Miracle-dz/UniFAR-FTUs huggingface dataset:
On bivalve phylogeny: a high‐level analysis of the Bivalvia (Mollusca) based on combined morphology and DNA sequence data

Abstract. Bivalve classification has suffered in the past from the crossed-purpose discussions among paleontologists and neontologists, and many have based their proposals on single character systems. More recently, molecular biologists have investigated bivalve relationships by using only gene sequence data, ignoring paleontological and neontological data. In the present study we have compiled morphological and anatomical data with mostly new molecular evidence to provide a more stable and robust phylogenetic estimate for bivalve molluscs. The data here compiled consist of a morphological data set of 183 characters, and a molecular data set from 3 loci: 2 nuclear ribosomal genes (18S rRNA and 28S rRNA), and 1 mitochondrial coding gene (cytochrome c oxidase subunit I), totaling ∼3 Kb of sequence data for 76 molluscs (62 bivalves and 14 outgroup taxa). The data have been analyzed separately and in combination by using the direct optimization method of Wheeler (1996), and they have been evaluated under 12 analytical schemes. The combined analysis supports the monophyly of bivalves, paraphyly of protobranchiate bivalves, and monophyly of Autolamellibranchiata, Pteriomorphia, Heteroconchia, Palaeoheterodonta, and Heterodonta s.l. , which includes the monophyletic taxon Anomalodesmata. These analyses strongly support the conclusion that Anomalodesmata should not receive a class status, and that the heterodont orders Myoida and Veneroida are not monophyletic. Among the most stable results of the analysis are the monophyly of Palaeoheterodonta, grouping the extant trigoniids with the freshwater unionids, and the sister-group relationship of the heterodont families Astartidae and Carditidae, which together constitute the sister taxon to the remaining heterodont bivalves. Internal relationships of the main bivalve groups are discussed on the basis of node support and clade stability.
Effects of fibrolytic enzymes in corn or barley diets on performance and carcass characteristics of feedlot cattle

A study was conducted to establish whether fibrolytic enzyme feed additives influence performance of feedlot cattle fed high grain diets, and to compare the effects of feeding diets of barley or corn on performance and carcass characteristics. Crossbred beef steers (408 kg) were offered high concentrate diets (95.1%, dry matter basis), consisting mainly of barley and barley silage or corn and corn silage. Concentrates were treated with either no enzyme or one of two enzyme mixtures. Calves were slaughtered after a 103- to 145-d feeding period at an average weight of 570 kg and 10.8 mm of backfat. Barley-fed calves grew faster (1.45 vs. 1.29 kg d−1), ate more dry matter (DM; 9.79 vs. 9.31 kg d−1), and converted DM to gain (6.85 vs. 7.35 kg DM kg−1gain) more efficiently compared with corn-fed calves (P < 0.001). Meat from barley-fed calves tended to be more highly marbled and was brighter in colour than meat from corn-fed calves, but diet had no effect on muscle score, rib eye area, or carcass leanness. Eff.
Sex differences in the brains of capuchin monkeys (Sapajus [Cebus] apella)

This study reports an analysis of 20 T1‐weighted magnetic resonance imaging scans from tufted capuchin monkeys (5 male, 15 female). We carried out a data‐driven, whole‐brain volumetric analysis on regional gray matter anatomy using voxel‐based morphometry. This revealed that males showed statistically significant expansion of a region of the hypothalamus, while females showed significant expansion in a distributed set of regions, including the cerebellum, early visual cortex, and higher‐order visual regions spanning occipital and temporal cortex. In order to elucidate the network connectivity of these regions, we employed probabilistic tractography on diffusion tensor imaging data. This showed that the female‐enlarged regions connect with distributed association networks across the brain. Notably, this contrasts with rodent studies, where sex differences are focused in deep, ancestral limbic regions involved in the control of reproductive behavior. Additionally, in our data set, for several regions, male and female volumetric measures were completely nonoverlapping. This contrasts with human studies, where sex differences in cortical regions have been reported but are characterized by overlapping rather than divergent male and female values. We suggest that these results can be understood in the context of the different lifetime experiences of males and females, which may produce increased experience‐dependent cortical plasticity in capuchins compared to rodents, and in humans compared to capuchins.
Contributions of Different Functional Groups to Contact Electrification of Polymers

