Miracle-dz/UniFAR-FTUs huggingface dataset:
identification of Three related genera salmonella citrobacter and proteus using API 20E, 16S-23S rDNA intergenic transcribed spacer fingerprinting, and 16S rDNA sequencing.

A total of 176 presumptive Salmonella strains isolated from different sources (food, environment, veterinary, and human) were analyzed by API 20E, serotyping, ITSF/ITSR-PCR and MINf/MINr-PCR. On the other hand, the 16S-23S rRNA intergenic transcribed spacer region was used to aid in their identification. Test results were confirmed by 16S rRNA sequencing. Of 176 suspected S. enterica isolates, API20E identified 105 (59.6%) as S. enterica, 42 (24%) as Citrobacter and 29 (16.4%) as Proteus. A total of 11 serotypes were found among 102 out of 105 Salmonella isolates. The remaining isolates were classified as untypeable by serotyping. When ITSF/ITSR-PCR and MINf/MINr-PCR were used, 101 out of 105 Salmonella isolates tested generated PCR products. Amplification of the spacer region between 16S-23S rRNA gene allowed discrimination of genera and facilitated species identification. Sequencing of 16S rRNA gene has identified 4 different species in proteus genus (P. mirabilis, P. penneri, P. vulgaris, and P. hausseri), 3 different species in Citrobacter genus (Citrobacter freundii, Citrobacter braakii, and Citrobacter youngae), and Salmonella enterica sub sp. enterica for all Salmonella isolates. The four suspect Salmonella isolates were definitively classified in Citrobacter genus. In conclusion, this study has demonstrated that API20E, serotyping associated to Salmonella specific PCR are accurate methods for S. enterica detection. In addition, PCR amplification of the 16S23S spacer region was suitable tool for identification of bacteria at genera and species level.
Genetic Improvement and Diversity in Snake River Wheatgrass (Elymus wawawaiensis) (Poaceae: Triticeae)

Abstract With the increased emphasis on using native plant materials in range revegetation programs in the western United States it is critical to identify genetically similar groups and develop native grasses that are competitive with invasive weeds, easy to establish, and persistent, and that produce high seed yield. A grass that shows appreciable drought tolerance on arid rangelands is Snake River wheatgrass (Elymus wawawaiensis J. Carlson & Barkworth). This study was designed to estimate genetic relationships and underlying genetic components for seed and forage trait improvement between plant introductions (PIs) of Snake River wheatgrass, 28 half-sib Snake River wheatgrass families (HSFs), and cultivars Secar and Discovery at Nephi, Utah, between 2005 and 2006. Based on molecular genetic diversity data in Snake River wheatgrass, with the exception of the PIs originating from Enterprise, Oregon, all other collections and cultivars are not genetically different and represent a common gene pool from which to develop improved Snake River wheatgrass germplasm. Selection in Snake River wheatgrass for total seed yield (g · plot−1), 100-seed weight (g), and seedling emergence from a deep planting depth had a positive effect. Further increases through selection and genetic introgression from hybridization with PIs will likely increase seed yield and 100-seed weight, but will not increase seedling emergence. Increases in dry matter yield (DMY) were observed after two cycles of selection in the HSFs compared to the PIs. There remains considerable genetic and phenotypic variation to further increase DMY in Snake River wheatgrass through selection and hybridization. Trends in forage nutritional quality were not observed after two cycles of selection in the HSFs or the PIs and will not likely result in improvement. Through recurrent selection, populations of Snake River wheatgrass have been and can be developed to more effectively establish and compete on annual weed–infested rangelands.
Lead and cadmium in wild birds in southeastern spain

The main purpose of this study was to monitor exposure to lead and cadmium in wild birds in Murcia, a southeastern region of Spain on the Mediterranean coast. This region lies on one of the African-European flyways. Samples of liver, kidney, brain, bone, and whole blood from several species of wild birds were obtained during 1993. We found a clear relationship between cadmium and lead concentrations in birds and their feedings habits. Vultures (Gyps fulvus) had the highest concentrations of lead (mean 40 μg/dl in blood), and seagulls (Larus argentatus and Larus ridibundus) the highest concentrations of cadmium (mean 4.43 μg/g in kidney). Insectivores had high concentrations of both metals, and diurnal and nocturnal raptors showed the lowest tissue concentrations. The finding that tissue and blood concentrations were generally not elevated suggests environmental (rather than acute) exposure. Birds from more industrialized areas of the region studied here had higher concentrations of both lead and cadmium.
The speed of sequence processing in biological neuronal networks

