Miracle-dz/UniFAR-FTUs huggingface dataset:
Rhizome and stolon development of bermudagrass cultivars in a transition-zone environment

ABSTRACT Bermudagrass (Cynodon spp.) is a warm season turfgrass that spreads by stolons and rhizomes. The present study aimed to increase knowledge on development of stolons and rhizomes in fertile (‘LaPaloma’ and ‘Yukon’) and sterile (‘Patriot’ and ‘Tifway’) cultivars of bermudagrass. A plot trial was established in May 2013 in Legnaro, northeastern Italy. Fertile cultivars were seeded while sterile cultivars were established by vegetative plugs. Turf samples were collected from autumn 2013 until summer 2015 on March, July, and October. Total length of stolons and rhizomes was measured and total dry weight was determined. The concentration of starch in stolons and rhizomes in October was also determined. The stolon and rhizome density per unit area, the rhizome specific weight, and the rhizome/stolon length and weight ratios were calculated. Sterile cultivars had higher stolon and rhizome density compared to fertile cultivars for both length. In all cultivars, the production of stolons was favoured over that of rhizomes and rhizomes began to develop more in the second season after establishment. Cultivars did not differ significantly in starch content, indicating no relationship between stolon and rhizome density and carbohydrate reserve accumulations. Abbreviations: LD: length density per unit area; WD: weight density per unit area; SW: specific weight; LR: rhizome-to-stolon length ratio; WR: rhizome-to-stolon weight ratio; TS: total starch per unit area
Evolutionary Analysis of the VP1 and RNA-Dependent RNA Polymerase Regions of Human Norovirus GII.P17-GII.17 in 2013–2017

Human norovirus (HuNoV) GII.P17-GII.17 (Kawasaki2014 variant) reportedly emerged in 2014 and caused gastroenteritis outbreaks worldwide. To clarify the evolution of both VP1 and RNA-dependent RNA polymerase (RdRp) regions of GII.P17-GII.17, we analyzed both global and novel Japanese strains detected during 2013–2017. Time-scaled phylogenetic trees revealed that the ancestral GII.17 VP1 region diverged around 1949, while the ancestral GII.P17 RdRp region diverged around 2010. The evolutionary rates of the VP1 and RdRp regions were estimated at ~2.7 × 10−3 and ~2.3 × 10−3 substitutions/site/year, respectively. The phylogenetic distances of the VP1 region exhibited no overlaps between intra-cluster and inter-cluster peaks in the GII.17 strains, whereas those of the RdRp region exhibited a unimodal distribution in the GII.P17 strains. Conformational epitope positions in the VP1 protein of the GII.P17-GII.17 strains were similar, although some substitutions, insertions and deletions had occurred. Strains belonging to the same cluster also harbored substitutions around the binding sites for the histo-blood group antigens of the VP1 protein. Moreover, some amino acid substitutions were estimated to be near the interface between monomers and the active site of the RdRp protein. These results suggest that the GII.P17-GII.17 virus has produced variants with the potential to alter viral antigenicity, host-binding capability, and replication property over the past 10 years.
Complete mitochondrail genome of Corydoras panda (Teleostei, Siluriformes, Callichthyidae, Corydoradinae)

Abstract We reported the complete mitochondrial genome yielded by next-generation sequencing of Corydoras panda in this study. The total length of the mitochondrial genome is 16,611 bp, with the base composition of 32.50% A, 26.30% T, 26.10% C, and 15.10% G, respectively. It contains two ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes, and a major non-coding control region (D-loop region). The arrangement of these genes is the same as that found in the Siluriformes. The complete mitogenomes of C. panda and other 18 species from Siluriformes were used for phylogenetic analysis using Neighbor-Joining method. The topology demonstrated that all species belong to nine genera are divided into three groups (Siluridae, Loricariidae, and Callichthyidae), and the C. panda was clustered with other species from genus Corydoras. Corydoras panda external morphological feature classification is consistent with the molecular classification results, so the information of the mitogenome could be used for future identification of Corydoras species.
Control of clathrin-mediated endocytosis by NIMA family kinases

