 score of 91.2% and 81.9%, respectively, on the 4th level. Moreover, our method can be used to predict the function of enzyme isoforms with considerable success. This methodology is broadly applicable for genome-wide prediction that can subsequently lead to automated annotation of enzyme databases and the identification of better/cheaper enzymes for commercial activities. AVAILABILITY The web-server can be freely accessed at http://hecnet.cbrlab. org/. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Interação do Trypanosoma cruzi com diferentes vetores: uso para o xenodiagnóstico

Data showing differences in the interaction (differentiation and multiplication) o/Trypanosoma cruzi Yand CL strains ("polar strains ”), in Triatoma infestans Panstrongylus megistus and Dipetalogaster maximus are presented. It is concluded that with T. infestans 40% of the individual bugs have accentuated resistance to infection with the Y strain of T. cruzi. P. megistus was found to be a good vector to the studied strains presenting good development and differentiation of the parasites with low percentage of rejection of infection. Better development and differentiation is shown by D. maximus which is indicated for xenodiagnosis in Chagas' disease. The authors suggest the presence of two factors responsible for this vector-parasite interaction: a resistance factor to infection, perhaps related to the presence of nutrients, and also a factor that regulates differentiation to metacyclic forms of T. cruzi.
Activity rhythm in the cave cricket Ceuthophilus Conicaudus hubbell

Nocturnal emergence of Ceuthophilus conicaudus Hubbell from Spider 'Cave (Carlsbad Caverns National Park) just after sunset was initiated by decreased light intensity with surface temperature, surface relative humidity, and moonlight intensity affecting the total number emerging each night. Air currents probably serve to orient cricket movements within the cave. Laboratory studies demonstrated a persistent endogenous rhythm in this cave cricket under constant environmental conditions. This rhythm was modified with light retarding activity and absence of food increasing activity. Decrease in activity in the light would be important in avoiding surface predators. Hunger could serve to stimulate activity while crickets are under constant cave conditions.
Efficacy and safety of camrelizumab combined with apatinib in advanced triple-negative breast cancer: an open-label phase II trial

Background Previous trials showed that antiangiogenesis or anti-programmed death protein 1/programmed death ligand 1 (PD-1/PD-L1) monotherapy only showed marginal effect in triple-negative breast cancer (TNBC). Preclinical studies demonstrated that antiangiogenic therapy could sensitize breast cancer to PD-1/PD-L1 blockade via reprogramming tumor microenvironment. Combinational treatment of checkpoint blockade and antiangiogenesis for TNBC has not been reported. Methods Patients with advanced TNBC with less than three lines of systemic therapy were enrolled in an open-label, non-comparative, two-arm, phase II trial at Sun Yat-sen Memorial Hospital. Camrelizumab (intravenously every 2 weeks) with apatinib orally at either continuous dosing (d1–d14) or intermittent dosing (d1–d7) was given until disease progression or unacceptable toxicities. Primary endpoint was objective response rate (ORR). Results From January 2018 to April 2019, 40 patients were enrolled, including 10 in the apatinib intermittent dosing cohort and 30 in the apatinib continuous dosing cohort. The ORR was 43.3% (13 of 30) in the continuous dosing cohort, while no objective response was observed in the intermittent dosing cohort. The disease control rate was 63.3% (19 of 30) in the apatinib continuous dosing cohort, and 40.0% (4 of 10) in the apatinib intermittent dosing cohort, respectively. The median progression-free survival (PFS) was 3.7 (95% CI 2.0 to 6.4) months and 1.9 (95% CI 1.8 to 3.7) months in the continuous dosing and intermittent dosing cohort, respectively. In the continuous dosing cohort, the median PFS of patients with partial response (8.3 months, 95% CI 5.9 to not reached) was significantly longer than that of patients with stable disease/progressive disease/not evaluable (2.0 months, 95% CI 1.7 to 3.0). The most common adverse events (AEs) included elevated aspartate aminotransferase/alanine aminotransferase and hand-foot syndrome. Overall, 26.7% and 20.0% of patients experienced grade ≥3 AEs in the continuous dosing and intermittent dosing cohort, respectively. In the continuous dosing cohort, a high percentage of baseline tumor-infiltrating lymphocytes (>10%) was associated with higher ORR and favorable PFS (p=0.029, 0.054, respectively). Conclusions The ORR by this chemo-free regimen was dramatically higher than previously reported ORR by anti-PD-1/PD-L1 antibody or apatinib monotherapy. Camrelizumab combined with apatinib demonstrated favorable therapeutic effects and a manageable safety profile in patients with advanced TNBC. Trial registration number NCT03394287.
Priming exercise increases Wingate cycling peak power output