Sequence processing has been proposed to be the universal computation performed by the neocortex. The Hierarchical Temporal Memory (HTM) model provides a mechanistic implementation of this form of processing. While the model accounts for a number of neocortical features, it is based on networks of highly abstract neuron and synapse models updated in discrete time. Here, we reformulate the model in terms of a network of spiking neurons with continuous-time dynamics to investigate how neuronal and synaptic parameters constrain the sequence-processing speed.
ON CHALIMINIA MUSTELOIDES (EUCYNODONTIA: TRITHELEDONTIDAE) FROM THE LATE TRIASSIC OF ARGENTINA, AND A PHYLOGENY OF ICTIDOSAURIA

Abstract A new specimen of Chaliminia musteloides Bonaparte is described from the upper section of the Los Colorados Formation (Late Carnian–Early Norian) of Argentina. A cladistic analysis of ictidosaurians supports its monophyly. Chaliminia and Elliotherium, grouped in the new subfamily Chalimininae, were placed as sister taxa to the new subfamily Pachygenelinae, which includes Pachygenelus, Diarthrognathus, and Tritheledon. Irajatherium is basal to both subfamilies as a stem Tritheledontidae. Riograndia represents the most basal non-tritheledontid ictidosaurian. The resulting tree topology agrees with the age of the fossil record of each ictidosaurian species. Although our analysis does not test the relationship of ictidosaurians with regard to Mammaliaformes, it is clear from our tree that ictidosaurians are closely related to them. Several derived characters seem to have been acquired convergently in both lineages and relate to food processing, development of primary chewing musculature and ancillary structures. In other aspects, ictidosaurians remained very conservative, or reverted to ancestral morphologies, such as the presence of interpterygoidal-vacuities. Analysis of the vacuities indicates that they represent an ancestral condition that facilitated the development of the mammalian skull base constituted by the reduced pterygoids, the basisphenoid, and posteriorly the development of the presphenoid by the ventral extension of the braincase. Possibly, the main factors in the remodeling of this area are the development of the sphenoid sinus and the forward and ventral expansion of the cranial cavity. The re-acquisition of interpterygoid vacuities among ictidosaurians could be the result of a paedomorphic (neotenic or progenetic) alteration of the developmental pattern.
Production of kepi grains using pure cultures as starters

Kepi is a refreshing, fermented dairy beverage that differs from other fermented milk products in that it is produced with a mixed microbial community which is confined to discrete grains. These grains can be recovered as a solid matrix at the end of the fermentation and then be reutilised as a starter to ferment the next batch of milk. The grain microbial community consists of a symbiotic association of yeasts and lactic acid bacteria, but the overall composition of the grains has not been completely elucidated. The microbes in the grains are embedded in a protein-polysaccharide Kefiran matrix, which appears essential for grain formation. The mechanism of grain formation is still not fully understood and it thus remains undecided which organism is really responsible for the production of this proteinpolysaccharide matrix. The aim of this study was to isolate, characterise and identify the microbes present in Kefiran from mass cultured South African grains and then to evaluate grain formation with these purified cultures isolated from Kefiran strings using a mass cultivation process. Sixteen strains of lactic acid bacteria and one yeast strain were isolated from Kefiran strings produced during the mass cultivation of South African Kepi grains. API technology, numerical clustering and DNA sequence comparisons were used to identify the purified isolates. The isolates were grouped into seven clusters by numerical clustering and clustering distance from selected reference and marker strains. The heterofermentative lactobacilli were identified as Lactobacillus parakefiri and Lb. kefiri and the homofermentative strains as Lb. delbrueckii ssp. bulgaricus, Lb. gallina rum, Lb. acidophilus and Lb. bavaricus. One isolate was found to be a member of the genus Lactobacillus, but was not positively identified to species level. Cultures isolated from Kefiran were evaluated for ability to grain formation by adding 1 x 10 cfu.ml:' bacteria and 1 x 108 cfu.ml' yeast to double pasteurised, full cream milk during the mass cultivation process. It was found that the control and all the cultures in double pasteurised milk showed grain accumulation indicating that other microbes were present in pasteurised and double pasteurised milk which had an influence on the grain forming ability. The cultures isolated from pasteurised and double pasteurised milk included members of the species Pediococcus, Acinetobacter, Lactococcus laetis ssp. lactis, Candida lipolytica, C. guilliermondii, Chryseobacterium meningosepticum, Pseudomonas putida and four isolates of the Bacillus cereus group. It was found that these rod-shaped "milk isolates" resulted in grain accumulation when inoculated into UHT milk and it was concluded that the "milk isolates" did contribute to grain formation. These isolates were then combined with the Stellenbosch University http://scholar.sun.ac.za
Measles virus and rinderpest virus divergence dated to the sixth century BCE

