Miracle-dz/UniFAR-FTUs huggingface dataset:
Shifts in diversification rates linked to biogeographic movement into new areas: an example of a recent radiation in the Andes

Acknowledgements We would like to thank S. Mathews for kindly sharing genomic DNA for some taxa used in this study. J. Sullivan, L. Harmon, E. Roalson, J. Beaulieu, B. Moore, N. Nürk, M. Pennell, T. Peterson, and two anonymous reviewers for helpful suggestions or comments on the manuscript. J. Beaulieu, L. Harmon, C. Blair and the University of Idaho Institute for Bioinformatics and Evolutionary Studies (NIH/NCRR P20RR16448 and P20RR016454) for computational aid. Funding for this work was provided by NSF DEB–1210895 to DCT for SUC, NSF DEB–1253463 to DCT, and Graduate Student Research Grants to SUC from the Botanical Society of America (BSA), the Society of Systematic Biologists (SSB), the American Society of Plant Taxonomists (ASPT), and the University of Idaho Stillinger Herbarium Expedition Funds. Premise of the study Clade specific bursts in diversification are often associated with the evolution of key innovations. However, in groups with no obvious morphological innovations, observed upticks in diversification rates have also been attributed to the colonization of a new geographic environment. In this study, we explore the systematics, diversification dynamics, and historical biogeography of the plant clade Rhinantheae in the Orobanchaceae, with a special focus on the Andean clade of the genus Bartsia L. Methods We sampled taxa from across Rhinantheae, including a representative sample of Andean Bartsia species. Using standard phylogenetic methods, we reconstructed evolutionary relationships, inferred divergence times among the clades of Rhinantheae, elucidated their biogeographic history, and investigated diversification dynamics. Key results We confirmed that the South American Bartsia species form a highly supported monophyletic group. The median crown age of Rhinantheae was determined to be ca. 30 Ma, and Europe played an important role in the biogeographic history of the lineages. South America was first reconstructed in the biogeographic analyses around 9 Ma, and with a median age of 2.59 Ma, this clade shows a significant uptick in diversification. Conclusions Increased net diversification of the South American clade corresponds with biogeographic movement into the New World. This happened at a time when the Andes were reaching the necessary elevation to host an alpine environment. Although a specific route could not be identified with certainty, we provide plausible hypotheses to how the group colonized the New World.
Molecular cloning and phylogenetic analysis of a novel BURP domain-containing gene from Camellia sinensis

BURP domain-containing proteins are a new class of plant-specific proteins that play important roles in the growth, development and stress response of plants. In this paper, a novel BURP domain-containing gene from Camellia sinensis (CsBDP, GenBank accession No. EU715397) was isolated and cloned using reverse transcription-polymerase chain reaction (RT-PCR) followed by 5′ and 3′ rapid amplification of cDNA ends (RACE) reactions. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and Western blot were then applied to detect the expression of CsBDP gene in Escherichia coli. Sequence comparison showed that the deduced protein sequence of CsBDP gene shared high sequence similarity to other BURP domain-containing proteins and contained four typical modules: an N-terminal hydrophobic region, a short conserved segment, a variable region containing two repeats of about 19 amino acids, which is unique for the RD22-like proteins of BURP family and a C-terminal BURP domain. Furthermore, phylogenetic tree revealed that the BURP protein family can be classified into eight subfamilies, and CsBDP was distinctly clustered into subfamily III with all RD22-like proteins. Therefore, CsBDP gene might be a stress-inducible gene and important for the stress tolerance of tea plant.
Attacking the SARS-CoV-2 Replication Machinery with the Pathogen Box’s Molecules