Endocytosis, the process by which cells internalize plasma membrane and associated cargo, is regulated extensively by posttranslational modifications. Previous studies suggested the potential involvement of scores of protein kinases in endocytic control, of which only a few have been validated within their native context. Here we show that the conserved NIMA-related kinases NEKL-2/NEK8/9 and NEKL-3/NEK6/7 (the NEKLs) control clathrin-mediated endocytosis in C. elegans. Loss of NEKLs leads to clathrin mislocalization and to a dramatic reduction in clathrin mobility at the apical membrane. Strikingly, reducing the levels of active AP2, the major clathrin adapter complex, rescues nekl mutant defects, whereas increased levels of active AP2 exacerbate nekl defects. Moreover, NEKL inhibition alleviates defects associated with reduced AP2 activity, attesting to the tight link between NEKL and AP2 functions. We also show that NEKLs are required for the clustering and internalization of membrane cargo and that human NEKs rescue defects in nekl mutant worms.
The Effect of Endotracheal Inflation Technique on Endotracheal Cuff Pressure

Abstract : Many surgical procedures require general anesthesia in which endotracheal intubation and mechanical ventilation is utilized in order to maintain adequate patient oxygenation. Endotracheal intubation, helps assure delivery of the adequate ventilation and prevention of aspiration of stomach contents into the lungs. In this study endotracheal cuff pressures were measured and correlated to currently utilized cuff inflation techniques. Data was analyzed using descriptive statistics. In 46% of the cases the cuffs were inflated using the pilot balloon palpation technique, 28% were inflated using the set volume technique, and 26% using the minimum occlusive pressure technique. Regardless of the technique used, none of the cuff pressures collected were found to be in the acceptable range of 18 to 25 mmHg. Thirteen percent of cuff pressures were below the minimum value required to prevent aspiration, and 87% of the sample were inflated above the maximum acceptable pressure, risking tracheal ischemia. These results suggest that the currently used techniques expose patients to excessive endotracheal cuff pressures.
Causal adaptation to visual input dynamics governs the development of complex cells in V1

Visual perception relies on cortical representations of visual objects that remain relatively stable with respect to the variation in object appearance typically encountered during natural vision (e.g., because of position changes). Such stability, known as transformation tolerance, is built incrementally along the ventral stream (the cortical hierarchy devoted to shape processing), but early evidence of position tolerance is already found in primary visual cortex (V1) for complex cells1. To date, it remains unknown what mechanisms drive the development of this class of neurons, as well as the emergence of tolerance across the ventral stream. Leading theories suggest that tolerance is learned, in an unsupervised manner, either from the temporal continuity of natural visual experience2–10 or from the spatial statistics of natural scenes11,12. However, neither learning principle has been empirically proven to be at work in the postnatal developing cortex. Here we show that passive exposure to temporally continuous visual inputs during early postnatal life is essential for normal development of complex cells in rat V1. This was causally demonstrated by rearing newborn rats with frame-scrambled versions of natural movies, resulting in temporally unstructured visual input, but with unaltered, natural spatial statistics. This led to a strong reduction of the fraction of complex cells, which also displayed an abnormally fast response dynamics and a reduced ability to support stable decoding of stimulus orientation over time. Conversely, our manipulation did not prevent the development of simple cells, which showed orientation tuning and multi-lobed, Gabor-like receptive fields as sharp as those found in rats reared with temporally continuous natural movies. Overall, these findings causally implicate unsupervised temporal learning in the postnatal development of transformation tolerance but not of shape tuning, in agreement with theories that place the latter under the control of unsupervised adaptation to spatial, rather than temporal, image statistics13–16.
Variant calling for cpn60 barcode sequence-based microbiome profiling

