Miracle-dz/UniFAR-FTUs huggingface dataset:
Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements

Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model misspecification, and data-type differences. Researchers must balance various trade-offs associated with locus length and evolutionary rate among other factors. The most commonly used reduced representation datasets for phylogenomics are ultraconserved elements (UCEs) and Anchored Hybrid Enrichment (AHE). Here, we introduce Rapidly Evolving Long Exon Capture (RELEC), a new set of loci that targets single exons that are both rapidly evolving (evolutionary rate faster than RAG1) and relatively long in length (greater than 1,500 bp), while at the same time avoiding paralogy issues across amniotes. We compare the RELEC dataset to UCEs and AHE in squamate reptiles by aligning and analyzing orthologous sequences from 17 squamate genomes, composed of ten snakes and seven lizards. The RELEC dataset (179 loci) outperforms AHE and UCEs by maximizing per-locus genetic variation while maintaining presence and orthology across a range of evolutionary scales. RELEC markers show higher phylogenetic informativeness than UCE and AHE loci, and RELEC gene trees show greater similarity to the species tree than AHE or UCE gene trees. Furthermore, with fewer loci, RELEC remains computationally tractable for full Bayesian coalescent species tree analyses. We contrast RELEC to and discuss important aspects of comparable methods, and demonstrate how RELEC may be the most effective set of loci for resolving difficult nodes and rapid radiations. We provide several resources for capturing or extracting RELEC loci from other amniote groups.
A CORDIC algorithm with fast rotation prediction and small iteration number

This work proposes a new CORDIC algorithm with merits of small number of rotation iterations, fast prediction of rotation sequence suited for parallel and pipelined operations, and fast simple variable scale factor decomposition and compensation. It has close to the minimum number of 0.8N iterations (including rotation and compensation) of the algorithm, but has the advantage of facilitating parallel and pipelined operations in realization over the latter algorithm.
Diverse functions of closely homologous actin isoforms are defined by their nucleotide, rather than their amino acid sequence

β- and γ-cytoplasmic-actin are nearly indistinguishable in their amino acid sequence, but are encoded by different genes that play non-redundant biological roles. The key determinants that drive their functional distinction are unknown. Here we tested the hypothesis that β- and γ-actin functions are defined by their nucleotide, rather than their amino acid sequence, using targeted editing of the mouse genome. Although previous studies have shown that disruption of β-actin gene critically impacts cell migration and mouse embryogenesis, we demonstrate here that generation of a mouse lacking β-actin protein by editing β-actin gene to encode γ-actin protein, and vice versa, does not affect cell migration and/or organism survival. Our data suggest that the essential in vivo function of β-actin is provided by the gene sequence independent of the encoded protein isoform. We propose that this regulation constitutes a global “silent code” mechanism that controls the functional diversity of protein isoforms.
Southeast Europe Journal of Soft Computing

In this study, shoe manufacturing is analyzed and specific production policy is developed for the men’s shoe making company. The main characteristic of the shoe manufacturing is that the daily production rate and processing times are highly volatile and subject to high variances depending on the model and rapidly changing trends. The aim of this study is to determine the optimum production policy over the combinations of the models which will be produced in daily working schedule. A simulation study was developed to see at what degree the variations of the models effect the throughput rate.
Efficacy and safety of a novel vaginal medical device in recurrent bacterial vaginosis: an international multicentre clinical trial