Abstract Purpose: The aim of the present study was to investigate the effect of priming exercise on Wingate performance and fatigue. Methods: Twelve recreationally active young male volunteers participated in the study (age: 25 ± 5 years; weight: 75.0 ± 7.5 kg; height: 177 ± 6 cm; BMI: 24.0 ± 1.7). During a first visit, participants performed a typical test and a supramaximal assessment of on a cycle ergometer, while during the next three visits, the participants performed in a random order a Wingate test (i) with no priming exercise, (ii) after priming exercise followed by a 15-min recovery (Priming15) and (iii) after priming exercise followed by a 30-min recovery (Priming30). Priming exercise lasted 6 min, at work rate corresponding to the gas exchange threshold (GET) plus 70% of the difference between the GET and . Results: The Priming 30 condition exhibited greater peak power output (595 ± 84 W) compared to the control (567 ± 85 W) and the Priming15 condition (569 ± 95 W) (P < .05). Regarding fatigue index, a tendency towards increased resistance to fatigue was observed in the Priming30 condition compared to the control and the Priming15 conditions (P = .072). Pre-Wingate lactate levels were found to be significantly different between the Priming15 (7.18 ± 3.09 mmol/L) and the Priming30 (4.87 ± 2.11 mmol/L) conditions (P < .05). Conclusions: Priming exercise of high intensity followed by a prolonged recovery leads to increased peak power in a subsequent Wingate test. Moreover, our data are consistent with the idea that a priming exercise-induced modest increase in blood lactate concentration at the onset of the following criterion bout is a key factor of performance.
A strategy for large-scale comparison of evolutionary- and reaction-based classifications of enzyme function

Abstract Determining the molecular function of enzymes discovered by genome sequencing represents a primary foundation for understanding many aspects of biology. Historically, classification of enzyme reactions has used the enzyme nomenclature system developed to describe the overall reactions performed by biochemically characterized enzymes, irrespective of their associated sequences. In contrast, functional classification and assignment for the millions of protein sequences of unknown function now available is largely done in two computational steps, first by similarity-based assignment of newly obtained sequences to homologous groups, followed by transferring to them the known functions of similar biochemically characterized homologs. Due to the fundamental differences in their etiologies and practice, `how’ these chemistry- and evolution-centric functional classification systems relate to each other has been difficult to explore on a large scale. To investigate this issue in a new way, we integrated two published ontologies that had previously described each of these classification systems independently. The resulting infrastructure was then used to compare the functional assignments obtained from each classification system for the well-studied and functionally diverse enolase superfamily. Mapping these function assignments to protein structure and reaction similarity networks shows a profound and complex disconnect between the homology- and chemistry-based classification systems. This conclusion mirrors previous observations suggesting that except for closely related sequences, facile annotation transfer from small numbers of characterized enzymes to the huge number uncharacterized homologs to which they are related is problematic. Our extension of these comparisons to large enzyme superfamilies in a computationally intelligent manner provides a foundation for new directions in protein function prediction for the huge proportion of sequences of unknown function represented in major databases. Interactive sequence, reaction, substrate and product similarity networks computed for this work for the enolase and two other superfamilies are freely available for download from the Structure Function Linkage Database Archive (http://sfld.rbvi.ucsf.edu).
Comprehensive analysis of the pre-ribosomal RNA maturation pathway in a methanoarchaeon exposes the conserved circularization and linearization mode in archaea

ABSTRACT The ribosomal RNA (rRNA) genes are generally organized as an operon and cotranscribed into a polycistronic precursor; therefore, processing and maturation of pre-rRNAs are essential for ribosome biogenesis. However, rRNA maturation pathways of archaea, particularly of methanoarchaea, are scarcely known. Here, we thoroughly elucidated the maturation pathway of the rRNA operon (16S-tRNAAla-23S-tRNACys-5S) in Methanolobus psychrophilus, one representative of methanoarchaea. Enzymatic assay demonstrated that EndA, a tRNA splicing endoribonuclease, cleaved bulge-helix-bulge (BHB) motifs buried in the processing stems of pre-16S and pre-23S rRNAs. Northern blot and quantitative PCR detected splicing-coupled circularization of pre-16S and pre-23S rRNAs, which accounted for 2% and 12% of the corresponding rRNAs, respectively. Importantly, endoribonuclease Nob1 was determined to linearize circular pre-16S rRNA at the mature 3′ end so to expose the anti-Shine–Dalgarno sequence, while circular pre-23S rRNA was linearized at the mature 5′ end by an unknown endoribonuclease. The resultant 5′ and 3′ extension in linearized pre-16S and pre-23S rRNAs were finally matured through 5′-3′ and 3′-5′ exoribonucleolytic trimming, respectively. Additionally, a novel processing pathway of endoribonucleolysis coupled with exoribonucleolysis was identified for the pre-5S rRNA maturation in this methanogen, which could be also conserved in most methanogenic euryarchaea. Based on evaluating the phylogenetic conservation of the key elements that are involved in circularization and linearization of pre-rRNA maturation, we predict that the rRNA maturation mode revealed here could be prevalent among archaea.
Crop Adaptation in On-Farm Management by Natural and Conscious Selection: A Case Study with Lentil