Polymers are commonly used to fabricate triboelectric nanogenerators (TENGs). Here, several polymer films with similar main chains but different functional groups on the side chain are employed to clarify the contributions of each functional group to contact electrification (CE). The results show that the electron‐withdrawing (EW) ability and density of these functional groups on the main chain can determine both the polarity and density of CE‐induced surface charges. Similar results are obtained for CE in both the polymer–polymer and polymer–liquid modes. A theoretical mechanism involving electron cloud overlap is proposed to explain all of these results. More importantly, the unsaturated groups on poly(tetrafluoroethylene) molecular chain are proved to have a much stronger EW ability than the saturated groups. The density of these unsaturated groups can be increased using a sputtering technique, suggesting that this is a facile and effective method of enhancing the performance of TENGs. These results clarify the correlation between the molecular structure and macroscopic electrification behavior of polymers.
SteadEye-Head—Improving MARG-Sensor Based Head Orientation Measurements Through Eye Tracking Data

This paper presents the use of eye tracking data in Magnetic AngularRate Gravity (MARG)-sensor based head orientation estimation. The approach presented here can be deployed in any motion measurement that includes MARG and eye tracking sensors (e.g., rehabilitation robotics or medical diagnostics). The challenge in these mostly indoor applications is the presence of magnetic field disturbances at the location of the MARG-sensor. In this work, eye tracking data (visual fixations) are used to enable zero orientation change updates in the MARG-sensor data fusion chain. The approach is based on a MARG-sensor data fusion filter, an online visual fixation detection algorithm as well as a dynamic angular rate threshold estimation for low latency and adaptive head motion noise parameterization. In this work we use an adaptation of Madgwicks gradient descent filter for MARG-sensor data fusion, but the approach could be used with any other data fusion process. The presented approach does not rely on additional stationary or local environmental references and is therefore self-contained. The proposed system is benchmarked against a Qualisys motion capture system, a gold standard in human motion analysis, showing improved heading accuracy for the MARG-sensor data fusion up to a factor of 0.5 while magnetic disturbance is present.
Burden of Osteoporotic Fractures Using Disability-Adjusted Life Years in South Korea

There is an increase in the number of patients with osteoporotic fractures due to the aging population in Korea. This study investigated the burden of osteoporotic fractures including hip, spine, and wrist fractures in the Korean population by estimating disability-adjusted life years (DALYs). The DALY for a given condition in a population captures years of life lost due to premature death and years of life lived with a disability and its severity and duration. To calculate DALYs from all relevant data collected for the 3 conditions, we used a DALY calculation template provided by the World Health Organization in 2014. DALYs per 100 000 for vertebral fractures (3168) were higher than those of hip fractures (2496) in women. Wrist fractures (1038) had the least burden, and the difference between men and women was the lowest. The aging population is expected to increase the burden of osteoporosis.
A Fully Integrated Assay Panel for Early Drug Metabolism and Pharmacokinetics Profiling

Evaluation and optimization of physicochemical and metabolic properties of compounds are a crucial component of the drug development process. Continuous access to this information during the design-make-test-analysis cycle enables identification of chemical entities with suitable properties for efficient project progression. In this study, we describe an integrated and automated assay panel (DMPK Wave 1) that informs weekly on lipophilicity, solubility, human plasma protein binding, and metabolic stability in rat hepatocytes and human liver microsomes. All assays are running in 96-well format with ultraperformance liquid chromatography–mass spectrometry (MS)/MS as read-out. A streamlined overall workflow has been developed by optimizing all parts of the process, including shipping of compounds between sites, use of fit-for-purpose equipment and information systems, and technology for compound requesting, data analysis, and reporting. As a result, lead times can be achieved that well match project demands across sites independently of where compounds are synthesized. This robust screening strategy is run on a weekly basis and enables optimization of structure-activity relationships in parallel with DMPK properties to allow efficient and informed decision making.
Applying VSM to Identify the Criminal Meaning of Texts