Several risk factors have been identified but the etiology and pathogenesis of Bacterial vaginosis (BV) are still not completely understood, and the recurrence rate of BV remains high despite adequate chemotherapy treatment. The primary objective of the study was to assess the effectiveness of a new vaginal medical device, which contains polycarbophil, 0.04 % lauryl glucoside, and glycerides (Polybactum® – Effik Italia), in reducing BV recurrence rate. This was a multicenter, open label, not comparative study performed in Italy and Romania. Female subjects over 18-years-old affected by recurrent BV were included. The latest episode was diagnosed by Amsel criteria 6-9 days before the start of the study and treated with vaginal metronidazole (gel 0.75% mg for 5 days or ovules 500 mg for 7 days). The recurrence was defined by at least 2 episodes in the previous 12 months. Polybactum® vaginal ovules, day 1-4-7, were started within the 12th and the 24th hr after the end of metronidazole therapy and repeated monthly for 3 cycles. The first 41 patients enrolled were evaluated for an interim analysis 6 months after the study started; 2 patients interrupted the trial, leaving 39 evaluable subjects. The recurrence rate was significantly reduced compared to previous published data (10.26% vs 40% p<0.001). In 35 patients without recurrence, the assessment of Lactobacillus vaginal flora performed by phase contrast microscopy evidenced a significant improvement form baseline (p=0.022) The Investigator global assessment of tolerability was excellent in 38 out of 39 cases. IMPORTANCE Bacterial vaginosis (BV) is the most common vaginal disorder in women of childbearing age. In BV, Lactobacillus species, which are predominant in a healthy vaginal flora, are replaced by anaerobes, mainly Gardnerella vaginalis. BV is responsible for more than 60% of vulvovaginal infections and has been linked to serious, potentially life-threatening conditions, including: pelvic inflammatory disease, postoperative infections, acquisition and transmission of the human immunodeficiency virus, preterm birth, and several adverse pregnancy outcomes. Our research showed that 3 monthly cycles of Polybactum® ovules administered after one course of metronidazole vaginal therapy can reduce the rate of Bacterial vaginosis recurrence and improve the vaginal milieu, favouring the growth of vaginal lactobacillus species. Taken together our results confirm that Polibactum® is a safe and effective treatment to reduce BV recurrence rate after a first line therapy with metronidazole.
Elevated atmospheric CO2 concentration improves water use efficiency and growth of a widespread Cerrado tree species even under soil water deficit

Changes in atmospheric CO2 levels are accompanied by ecological interactions involving other environmental factors, such as drought, which can severely alter the water balance of plants, thereby influencing sap flow, gas exchange, and plant growth. The objective of this study was to evaluate the water use economy, leaf gas exchange, and growth of young plants of the species Lafoensia pacari subjected to high concentrations of atmospheric CO2 ([CO2]) and soil water deficit. Increased vapor pressure deficit was observed from 1200 to 1800 hours. Plants under elevated [CO2] exhibited increased leaf photosynthesis, resulting in improved growth. Specific leaf area was lower in plants under high [CO2], mainly after soil water deficit treatment. Daily irrigated plants growing under ambient [CO2] had higher stem sap flow velocity (cm h-1) and hourly sap flow (kg h-1), mainly during the hottest hours of the day, than plants under high [CO2]. Improved water use by plants growing under high [CO2] may result in increased availability of water in the soil, partially offsetting future drought events and extending the growth period.
Effects of pre-anthesis drought stress on yield components and seed quality of rice (Oryza sativa L.)

Sufficient supply of high quality planting materials is vital for a successful rice production. Pre-anthesis drought stress significantly reduces yield components of the lowland cultivated rice hence scientific information on its effect on seed quality is still very much lacking. This study was conducted to compare the effects of pre-anthesis drought stress on yield components and seed quality of two rice genotypes, a drought tolerant Moroberekan (V1), and local drought susceptible MR297 (V2). Three durations of drought stress used in this study were well-watered condition (S1), five days stress duration (S2), and ten days stress duration (S3). Complete (100%) spikelet sterility was observed for MR297 as compared with Moroberekan (31%) under S3. The seed germination rate of Moroberekan was significantly lower (p<0.05) under S1 (48%) as compared with S2 (80%) and S3 (70%). However, embryo of the non-germinated seeds of Moroberekan were still alive based on tetrazolium test thus indicated that the seeds were still viable yet dormant. In contrast, seed germination rate of MR297 was not affected by pre-anthesis drought stress (88% for S1 compared to 93% for S2). Therefore, seeds of MR297 produced under pre-anthesis drought stressed condition could be safely distributed in rice seeds supply chain.
Morphometric analysis of fossil hylobatid molars from the Pleistocene of southern China