The world is currently facing a pandemic caused by the new 2019 coronavirus disease (COVID-19), caused by SARS-CoV-2. Among the fundamental processes of this virus are viral transcription and replication. They allow the synthesisof genetic material and the consequent multiplication of the virus to infect other cells or organisms. These are performed by a multi-subunit machinery of various nonstructural proteins (nsp); among which the RNA-dependent RNApolymerase (RdRp or nsp12) is the most important, and, at the same time, conserved among coronaviruses. The structure of this protein (PDB ID: 6M71) was used as a target in the application of computational strategies for drugsearch, like virtual screening and molecular docking. The region considered for virtual screening has three important amino acids for protein catalysis: T680 (located in Motif A), N691 and D623 (located in Motif B), where a grid box was located. In turn, applying the concept of drug repositioning isconsidered as a quick response in the treatment of sudden outbreaks of diseases. Here, we used the Pathogen Box, a database of chemical compounds analyzed for the treatment against malaria, which were filtered under the criteria of selecting those that do not present any violation of Lipinski'sRule of Five. At the same time, the Remdesivir, Beclabuvir and Sofosbuvir drug, previously used in in silico and clinical studies for inhibition of nsp12, were used as positive controls. The results showed a Top10 potential target inhibitors, with binding energy higher than those of the positive controls, of which TCMDC-134153 and TCMDC-135052, both with -7.53 kcal/mol, present interactions with the three important residues of the nsp12 catalytic site. These proposed ligands would be used for subsequent validation by molecular dynamics, where they can beconsidered as drugs for the development of effective treatments against this new pandemic.
Drivers of Credit Penetration in Eastern India

This article highlights that the eastern region of India continues to lag behind other regions in harnessing the potential of bank credit as an instrument to promote growth and development, notwithstanding concerted policy efforts to further financial inclusion in the region. While enhancing access to credit remains critical to strengthen credit penetration in the region, empirical findings suggest that factors influencing demand for credit – per capita income, level of industrial activity and availability of infrastructure such as road network and power supply – also matter.
Fecundity and brood loss in four species of fiddler crabs, genus Uca (Brachyura: Ocypodidae), in the mangroves of Inhaca Island, Mozambique

In this study, four species of fiddler crabs (Uca) at Inhaca Island, Mozambique, were studied: their fecundity determined and egg loss between the first and last embryonic development stage evaluated. Ovigerous female crabs were collected throughout February to March (wet season) of 2006, during day-time at low tide, in Ponta Rasa (U. annulipes and U. inversa) and Saco (U. chlorophthalmus and U. vocans) mangroves. Average brood size increased significantly with female and species size, ranging from 932 (CW = 8.51 mm) in U. annulipes, to 18,057 (CW = 23.5 mm) in U. vocans. The number of embryos decreased significantly over the incubation period for each species. Brood loss from embryonic stage I to stage IV for U. annulipes, U. inversa, U. chlorophthalmus and U. vocans was 12.3%, 14%, 43.2% and 23.6%, respectively (P < 0.05). Positive allometry was recorded for all species in the early development stage, however, due to the higher relative brood loss in larger females (U. vocans), when comparing the number of embryos in late developmental stage, a negative allometry was possible to observe. The average volume of embryos at the same stage differed among species although significant differences were found between embryonic stages for all species. Embryo volume increased 96.1%, 93.3%, 92.9% and 96.3% in, respectively, U. annulipes, U. inversa, U. chlorophthalmus and U. vocans (P < 0.05). Differences in brood loss were attributed to habitat substrate and structure, stress factors and behavioural aspects.
Effects of Multiple Mycotoxins and a Hydrated Sodium Calcium Aluminosilicate in Poultry 1

Effects of feeding a combination of mycotoxins at naturally occurring levels in broiler chicks and turkey poults were evaluated. The efficacy of a hydrated sodium calcium aluminosilicate (HSCAS) to ameliorate the effects of the combination of mycotoxins was also determined. Day-old chicks and poults were randomly assigned to each of four dietary treatments for 21 days. A 2 x 2 factorial arrangement was used with treatments containing either no mycotoxins or multiple mycotoxins (MM) with 0 or 1% HSCAS. The MM consisted of 1 mg deoxynivalenol, 5 mg moniliformin, 5 mg fumonisin B, 100 µg aflatoxin B, 1 mg 1 1 zearalenone, and 0.5 mg ochratoxin A per kg diet. In experiment 1, feed intake and BW gain were decreased (P 0.05) by dietary treatments. Relative spleen weights, serum albumin, protein, globulin, and calcium levels were decreased (P < 0.05) in poults fed MM. Mean cell volume was decreased (P < 0.05) in poults fed diets containing HSCAS. Data indicate that a combination of low levels of mycotoxins decreased chick performance and altered several hematological and serum biochemical values in poults. Addition of HSCAS to diets containing MM did not prevent the negative effects observed in chicks and poults.
Electronic games in child and adolescent health care: an integrative review