Amplification and sequencing of conserved genetic barcodes such as the cpn60 gene is a common approach to determining the taxonomic composition of microbiomes. Exact sequence variant calling has been proposed as an alternative to previously established methods for aggregation of sequence reads into operational taxonomic units (OTU). We investigated the utility of variant calling for cpn60 barcode sequences and determined the minimum sequence length required to provide species level resolution. Sequence data from the 5’ region of the cpn60 barcode amplified from the human vaginal microbiome (n=25), infant stool (n=47), and a mock community were used to compare variant calling to de novo assembly of reads, and mapping to a reference sequence database. Results were compared in terms of number of OTU formed, resolution of OTU sequences, and overall community composition. Variant calling resulted in high resolution profiles that were consistent in composition to those generated with previous methods but with significant logistical advantages. Variant calling is rapid, achieves high resolution of taxa, and does not require reference sequence data. Our results further demonstrate that 150 bp from the 5’ end of the cpn60 barcode sequence is sufficient to provide species-level resolution of microbiota.
The human Shu complex functions with PDS5B and SPIDR to promote homologous recombination

Abstract RAD51 plays a central role in homologous recombination during double-strand break repair and in replication fork dynamics. Misregulation of RAD51 is associated with genetic instability and cancer. RAD51 is regulated by many accessory proteins including the highly conserved Shu complex. Here, we report the function of the human Shu complex during replication to regulate RAD51 recruitment to DNA repair foci and, secondly, during replication fork restart following replication fork stalling. Deletion of the Shu complex members, SWS1 and SWSAP1, using CRISPR/Cas9, renders cells specifically sensitive to the replication fork stalling and collapse caused by methyl methanesulfonate and mitomycin C exposure, a delayed and reduced RAD51 response, and fewer sister chromatid exchanges. Our additional analysis identified SPIDR and PDS5B as novel Shu complex interacting partners and genetically function in the same pathway upon DNA damage. Collectively, our study uncovers a protein complex, which consists of SWS1, SWSAP1, SPIDR and PDS5B, involved in DNA repair and provides insight into Shu complex function and composition.
Selenium-enriched probiotics improve hepatic protection by regulating pro-inflammatory cytokines and antioxidant capacity in broilers under heat stress conditions

Objective: High ambient temperature in poultry is a challenging and fatal stress among environmental factors. It affects the production quality, damages the liver, and increases mortality in broilers. The present study is focused to explore appropriate utilization of Selenium (Se) as a feed additive in broiler chickens against high temperature. Materials and Methods: Day-old male broiler chickens (Ross 308) (n = 200) were grouped according to the supplements used in their basal diets such as: corn-soybean basal diet as control (Con), a basal diet containing sodium selenite, basal diet with probiotics, and a basal diet containing selenium-enriched probiotics (SP). At the end of the experimental period of 42 days, the liver was isolated and was used to determine the antioxidant capacity through a spectrophotometer. Inflammatory and anti-inflammatory cytokines production in the liver was measured through a real-time polymerase chain reaction. Results: Hepatic analyses revealed the decreased level of malondialdehyde, whereas glutathione, glutathione peroxidase (GSH-Px), and superoxide dismutase levels were increased in the SP group. Furthermore, supplementation of SP significantly up-regulated the mRNA expression of glutathione peroxidase 1 (GPx1), GPx4, IL6, and IL10 and down-regulated the expression of pro-inflammatory cytokines. Conclusion: It is thus concluded that SP as a potential nutritive supplement may facilitate hepatic protection by suppressing hepatic oxidation, inflammation, and necrosis during the high ambient temperature of summer.
Different languages, similar encoding efficiency: Comparable information rates across the human communicative niche

Human languages encode similar average information rates (~39 bits/s) despite their remarkable differences. Language is universal, but it has few indisputably universal characteristics, with cross-linguistic variation being the norm. For example, languages differ greatly in the number of syllables they allow, resulting in large variation in the Shannon information per syllable. Nevertheless, all natural languages allow their speakers to efficiently encode and transmit information. We show here, using quantitative methods on a large cross-linguistic corpus of 17 languages, that the coupling between language-level (information per syllable) and speaker-level (speech rate) properties results in languages encoding similar information rates (~39 bits/s) despite wide differences in each property individually: Languages are more similar in information rates than in Shannon information or speech rate. These findings highlight the intimate feedback loops between languages’ structural properties and their speakers’ neurocognition and biology under communicative pressures. Thus, language is the product of a multiscale communicative niche construction process at the intersection of biology, environment, and culture.
Sinking with the Ship: How Does Involuntary Job Displacement Affect Health Insurance?