Generally, to define the belonging of a text to a specific theme or domain, we can use approaches to text classification. However, the task becomes more complicated when there is no train corpus, in which the set of classes and the set of documents belonged to these classes are predetermined. We suggest using the semantic similarity of texts to determine their belonging to a specific domain. Our train corpus includes news articles containing criminal information. In order to define whether the theme of input documents is close to the theme of the train corpus, we propose to calculate the cosine similarity between documents of the corpus and the input document. We have empirically established the average value of the cosine similarity coefficient, in which the document can be attributed to the highly specialized documents containing criminal information. We evaluate our approach on the test corpus of articles from the news sites of Kharkiv. F-measure of the document classification with criminal information achieves 96 %.
Beyond Freezing: Temporal Expectancy of an Aversive Event Engages the Amygdalo-Prefronto-Dorsostriatal Network.

During Pavlovian aversive conditioning, a neutral conditioned stimulus (CS) becomes predictive of the time of arrival of an aversive unconditioned stimulus (US). Using a paradigm where animals had to discriminate between a CS+ (associated with a footshock) and a CS- (never associated with a footshock), we show that, early in training, dynamics of neuronal oscillations in an amygdalo-prefronto-striatal network are modified during the CS+ in a manner related to the CS-US time interval (30 or 10 s). This is the case despite a generalized high level of freezing to both CS+ and CS-. The local field potential oscillatory power was decreased between 12 and 30 Hz in the dorsomedial striatum (DMS) and increased between 55 and 95 Hz in the prelimbic cortex (PL), while the coherence between DMS, PL, and the basolateral amygdala was increased in the 3-6 Hz frequency range up to the expected time of US arrival only for the CS+ and not for the CS-. Changing the CS-US interval from 30 to 10 s shifted these changes in activity toward the newly learned duration. The results suggest a functional role of the amygdalo-prefronto-dorsostriatal network in encoding temporal information of Pavlovian associations independently of the behavioral output.
Air Temperature During Seed Filling and Soybean Seed Germination and Vigor

High temperature stress during seed filling in controlled environments reduces soybean [Glycine max (L.) Merrill] seed germination and vigor, but the effect of high temperature in the field has not been determined. Seeds of two soybean cultivars (Hutcheson, maturity group [MG] V, and DP4690, MG IV) were produced in the field in Kentucky, Mississippi, Arkansas, and Texas in 2000 to 2002. Air temperature during seed filling was monitored and brown (mature) pods were harvested, hand threshed, and all shriveled and abnormal seeds were removed before determining standard germination and vigor (accelerated-aging germination). Mean maximum temperatures during seed filling (growth stage R5 to R7) ranged from 24.0 (Kentucky) to 37.6 degrees C (Texas). When seed lots infected with Phomopsis longicolla (Hobbs) were removed from the analysis, standard germination and accelerated-aging germination (AA) decreased as mean maximum temperature during seed filling increased, but the decrease was significant (P = 0.05) only for Hutcheson. Standard germination of Hutcheson declined linearly (r2 = 0.49) from near 100% at 24 degrees C to 85% at 36 degrees C, while the decrease in AA was curvilinear (R2 = 0.86) and germination reached 11% at 36 degrees C. Seeds of Hutcheson were more sensitive to high temperature than seeds of DP4690 and seed vigor (AA) was much more sensitive to high-temperature stress than was standard germination. Our findings support the results of experiments in controlled environments by demonstrating that high temperature during seed filling in the field, without seed infection with P. longicolla or physical injury, reduced soybean seed germination and vigor.
A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis

Background The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has been growing exponentially, affecting over 4 million people and causing enormous distress to economies and societies worldwide. A plethora of analyses based on viral sequences has already been published both in scientific journals and through non–peer-reviewed channels to investigate the genetic heterogeneity and spatiotemporal dissemination of SARS-CoV-2. However, a systematic investigation of phylogenetic information and sampling bias in the available data is lacking. Although the number of available genome sequences of SARS-CoV-2 is growing daily and the sequences show increasing phylogenetic information, country-specific data still present severe limitations and should be interpreted with caution. Objective The objective of this study was to determine the quality of the currently available SARS-CoV-2 full genome data in terms of sampling bias as well as phylogenetic and temporal signals to inform and guide the scientific community. Methods We used maximum likelihood–based methods to assess the presence of sufficient information for robust phylogenetic and phylogeographic studies in several SARS-CoV-2 sequence alignments assembled from GISAID (Global Initiative on Sharing All Influenza Data) data released between March and April 2020. Results Although the number of high-quality full genomes is growing daily, and sequence data released in April 2020 contain sufficient phylogenetic information to allow reliable inference of phylogenetic relationships, country-specific SARS-CoV-2 data sets still present severe limitations. Conclusions At the present time, studies assessing within-country spread or transmission clusters should be considered preliminary or hypothesis-generating at best. Hence, current reports should be interpreted with caution, and concerted efforts should continue to increase the number and quality of sequences required for robust tracing of the epidemic.
Effect of serum 25‐hydroxyvitamin D levels on sperm quality and assisted reproductive technology outcomes for men of infertile Chinese couples

Vitamin D insufficiency/deficiency is highly prevalent in China, but its effect on sperm quality and outcomes of assisted reproductive technology (ART) in men from infertile couples is not clear. This study aimed to explore the association of serum 25‐hydroxyvitamin D (25OHD) levels and semen parameters, as well as ART outcomes for men from infertile couples.
Associations and abundance of sea urchins and abalone on shallow subtidal reefs in southern New South Wales

The densities of the abalone Haliotis rubra and the sea urchin Centrostephanus rodgersii were estimated at five localities on the southern coast of New South Wales. Abalone were most abundant at localities south of Eden but were patchy at all localities and sites. There was no clear pattern in the abundance of C. rodgersii among localities but there was considerable variation among sites within localities. Densities of abalone and sea urchins were negatively associated within 10-m2 transects at 20% of sites. At the smallest nearest-neighbour scale, the two species were segregated. The population structures of abalone differed considerably among sites; some populations consisted of single size cohorts, whereas others were much more complex. Abalone large enough to be collected legally were rare at all localities and comprised less than 10% of the total population. Possible reasons for the negative associations between H. rubra and C. rodgersii are discussed.
Changes in long-chain fatty acid composition of milk fat globule membrane and expression of mammary lipogenic genes in dairy cows fed sunflower seeds and rumen-protected choline.

The aim of this experiment was to investigate the effect of dietary supplementation of crushed high oleic sunflower seeds (HOS) and rumen-protected choline (RPC) on the fatty acid (FA) profile of phospholipids and sphingomyelin and mammary transcription of genes that are important for milk fat synthesis and de novo synthesis of sphingolipids. Twenty-four cows were divided into four groups that either received an unsupplemented diet (Control), the Control diet supplemented with 50 g RPC per day, a diet supplemented with HOS at 10% of dry matter, or RPC and HOS in combination (RPC + HOS). RPC supplementation had no effect on the FA composition of milk or sphingomyelin. Cows receiving RPC and RPC + HOS had increased incorporation of C22:5 (n-3) into phospholipids. Milk FA proportion of C18:0 and C18:1 isomers was increased in cows receiving HOS (HOS and RPC + HOS). Sphingomyelin proportion of C22:0 was increased in cows receiving HOS and RPC + HOS, at the expense of C23:0. HOS supplementation further increased the proportion of unsaturated fatty acids (UFA) in milk phospholipids. HOS supplementation increased mammary transcription of UDP-glucose ceramide glycosyltransferase (UGCG), sterol response element-binding protein cleavage-activating protein (SCAP) and peroxisome proliferation-activated receptor Gamma subunit C 1b (PPARGC1b), and reduced transcription of insulin induced gene 1 (INSIG1) and fatty acid-binding protein 3 (FABP3). Dietary supplementation of RPC increased mammary transcription of fatty acid desaturase 1 (FADS1) and longevity assurance gene 2 (LASS2), and reduced transcription of sphingomyelin synthase (SGMS). The results show that the FA profile of milk phospholipids is sensitive to dietary lipid supplementation and, to a minor degree, RPC supplementation. Furthermore, transcription of genes that are important for milk fat synthesis and sphingolipids synthesis is affected by dietary supplementation of RPC and HOS.
Desempenho produtivo de bovinos Nelore de diferentes classes sexuais alimentados com dietas contendo dois níveis de oferta de concentrado