Universidade Federal da Bahia, Salvador, BA, Brazil. Confl icts of interest: nothing to declare. Abstract In the current context we fi nd games that involve advanced technologies, such as the use of notebooks, smartphones and video games, whether in the hospital, outpatient, medical clinic, or home setting, these innovative devices are integrated into health promotion, prevention, treatment, and recovery. This study aimed to describe, using an integrative review, the use of electronic games in child and adolescent health care. This was a review of national and international literature; articles published between the years 2007 and 2017, which addresses the implications of electronic game usage. Data collection was performed between January and April of 2018, in the Virtual Health Library (VHL), selecting databases (MEDLINE, LILACS and BDENF) using the VHL Health Sciences Descriptors (DeCS). The following descriptors were used: “Criança hospitalizada/ Hospitalized Child”; “Jogos de vídeo/Video Games”; “Promoção da saúde/Health Promotion”. The analysis was performed from the fi nal sample of 11 articles. The literature addresses issues related to the use of electronic games. Issues related to health promotion, prevention, treatment and recovery in situations of chronic diseases, and the stimulation of physical activities were evidenced in the study. This fi ndings showed the relevance for health professionals, especially nurses, to know that electronic games can help in the care for children with acute or chronic diseases, whether or not they are hospitalized.
International Satellite Cloud Climatology Project (ISCCP) Stage DX Pixel Level Cloud Product - Revised Algorithm in Native (NAT) Format (ISCCP_DX_NAT)

Since 1983 an international group of institutions has collected and analyzed satellite radiance measurements from up to five geostationary and two polar orbiting satellites to infer the global distribution of cloud properties and their diurnal, seasonal and interannual variations. The primary focus of the first phase of the project (1983-1995) was the elucidation of the role of clouds in the radiation budget (top of the atmosphere and surface). In the second phase of the project (1995 onwards) the analysis also concerns improving understanding of clouds in the global hydrological cycle. [Location=TROPOSPHERE] [Temporal_Coverage: Start_Date=1983-07-01; Stop_Date=] [Spatial_Coverage: Southernmost_Latitude=-90; Northernmost_Latitude=90; Westernmost_Longitude=-180; Easternmost_Longitude=180] [Data_Resolution: Latitude_Resolution=30 Km; Longitude_Resolution=30 Km; Temporal_Resolution=3 Hourly].
High effective inbreeding coefficients correlate with morphological abnormalities in populations of South Australian koalas (Phascolarctos cinereus)