Numerous job cuts during the 2001 recession and the subsequent sluggish recovery have no doubt added to the growing number of Americans without health insurance, yet little evidence exists on how involuntary job displacement is causally related to health insurance status. Prior research indicates that workers who are about to be displaced earn less than their non displaced counterparts, and that wage losses associated with displacement actually start prior to the date of separation. In this paper, I use panel and cross sectional data to test whether workers about to be displaced differ in their health insurance coverage from their employer relative to similar workers who are not displaced, and if so, how far back in time these health insurance losses occur. I also test the extent to which other sources of health insurance cushion the effects of displacement on health insurance. I find that workers who are subsequently displaced from jobs are less likely to have own-employer provided health insurance than otherwise similar workers who are not displaced, and that this difference starts up to two years prior to displacement. Other sources of health insurance play an important role in protecting the health insurance coverage of these workers, even in the pre-displacement period.
The mental health of newly remanded prisoners, the prison reception health screen and the resulting management of mental disorder at Durham prison

Recent cross-sectional studies have confirmed that the prevalence of mental disorder in English prisons is high but they provide little insight into the fate of the mentally disordered in prison. This thesis concentrates on a longitudinal study of mental disorder in 569 unconvicted adult male remand prisoners received into Durham prison between 1 October 1995 and 30 April 1996. Subjects were interviewed at reception by psychiatric researchers and monitored throughout the remand period. The data collected was used to establish the prevalence of mental disorder and substance misuse at reception into prison, effectiveness of prison reception screening, number of mentally disordered subjects identified and referred for psychiatric assessment, nature of psychiatric interventions, and final disposal of all subjects. Additional research was undertaken at Durham to evaluate health care provision at this prison, and, in order to comment on the generalisability of the findings, health care facilities at other prisons in England and Wales were investigated. More than a quarter of subjects at Durham prison were suffering from mental disorder. Serious disorders were especially prevalent and one in twenty remands was acutely psychotic. Drug and alcohol misuse was the norm. More than half of our subjects received current substance abuse or dependence diagnoses.
Molecular identification of Tilletia controversa and T. caries, the causal agent of wheat dwarf and common bunt

Common and dwarf bunt of wheat are recognized as being caused by three closely related species, Tilletia caries and T. laevis as common bunt, and T. controversa as dwarf bunt. The morphological characteristics of two species including T. controversa and T. caries were studied from wheat grown in two provinces of Iran, Lorestan and Chaharmahal–o-Bakhtiari during 2014-2015. In this study, morphological characters could not completely distinguish these pathogens, as in some properties, they showed similarity to T. laevis. So, a collection of twenty wheat bunt isolates was used to compare species in morphological characteristics and phylogenetic relationships. Phylogenetic analyses were presented based on three PCR amplified nuclear DNA fragments including elongation factor 1 alpha (EF1α), the second largest subunit of RNA polymerase II (RPB2) genes and ITS-rDNA region. Maximum likelihood (ML) method was used to determine the phylogenetic relationship among isolates using MEGA v.6 and BEAUti and BEAST v1.6. 1 software. Maximum likelihood bootstrap (BS) values and Bayesian posterior probabilities (PP) values were applied as criteria for strongly supported clades. Two species including T. controversa and T. caries were distinguished as different species with DNA sequence information.
Larval Prey Preference of Pond-breeding salamander Hynobius tokyoensis Living in a Stream