On-farm management of landraces or older cultivars of crop plants is often recommended to combine conservation and use of genetic resources, but experimental studies on on-farm management are hard to find, particularly in industrialized countries. To investigate whether on-farm management results in regional adaptation and enhances crop biodiversity, an experiment with lentils (Lens culinaris Medik.) was designed. Lentil production has almost ceased to exist in central Europe, but lentils may still be found in gene banks and have remained a popular food. Three landraces were evaluated on three farms in Germany; at each farm, three populations evolved, based on three selection methods: (i) natural selection, (ii) visual mass selection, and (iii) selection for yield of single plant progenies. These selection methods were applied for two to four years. The nine populations developed for each landrace (three methods × three locations) were grown in a comparative trial on two of the farms. In most cases, populations selected at a specific location were at this location superior in yield to populations selected at other locations, indicating that on-farm management can result in site-specific adaptation. Significant changes in morphological and phonological traits occurred. For one landrace, natural selection increased seed weight. The response to different selection methods largely depended on landrace and selection site, and no method was generally superior. In conclusion, on-farm management is a useful approach to maintain, use, and develop plant genetic resources. Natural selection as the most cost-efficient method is recommended.
Effects of dietary additions of modified tall oil, chromium nicotinate, and L-carnitine on growth performance, carcass characteristics, and bacon characteristics of growing-finishing pigs

Eighty gilts were supplemented with modified tall oil (MTO), chromium nicotinate (CrNic), and L-carnitine to determine effects on growth and meat quality characteristics. Pigs were assigned to one of eight treatments in a 2 × 2 × 2 factorial with main effects of MTO (0 or 0.5%), CrNic (0 or 50 μg kg-1), and L-carnitine (0 or 50 mg kg-1). Pigs fed MTO had increased (P = 0.03) average daily gain and pigs fed CrNic had improved (P = 0.02) gain:feed. Bellies from pigs supplemented with MTO with no CrNic were firmer (P 0.05) were detected for longissimus muscle (LM) visual or objective color values. Furthermore, no differences (P > 0.05) were detected for LM Warner-Bratzler shear force or sensory traits. Bacon from pigs fed MTO had firmer (P < 0.05) slices than bacon from pigs fed no MTO.These data suggest improvements in growth performance from addition of 0.50% MTO and(or) 50 μg kg-1 CrNic to diets of finishing gilts. Supplementi.
Hispaniolanthus: A New Genus of Capparaceae Endemic to Hispaniola

Abstract. Hispaniolanthus (Capparaceae), a new genus segregated from Capparis, is described and illustrated. It is characterized by short simple hairs, minute stipules, spiral phyllotaxy, juvenile individuals with linear leaf blades, mature individuals with their young leaves conduplicate, flowers axillary and subterminal, solitary and/or rarely paired, without peduncles and on remarkably long-pedicels. The calyx is decussate with closed aestivation, bearing sepals similar in size to that of the petals, four erect to divergent nectary scales, and ca. 30 to 45 stamens on short filaments, 1.5–2.0 cm long. Hispaniolanthus is a monospecific genus known only from dry forests of western Haití, facing the Island of Gonaïves. It is represented by the new combination herewith transferred from Capparis: Hispaniolanthus dolichopodus. Its putative relationships with the morphologically closer genera of Capparaceae are discussed.
Surface‐Based Atlases of Cerebellar Cortex in the Human, Macaque, and Mouse

Abstract: This study describes surface reconstructions and associated flat maps that represent the highly convoluted shape of cerebellar cortex in three species: human, macaque, and mouse. The reconstructions were based on high‐resolution structural MRI data obtained from other laboratories. The surface areas determined for the fiducial reconstructions are about 600 cm2 for the human, 60 cm2 for the macaque, and 0.8 cm2 for the mouse. As expected from the ribbon‐like pattern of cerebellar folding, the cerebellar flat maps are elongated along the axis parallel to the midline. However, the degree of elongation varies markedly across species. The macaque flat map is many times longer than its mean width, whereas the mouse flat map is only slightly elongated and the human map is intermediate in its aspect ratio. These cerebellar atlases, along with associated software for visualization and for mapping experimental data onto the atlas, are freely available to the neuroscience community (see http://brainmap.wustl.edu).