Objetivou-se avaliar os efeitos de classe sexual e nivel de oferta de concentrado sobre o desempenho, o consumo e a digestibilidade dos nutrientes em bovinos Nelore. Trinta e cinco animais, 12 machos inteiros, 11 machos castrados e 12 femeas, provenientes de um mesmo grupo contemporâneo, foram distribuidos aleatoriamente a dois tratamentos, correspondentes aos niveis de oferta de concentrado, 0,6 e 1,2% do peso corporal, respectivamente. Os animais foram alimentados individualmente durante 112 dias, sendo abatidos ao final do experimento, com um grupo referencia abatido ao inicio. Os machos inteiros foram mais eficientes, pois apresentaram maior peso final e de corpo vazio, como resultado da maior taxa de crescimento em relacao as femeas, ficando os machos castrados em posicao intermediaria. Os consumos relativos de materia seca e de todos os demais nutrientes foram superiores nas femeas em relacao aos machos inteiros, de modo que os castrados apresentaram valores intermediarios. As digestibilidades, a excecao do extrato etereo, nao foram afetadas pela classe sexual. As digestibilidades da materia seca e materia orgânica foram superiores para a dieta com nivel de oferta de concentrado de 1,2% do PV. Classe sexual afetou o crescimento e a capacidade de consumo dos animais, porem nao teve efeito sobre a digestibilidade dos nutrientes da dieta. Niveis de oferta de concentrado de 0,6 e 1,2% do PV nao foram suficientes para promover diferencas no desempenho de bovinos Nelore, independentemente de classe sexual.
Environmental Factors Affecting Nest-Site Selection and Breeding Success of the White Stork (Ciconia ciconia) in Western Turkey

Abstract We investigated nest site selection and breeding success of White Storks (Ciconia ciconia) in relation to geographical features, weather, and land use in western Turkey. Locations of nests in relation to altitude, distance to the nearest river and stream, slope, and aspect were examined between 2008 and 2010 in Sındırgı District. Population dynamics of breeding White Storks were surveyed in the central town in 1984, 1987, and between 1992 and 2010. White Storks nested in only 17 of 74 settlements. Twenty-six of 46 nests were occupied in 2010 with a mean density of 1.72 breeding pairs/km2. Settlements with nests were significantly lower (x ± SD) in elevation (283.3 ± 77.3 vs. 622.5 ± 230.7 m) and closer to the nearest river (1,646.2 ± 1,004.5 vs. 4,101.7 ± 3,231.5 m) than settlements without nests. No significant difference was found between the mean aspects of the settlements and the distances to the nearest stream between these two groups of settlements. The number of breeding pairs and fledglings had a significantly decreasing trend throughout the study period. The number of breeding pairs was positively correlated with the annual total area of crop fields and negatively correlated with the total area of fruit production. The number of breeding pairs was positively correlated with total and maximum precipitation in April, but breeding success was negatively correlated with mean total precipitation and mean maximum precipitation during the breeding season.