Older origins of measles virus Animal domestication by humans is thought to have given many pathogens an opportunity to invade a new host, and measles is one example of this. However, there is controversy about when measles emerged in humans, because the historical descriptions of measles are relatively recent (late ninth century CE). The controversy has persisted in part because ancient RNA is thought to be a poor target for molecular clock techniques. Düx et al. have overcome the ancient RNA challenge by sequencing a measles virus genome obtained from a museum specimen of the lungs of child who died in 1912 (see the Perspective by Ho and Duchêne). The authors used these and other more recent sequencing data in a Bayesian molecular clock–modeling technique, which showed that measles virus diverged from rinderpest virus in the sixth century BCE, indicating an early origin for measles possibly associated with the beginnings of urbanization. Science, this issue p. 1367; see also p. 1310 Measles virus diverged from rinderpest virus in the sixth century BCE, indicating an early origin for human measles. Many infectious diseases are thought to have emerged in humans after the Neolithic revolution. Although it is broadly accepted that this also applies to measles, the exact date of emergence for this disease is controversial. We sequenced the genome of a 1912 measles virus and used selection-aware molecular clock modeling to determine the divergence date of measles virus and rinderpest virus. This divergence date represents the earliest possible date for the establishment of measles in human populations. Our analyses show that the measles virus potentially arose as early as the sixth century BCE, possibly coinciding with the rise of large cities.
Biodiversity and Litter Decomposition in Terrestrial Ecosystems

▪ Abstract We explore empirical and theoretical evidence for the functional significance of plant-litter diversity and the extraordinary high diversity of decomposer organisms in the process of litter decomposition and the consequences for biogeochemical cycles. Potential mechanisms for the frequently observed litter-diversity effects on mass loss and nitrogen dynamics include fungi-driven nutrient transfer among litter species, inhibition or stimulation of microorganisms by specific litter compounds, and positive feedback of soil fauna due to greater habitat and food diversity. Theory predicts positive effects of microbial diversity that result from functional niche complementarity, but the few existing experiments provide conflicting results. Microbial succession with shifting enzymatic capabilities enhances decomposition, whereas antagonistic interactions among fungi that compete for similar resources slow litter decay. Soil-fauna diversity manipulations indicate that the number of trophic levels, spec.
Pleiotropic Effect of GNP1 Underlying Grain Number per Panicle on Sink, Source and Flow in Rice