Habitats for pond-breeding salamanders are declining as a result of land development and management abandonment. In that context, a pond-breeding salamander Hynobius tokyoensis has recently been known to breed in small streams. However, little is known about the ecology of pond-breeding salamander larvae, such as food, in small streams. Here, to gain insight into foraging ecology of Hynobius tokyoensis larvae in small steams, we investigated the potential prey items in nine small streams running through secondary forests in Hachiouji City, Tokyo, Japan. In addition, we hypothesized that H. tokyoensis larvae preferentially predate active prey invertebrates over less-active prey because they are generalist, sit-and-wait predators. To test this hypothesis, we experimentally examined predation frequencies by H. tokyoensis larvae on the two major arthropod species (isopods and Plecoptera larvae) and activity (i.e., movement frequencies and distances) of the potential prey. As a result, isopods (Asellus hilgendorfii) and Plecoptera (Nemouridae larvae) are the two dominant aquatic invertebrates in small streams inhabited by H. tokyoensis, larval salamanders consumed more isopods than Plecoptera larvae and isopods are more active than Plecoptera larvae. Taken together, we concluded that isopods should be the main prey for salamander larvae inhabiting small streams due to their high abundance and conspicuous activities.
Obtenção de SNPs, reação do feijoeiro comum à ferrugem da soja e piramidação de genes de resistência a Uromyces appendiculatus

Single nucleotide polymorphisms (SNPs) were discovered in common bean (Phaseolus vulgaris L.) via resequencing of sequence-tagged sites (STSs) developed by PCR primers designed to soybean shotgun and BAC-end sequences, and to common bean genes and microsatellite flanking regions. DNA fragments harboring SNPs were identified in single amplicons from six contrasting P. vulgaris genotypes of the Andean (‘Jalo EEP558’, ‘G19833’, and ‘AND277’) and Mesoamerican (‘BAT 93’, ‘DOR 364’, and ‘Rudá’) gene pools. These genotypes are the parents of three common bean RIL mapping populations. From an initial set of 1,880 PCR primer pairs tested, 265 robust STSs were obtained, amplified and sequenced in each one of the six common bean genotypes. In the resulting 131,120 bp of aligned sequence, a total of 677 SNPs were identified, including 555 single-base changes (295 transitions and 260 transversions) and 122 small nucleotide insertions/deletions (indels). The frequency of SNPs was 5.16 SNPs/Kb and the mean nucleotide diversity expressed as Halushka’s theta was 0.00226. This work represents one of the pioneer efforts aiming to detect SNPs in P. vulgaris. The SNPs identified are an important resource to common bean geneticists for quantitative trait loci (QTLs) discovery, marker-assisted selection and for map-based cloning. They will be also useful for diversity analysis and microsynteny studies among legume species.
Growth response and carcass characteristics of broiler chickens on different daily feeding frequency

A total of 99 day old broiler chicks were used in a 56 day trial to determine the growth response and carcass characteristics of broiler Chickens on different daily feeding frequency. They were randomly allotted into three treatment groups (T1, T2, T3). T1 were fed once a day, T2 were fed twice a day while T3 were fed thrice a day. All treatments were fed with the same quality and quantity of feed. Data obtained include; weight gain, feed intake, feed conversion ratio, and carcass traits of the broiler chickens. Results obtained revealed no significant (P>0.05) difference among the growth parameters observed except the final weight. Birds fed twice a day recorded the highest final weight (2295.50g) followed by those fed once a day (2236.30g) and thrice a day (2230.30g) respectively. No significant differences (P>0.05) among dietary treatments were observed on carcass parameters measured except the live weight, drumstick and heart. The live weight of the experimental animals ranged significantly from birds fed once a day (2366.67g) to those fed thrice a day (2783.30g). Birds fed twice a day and thrice a day had similar (P>0.05) drumstick values but significantly (P<0.05) higher than those fed once. Animals fed twice a day (0.58) recorded the highest heart weight followed by those fed once a day (0.45) and thrice a day (0.48) that was statistically similar. Based on the results of this study, it was concluded that birds fed frequently at least twice a day performed better compared with birds fed once a day.