This study investigates the morphological variation and taxonomic affinities of 28 fossil gibbon molars from eight newly discovered Pleistocene cave sites in the area of Chongzuo, Guangxi Zhuang Autonomous Region, China. A recent descriptive analysis demonstrated that these fossil teeth form a uniform group that can be assigned to a single species of Nomascus . In this contribution, a two-dimensional morphometric approach is employed to examine the Chongzuo specimens in comparison with a large sample of extant hylobatids, as well as with previously reported hylobatid dental remains from the Pleistocene of China. Buccolingual and mesiodistal measurements and crown outline areas reveal that the Chongzuo molars correspond most closely with Nomascus and, to a lesser extent, Hoolock . Crown shape was investigated using elliptical Fourier analysis. Our results show that the Chongzuo specimens fall in most cases either within the range of variation of extant Nomascus to the exclusion of all other hylobatid genera, or their distance from the cluster represented by the Nomascus sample is relatively small. Similarly, the Mahalanobis distances for crown shape show a trend towards smaller morphological distances between the Chongzuo specimens and Nomascus , followed by Hoolock and Hylobates . The Chongzuo molars are also morphometrically distinct from Bunopithecus sericus , but fall within the range of overlap of other Pleistocene hylobatid dental remains from southern China. The balance of evidence indicates that the Chongzuo teeth can be attributed to cf. Nomascus . The fossil teeth are sufficiently distinct from those of extant Nomascus that they may represent an extinct species.
Estimating density and detection of bobcats in fragmented midwestern landscapes using spatial capture–recapture data from camera traps

Camera‐trapping data analyzed with spatially explicit capture–recapture (SCR) models can provide a rigorous method for estimating density of small populations of elusive carnivore species. We sought to develop and evaluate the efficacy of SCR models for estimating density of a presumed low‐density bobcat (Lynx rufus) population in fragmented landscapes of west‐central Illinois, USA. We analyzed camera‐trapping data from 49 camera stations in a 1,458‐km area deployed over a 77‐day period from 1 February to 18 April 2017. Mean operational time of cameras was 52 days (range= 32–67 days). We captured 23 uniquely identifiable bobcats 113 times and recaptured these same individuals 90 times; 15 of 23 (65.2%) individuals were recaptured at ≥2 camera traps. Total number of bobcat capture events was 139, of which 26 (18.7%) were discarded from analyses because of poor image quality or capture of only a part of an animal in photographs. Of 113 capture events used in analyses, 106 (93.8%) and 7 (6.2%) were classified as positive and tentative identifications, respectively; agreement on tentative identifications of bobcats was high (71.4%) among 3 observers. We photographed bobcats at 36 of 49 (73.5%) camera stations, of which 34 stations were used in analyses. We estimated bobcat density at 1.40 individuals (range= 1.00–2.02)/100 km. Our modeled bobcat density estimates are considerably below previously reported densities (30.5 individuals/ 100 km) within the state, and among the lowest yet recorded for the species. Nevertheless, use of remote cameras and SCR models was a viable technique for reliably estimating bobcat density across west‐central Illinois. Our research establishes ecological benchmarks for understanding potential effects of colonization, habitat fragmentation, and exploitation on future assessments of bobcat density using standardized methodologies that can be compared directly over time. Further application of SCR models that quantify specific costs of animal movements (i.e., least‐cost path models) while accounting for landscape connectivity has great utility and relevance for conservation and management of bobcat populations across fragmented Midwestern landscapes. © 2019 The Wildlife Society.
Deciphering cell lineage specification during male sex determination with single-cell RNA sequencing