Rice yield potential is largely determined by the balance among source capacity, sink strength, and flow fluency. Our previous study indicated that the gene GNP1 encoding gibberellin biosynthesis gene GA20ox1 affects grain number per panicle (GNP) in rice, thus resulting in increase of grain yield. To clarify GNP1 effect on sink, source and flow in regulating rice grain yield, we compared Lemont, a japonica (geng) cultivar, with its near-isogenic line (NIL-GNP1TQ) in Lemont background with introgression of the allele at GNP1 from Teqing, a high-yielding indica (xian) cultivar. NIL-GNP1TQ exhibited averagely 32.8% more GNP than Lemont with the compensation by reduced seed setting rate, panicle number and single-grain weight. However, NIL-GNP1TQ still produced averagely 7.2% higher grain yield than Lemont in two years, mainly attributed to significantly more filled grain number per panicle, and greater vascular system contributing to photoassimilates transport to spikelets. The significantly decreased grain weight of superior spikelets (SS) in NIL-GNP1TQ was ascribed to a significant decrease of grain size while the significantly decreased grain weight of inferior spikelets (IS) ascribed to both grain size and poor grain-filling as compared with Lemont. The low activities of key enzymes of carbon metabolism might account for the poor grain-filling in IS, which resulted in more unfilled grains or small grain bulk density in NIL-GNP1TQ. In addition, low seed setting rate and grain weight of IS in NIL-GNP1TQ might be partially resulted from significantly lower carbohydrate accumulation in culms and leaf sheath before heading compared with Lemont. Our results indicated that significantly increased GNP from introgression of GNP1TQ into Lemont did not highly significantly improve grain yield of NIL-GNP1TQ as expected, due primarily to significant low sink activities in IS and possible insufficient source supply which didn’t fully meet the increased sink capacity. The results provided useful information for improving rice yield potential through reasonably introgressing or pyramiding the favorable alleles underlying source-related or panicle number traits by marker-assisted selection.
A Chloroplast COR413 Protein From Physcomitrella patens Is Required for Growth Regulation Under High Light and ABA Responses

COR413 genes belong to a poorly characterized group of plant-specific cold-regulated genes initially identified as part of the transcriptional activation machinery of plants during cold acclimation. They encode multispanning transmembrane proteins predicted to target the plasma membrane or the chloroplast inner membrane. Despite being ubiquitous throughout the plant kingdom, little is known about their biological function. In this study, we used reverse genetics to investigate the relevance of a predicted chloroplast localized COR413 protein (PpCOR413im) from the moss Physcomitrella patens in developmental and abiotic stress responses. Expression of PpCOR413im was strongly induced by abscisic acid (ABA) and by various environmental stimuli, including low temperature, hyperosmosis, salinity and high light. In vivo subcellular localization of PpCOR413im-GFP fusion protein revealed that this protein is localized in chloroplasts, confirming the in silico predictions. Loss-of-function mutants of PpCOR413im exhibited growth and developmental alterations such as growth retardation, reduced caulonema formation and hypersensitivity to ABA. Mutants also displayed altered photochemistry under various abiotic stresses, including dehydration and low temperature, and exhibited a dramatic growth inhibition upon exposure to high light. Disruption of PpCOR413im also caused altered chloroplast ultrastructure, increased ROS accumulation, and enhanced starch and sucrose levels under high light or after ABA treatment. In addition, loss of PpCOR413im affected both nuclear and chloroplast gene expression in response to ABA and high light, suggesting a role for this gene downstream of ABA in the regulation of growth and environmental stress responses. Developmental alterations exhibited by PpCOR413im knockout mutants had remarkable similarities to those exhibited by hxk1, a mutant lacking a major chloroplastic hexokinase, an enzyme involved in energy homeostasis. Based on these findings, we propose that PpCOR413im is involved in coordinating energy metabolism with ABA-mediated growth and developmental responses.
Primate Taxonomy: Inflation or Real?*

This article reviews changes in primate taxonomy, especially those pertaining to the meaning of the term species, since its inception two and a half centuries ago. Despite continuing discoveries and the involvement of competent practitioners, the adoption of the polytypic species concept, especially underpinned by the biological species concept, ensured that primate taxonomy was in a sorry state by the middle of the twentieth century. In the latter half of the twentieth century, a gradual rethinking of the nature of species took place, and many different species concepts were proposed. The phylogenetic species concept has been widely adopted over the past ∼20 years, sustained by a gradual realization that species are evolutionary lineages. This review provides examples of how the old way of thinking about species hampered our understanding of primate biodiversity and of how the phylogenetic species concept (or the diagnosability criterion under the general lineage concept) has clarified matters, opening them up for discussion. The adoption of this evolutionary view of species has implications for conservation, particularly because it increases recognition of biodiversity.
A check list of the pseudoscorpions of South Africa (Arachnida: Pseudoscorpiones).