Koalas have undergone a series of sequential founding events on islands in south‐eastern Australia in recent times. Populations in South Australia at the Eyre Peninsula and Mt Lofty Ranges were founded in the 1960s from a colony on Kangaroo Island. The Kangaroo Is. colony was derived from animals introduced to French Island from mainland Victoria over a century ago. In this study, we first use microsatellite markers to quantify levels of genetic variation within the South Australian koala populations and the relatively unperturbed Strzelecki Ranges population from mainland Victoria. This analysis revealed low levels of allelic diversity (1.7 ± 0.2 to 2.7 ± 0.5) and heterozygosity (0.208 ± 0.088 to 0.340 ± 0.110) in the three South Australian koala populations relative to the Strzelecki Ranges population, which has the highest levels of allelic diversity (4.7 ± 1.1) and heterozygosity (0.476 ± 0.122) in Victoria. Second, we measured the incidence of testicular aplasia, a unilateral or bilateral failure in testicular development, in the Eyre Peninsula and Kangaroo Is. populations, and in the ultimate founding population at French Is. Testicular aplasia was present at a frequency of 4.3% in French Is. , 12.8% in Kangaroo Is. and 23.9% in the Eyre Peninsula, but was undetectable in the non‐bottlenecked Pilliga State Forest population of New South Wales. The incidence of testicular aplasia correlated positively with effective inbreeding coefficients derived from heterozygosity values (0.13 ± 0.06 in the Pilliga State Forest, 0.57 ± 0.17 in French Is., 0.63 ± 0.12 on Kangaroo Is. and 0.77 ± 0.12 in the Eyre Peninsula), which may indicate inbreeding depression. These findings are of concern when evaluating the long‐term conservation and viability of the South Australian koala populations, which may benefit from genetic augmentation in the future. Finally, unconfirmed reports suggested that animals from other states in Australia were introduced into the Mt Lofty Ranges population. Therefore, we quantified differentiation between the three South Australian populations and the Strzelecki Ranges and French Is. populations, based on microsatellites and mtDNA d‐loop region variation. R‐statistics and Goldstein's delta mu square distance revealed that differentiation at nuclear loci between populations paralleled known recent population history, except for the close relationship between Mt Lofty Ranges and French Is. This suggested a recent contribution to the Mt Lofty Ranges populations of animals derived from the French Is. translocation program. Furthermore, mtDNA d‐loop analysis found no evidence of contributions to the gene pool from animals of New South Wales or Queensland stock, implying that the population was derived exclusively from Victorian stock.
Homogeneity Test Of Hardy-weinberg Deviations In Brazilian Littorinids: Evidence For Selection?

Echinolittorina lineolata, Littoraria flava and L. angulifera (Gastropoda: Littorinidae) have a wide distribution along the Brazilian coast. The aim of this study was to evaluate the occurrence of Hardy-Weinberg disequilibrium in these species and to verify if there is a pattern in deviations. Isozyme analyses were done on 20 populations of E. lineolata, nine of L. flava and 10 of L. angulifera, collected along 4,000 km of the Brazilian coast. Sixteen polymorphic loci were analysed in E. lineolata, 15 in L. angulifera and 17 in L. flava. Most populations showed heterozygote deficiency in several loci. A homogeneity test among loci showed heterogeneous F I S values in most populations. This result ruled out inbreeding and the Wahlund effect as the main causes of departure in these populations. In all littorinid species, at least one PGM locus had homogeneous F I S values. This finding may suggest that this enzyme could have an important role in the fitness of these periwinkles.
Distribution, abundance and biomass of epiphyte‐lianoid communities in a New Zealand lowland Nothofagus‐podocarp temperate rain forest: tropical comparisons

In tropical rain forests, epiphytes can contribute significantly to species diversity and biomass, a feature not generally associated with temperate forest systems. This study investigates epiphyte‐liane diversity and biomass on three host trees (two Dacrycarpus dacrydioides [Podocarpaceae] and one Nothofagus menziesii [Fagaceae]).
Partitioning and reorganization of hierarchical circuits for DFT

To make VLSI circuits more testable, design-for-testability (DFT) and built-in self-test (BIST) techniques are often employed. These techniques typically assume a register/gate level decomposition of the overall circuit. In general, the given user hierarchy is not appropriate for embedding various testable design methodologies (TDMs). This paper describes a new canonical partitioning of a circuit into disjoint subcircuits, referred to as clouds and registers. A salient feature of this partitioning is the attempt to preserve the user hierarchy as much as possible. This enables easy identification of equivalence among various clouds of the circuit. The authors also show how this canonical partitioning can be used for three specific TDMs, namely full scan, partial scan and BILBO designs. For the case of full scan, deterministic tests are generated for one cloud in each equivalence class, and replicated for all clouds in that class. These tests are organized to form a test set for the entire circuit. Test vectors are edited to correspond to the order of flip-flops in the scan paths of the circuit. Analytical expressions for the reduction in the number of test vectors due to this canonical partitioning are derived and substantiated with experimental results. <<ETX>>
Expression of Genes Involved in Proanthocyanidin Biosynthesis during Fruit Development in a Chinese Pollination-constant, Nonastringent (PCNA) Persimmon, `Luo Tian Tian Shi'