The gonad is a unique biological system for studying cell fate decisions. However, major questions remain regarding the identity of somatic progenitor cells and the transcriptional events driving cell differentiation. Using time course single cell RNA sequencing on XY mouse gonads during sex determination, we identified a single population of somatic progenitor cells prior sex determination. A subset of these progenitors differentiate into Sertoli cells, a process characterized by a highly dynamic genetic program consisting of sequential waves of gene expression. Another subset of multipotent cells maintains their progenitor state but undergo significant transcriptional changes that restrict their competence towards a steroidogenic fate required for the differentiation of fetal Leydig cells. These results question the dogma of the existence of two distinct somatic cell lineages at the onset of sex determination and propose a new model of lineage specification from a unique progenitor cell population.
Conjugative Delivery of CRISPR-Cas9 for the Selective Depletion of Antibiotic-Resistant Enterococci

The innovation of new therapies to combat multidrug-resistant (MDR) bacteria is being outpaced by the continued rise of MDR bacterial infections. Of particular concern are hospital-acquired infections (HAIs) that are recalcitrant to antibiotic therapies. The Gram-positive intestinal pathobiont Enterococcus faecalis is associated with HAIs, and some strains are MDR. Therefore, novel strategies to control E. faecalis populations are needed. ABSTRACT The innovation of new therapies to combat multidrug-resistant (MDR) bacteria is being outpaced by the continued rise of MDR bacterial infections. Of particular concern are hospital-acquired infections (HAIs) that are recalcitrant to antibiotic therapies. The Gram-positive intestinal pathobiont Enterococcus faecalis is associated with HAIs, and some strains are MDR. Therefore, novel strategies to control E. faecalis populations are needed. We previously characterized an E. faecalis type II CRISPR-Cas system and demonstrated its utility in the sequence-specific removal of antibiotic resistance determinants. Here, we present work describing the adaption of this CRISPR-Cas system into a constitutively expressed module encoded on a pheromone-responsive conjugative plasmid that efficiently transfers to E. faecalis for the selective removal of antibiotic resistance genes. Using in vitro competition assays, we show that these CRISPR-Cas-encoding delivery plasmids, or CRISPR-Cas antimicrobials, can reduce the occurrence of antibiotic resistance in enterococcal populations in a sequence-specific manner. Furthermore, we demonstrate that deployment of CRISPR-Cas antimicrobials in the murine intestine reduces the occurrence of antibiotic-resistant E. faecalis by several orders of magnitude. Finally, we show that E. faecalis donor strains harboring CRISPR-Cas antimicrobials are immune to uptake of antibiotic resistance determinants in vivo. Our results demonstrate that conjugative delivery of CRISPR-Cas antimicrobials may be adaptable for future deployment from probiotic bacteria for exact targeting of defined MDR bacteria or for precision engineering of polymicrobial communities in the mammalian intestine.
The complete mitochondrial genome of Rhynchocypris oxycephalus (Teleostei: Cyprinidae) and its phylogenetic implications

Abstract Rhynchocypris oxycephalus (Teleostei: Cyprinidae) is a typical small cold water fish, which is distributed widely and mainly inhabits in East Asia. Here, we sequenced and determined the complete mitochondrial genome of R. oxycephalus and studied its phylogenetic implication. R. oxycephalus mitogenome is 16,609 bp in length (GenBank accession no.: MH885043), and it contains 13 protein‐coding genes (PCGs), two rRNA genes, 22 tRNA genes, and two noncoding regions (the control region and the putative origin of light‐strand replication). 12 PCGs started with ATG, while COI used GTG as the start codon. The secondary structure of tRNA‐Ser (AGN) lacks the dihydrouracil (DHU) arm. The control region is 943bp in length, with a termination‐associated sequence, six conserved sequence blocks (CSB‐1, CSB‐2, CSB‐3, CSB‐D, CSB‐E, CSB‐F), and a repetitive sequence. Phylogenetic analysis was performed with maximum likelihood and Bayesian methods based on the concatenated nucleotide sequence of 13 PCGs and the complete sequence without control region, and the result revealed that the relationship between R. oxycephalus and R. percnurus is closest, while the relationship with R. kumgangensis is farthest. The genus Rhynchocypris is revealed as a polyphyletic group, and R. kumgangensis had distant relationship with other Rhynchocypris species. In addition, COI and ND2 genes are considered as the fittest DNA barcoding gene in genus Rhynchocypris. This work provides additional molecular information for studying R. oxycephalus conservation genetics and evolutionary relationships.
Effects of different dietary carbohydrate on growth performance and liver histology of Nile tilapia, Oreochromis niloticus fingerlings