A check list of the Pseudoscorpiones of the class Arachnida of South Africa is presented. A total of 135 species and 10 subspecies of pseudoscorpions are known from South Africa, represented by seven superfamilies, 15 families and 65 genera. This represents about 4.4 of the world fauna. Of the 135 species, 97 species (73 ) are known only from South Africa, 33 species have a wider distribution pattern throughout the Afrotropical Region and three are cosmopolitan. This study forms part of the South African National Survey of Arachnida (SANSA).
A Photovoltaic System Investment Game for Assessing Network Hosting Capacity Allocations

The rapid rise of PV installations in low-voltage (LV) distribution networks means that they are likely to exceed network hosting capacity. For this reason, distribution network service providers (DNSP) have begun to mandate connection codes, such as inverter Volt/Var control and/or PV active power curtailment, to mitigate the resulting network problems. This approach manages the network state, but may cause an existing PV system to become inefficient as it is curtailed more often. This paper investigates the effects on overall economic efficiency and individual customer welfare of natural uncoordinated rooftop PV investment processes that arise when customers invest in PV systems independently to maximize their individual welfare. We develop a novel game-theoretic framework that computes the annual payoffs to customers for different PV investment sizes, given the installations of other customers. This calculation is based on an optimal AC power flow model that includes inverter connection standards that link customers' annual payoffs via their effects on AC network voltages and consequent PV curtailment responses. We show that the interaction of PV investments produces a concave potential game with continuous action sets, which has a pure Nash equilibrium that can be found using an adaptive learning process. Then, to evaluate the efficiency of the investments under the game model, we compute an centrally-coordinated PV investment profile, found by solving an optimal PV sizing problem that maximizes social welfare across all customers. Comparing the value of investment patterns for the game and the centrally-coordinated optimization shows: (i) the inefficiency of the Nash equilibrium is 1.4, which indicates the efficiency loss resulting from uncoordinated PV investments, and (ii) the inequity of a skewed distribution of benefits, penalising customers closer to the distribution transformer and benefiting those towards the end of the feeder. This model provides a quantitative tool for evaluating policies and regulations that improved coordination and allocation of PV hosting capacity (and that of other energy distributed energy resources) between customers on LV feeders.
Peroxisome proliferator-activated receptor-γ coactivator 1α (PGC-1α) regulates triglyceride metabolism by activation of the nuclear receptor FXR

Peroxisome proliferator-activated receptor-γ coactivator 1α (PGC-1α) has been shown to regulate adaptive thermogenesis and glucose metabolism. Here we show that PGC-1α regulates triglyceride metabolism through both farnesoid X receptor (FXR)-dependent and -independent pathways. PGC-1α increases FXR activity through two pathways: (1) it increases FXR mRNA levels by coactivation of PPARγ and HNF4α to enhance FXR gene transcription; and (2) it interacts with the DNA-binding domain of FXR to enhance the transcription of FXR target genes. Ectopic expression of PGC-1α in murine primary hepatocytes reduces triglyceride secretion by a process that is dependent on the presence of FXR. Consistent with these in vitro studies, we demonstrate that fasting induces hepatic expression of PGC-1α and FXR and results in decreased plasma triglyceride levels in wild-type but not in FXR-null mice. Our data suggest that PGC-1α plays an important physiological role in maintaining energy homeostasis during fasting by decreasing triglyceride production/secretion while it increases fatty acid β-oxidation to meet energy needs.
Image compressed sensing recovery via adaptive dictionary learning

This paper addresses the image compressed sensing recovery problem. To improve the recovery quality, instead of using a fixed dictionary that is generally a universal one trained in an off-line manner for sparse representations of image patches, we adopt an adaptive dictionary learning strategy. Inspired by the monotone fast iterative shrinkagethresholding algorithm, a dictionary learning algorithm is introduced in this work. Also, we abandon the classic method that breaks an image into fully overlapping patches, and propose a new overlapping patches extraction method, which decreases the number of patches and saves much run-time, while achieves similar recovery qualities.