Expression patterns of the genes involved in condensed tannin (CT) biosynthesis during fruit development was investigated in a Chinese pollination-constant, nonastringent (PCNA) persimmon (Diospyros kaki Thunb.) ʻLuo Tian Tian Shiʼ. The transcript levels of phenylalanine ammonia-lyase (PAL) and dihydrofl avonol reductase (DFR) in ʻLuo Tian Tian Shiʼ were detected at high levels throughout the fruit growth. Chalcone synthase (CHS) and fl avonol 3-hydroxylase (F3H) also continued to be transcribed during fruit growth, although their levels decreased earlier than PAL and DFR. In contrast, expression levels of these genes declined into undetectable levels at an early stage of fruit development in Japanese PCNA persimmon. In addition, anthocyanidin reductase (ANR), which encodes a key enzyme of the proanthocyanidin biosynthesis, was transcribed at high levels in ʻLuo Tian Tian Shiʼ during fruit growth, but not in Japanese PCNA persimmon. By contrast, the expression of D. kaki serine carboxypeptidase-like protein 1 (DkSCPL1) that was obtained from suppression subtractive hybridization (SSH) analysis between artifi cially astringency-removed fruit and astringent fruit in a different experiment, declined earlier than the other fl avonoid biosynthesis genes in ʻLuo Tian Tian Shiʼ, coincident with the termination of the tannin cell development. In the F1 progeny of the cross between ʻLuo Tian Tian Shiʼ and Japanese PCNA ʻTaishuʼ, similar expression patterns were obtained among segregated PCNA and astringent offspring. These results indicate that Chinese PCNA is different from Japanese PCNA in expression of the genes involved in CT biosynthesis. In conclusion, we clarifi ed that expression of the genes (PAL to ANR, but not SCPL) involved in fl avonoid biosynthesis was continuous in the Chinese PCNA cultivar, despite the termination of tannin cell development.
Untangling the influence of phylogeny, soil and climate on leaf element concentrations in a biodiversity hotspot

Summary 1. Plant elemental properties are fundamentally important for physiology and biogeochemical cycling in ecosystems. No study has examined foliar elements and their interaction with soil and climate conditions at large geographic scales in Karst areas of China, a biodiversity hotspot in the world. Yet such information is important for understanding the functional diversity of nutrient strategies and the physiological adaptations of plants to climatic and edaphic heterogeneity. 2. We assessed the influence of phylogeny, soil type and the climate on leaf element concentrations in a clade of taxonomically diverse Karst plants from the subfamily Didymocarpoideae under an explicit phylogenetic framework. We measured leaf concentrations of seven elements and evaluated soil properties for 422 populations of 177 Didymocarpoideae species. The phylogenetic signals present in the leaf element concentrations and in soil and climatic variables were quantified at both the subfamily (Didymocarpoideae) and genus (Primulina) levels. The correlations between leaf elements and soil and climate conditions were analysed at these two phylogenetic scales. 3. The Didymocarpoideae subfamily is generally characterized by higher Ca and Mg contents relative to other plants in China. Across the subfamily, a strong phylogenetic signal is detected for all of the leaf elements analysed as well as for most soil and climate variables, whereas the genus Primulina exhibits no significant phylogenetic signal in leaf elements or in most soil variables. 4. We detected an influence of both soil and climatic conditions on leaf element concentrations. However, the patterns of the relationships between leaf elements and soil and climate variables vary at the subfamily and genus levels. The phylogeny has a stronger effect than soil and climatic factors on leaf element concentrations at the subfamily level, while the leaf element contents within the genus Primulina are mostly influenced by environmental conditions. We conclude that the influences of taxonomy, soil and climate on leaf element concentrations are dependent on the phylogenetic scale of analysis.