The experimental study was conducted to investigate the effects of different dietary carbohydrate sources on growth performance, blood parameters, body compostion and liver histology of fingerlings Nile tilapia (Oreochromis niloticus). Fish were distributed into six treatments and each treatment was represented in three replicates of glass aquaria, which contain 25 fish in each aquarium with an initial body weight of 9.2±0.037g. Six diets were formulated by using three different sources of carbohydrate (wheat bran, corn and sorghum) and each source was incorporated as two levels (15 and 30%) of the diet. Eighteen full glass aquaria measuring (75×40×35cm) were used for rearing fish. The experimental lasted 90 days after start. The results demonstrated that the growth performance parameters in terms of weight gain (WG) and specific growth rate (SGR) were shown the highest values for fish fed with sorghum compared with the other diets. In the same manner thenutrient utilization parameters from protein efficiency ratio (PER), feed conversion ratio (FCR) and net protein utilization (NPU) were increased with dietary sorghum starch in the two levels. No significance differences (P>0.01) were detected in RBCs, red blood cells, WBCs, white blood cells, PL, platelates, HB, haemoglobin and HCT, haematocrit between tested diets. Whole body composition of fish not affected with different dietary carbohydrate sources. However, histopathological examinations showed that sorghum supplemented with low dose improve liver and spleen structures. Based on growth performance, feed utilization, body composition and histopathological examination results, the appropriate dietary sorghum can incorporated up to 30% in feed formulation, without compromising effects on growth parameters, proximate composition and liver structure of Nile tilapia (Oreochromis niloticus) fingerlings.
A low supply voltage high PSRR voltage reference in CMOS process

This paper describes a bandgap voltage reference circuit that operates with a 3 V power supply and is compatible with a digital CMOS process. The use of a simple circuit topology results in a small silicon area of 0.07 mm/sup 2/, a power consumption of 1 mW and a high power supply rejection over a wide frequency band. The circuit realizes a temperature coefficient of 85 ppm//spl deg/C and a standard deviation of 20 mV without trimming. >
The phylogeographic history of amphitropical Callophyllis variegata (Florideophyceae, Rhodophyta) in the Pacific Ocean

Copyright © 2019 The Korean Society of Phycology 91 http://e-algae.org pISSN: 1226-2617 eISSN: 2093-0860 The phylogeographic history of amphitropical Callophyllis variegata (Florideophyceae, Rhodophyta) in the Pacific Ocean Trevor T. Bringloe*, Erasmo C. Macaya and Gary W. Saunders Centre for Environmental and Molecular Algal Research (CEMAR), Biology Department, University of New Brunswick, P.O. Box 4400, Fredericton, New Brunswick E3B 5A3, Canada Laboratorio de Estudios Algales (ALGALAB), Departamento de Oceanografía, Universidad de Concepción, Casilla 160-C, Concepción, Chile Millenium Nucleus Ecology and Sustainable Management of Oceanic Islands (ESMOI) Centro FONDAP de Investigaciones en Dinámica de Ecosistemas Marinos de Altas Latitudes (IDEAL), Independencia 631, Valdivia, Chile