Miracle-dz/UniFAR-FTUs huggingface dataset:
A Preliminary Study of Biliary Microbiota in Patients with Bile Duct Stones or Distal Cholangiocarcinoma

Background and Objective The distal cholangiocarcinoma (dCCA) is associated with many factors: genes, environment, infection, etc. The current changes in biliary flora are thought to be involved in the formation of many gastrointestinal tract (GIT) diseases, like colon adenocarcinoma. Therefore we want to investigate whether the dCCA has a certain correlation with biliary microecology, and to detect specific strains. Methods A total of 68 adults were enrolled, of whom 8 with dCCA, 16 with recurrent choledocholithiasis, and 44 with the onset of common bile duct stones. Endoscopic Retrograde Cholangiopancretography (ERCP) was utilized to collect bile samples for DNA extraction and 16S rRNA gene sequencing, followed by analysis of bile microbiota composition. Results First, Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria are the most dominant phyla in the bile of patients with dCCA and the onset of common bile duct stoes. Secondly, compared with the onset of common bile duct stones patients, we got a significant increase in the phylum Gemmatimonadetes, Nitrospirae, Chloroflexi, Latescibacteria, and Planctomycetes in dCCA patients. Finally, at the genus level, we obtained sequencing results of 252 bacterial genera from patients with dCCA, recurrent choledocholithiasis, and the new onset of common bile duct stones, revealing heterogeneity among individuals. Conclusion To the best of our knowledge, this is the first study of the dysbiosis of bile flora in patients with dCCA. This micro-ecological disorder may be a decisive factor in the formation of dCCA. At the same time, for the first time, this study provides a test chart of biliary microbial populations that may be associated with recurrent choledocholithiasis. The compositional changes of the core microbial group of the biliary tract have potentially important biological and medical significance for the microbiological biliary disorders of dCCA.
A dopamine-induced gene expression signature regulates neuronal function and cocaine response

Single-nucleus RNA-seq reveals a dynamic and cell-specific gene program in striatal neurons that contributes to cocaine response. Drugs of abuse elevate dopamine levels in the nucleus accumbens (NAc) and alter transcriptional programs believed to promote long-lasting synaptic and behavioral adaptations. Here, we leveraged single-nucleus RNA-sequencing to generate a comprehensive molecular atlas of cell subtypes in the NAc, defining both sex-specific and cell type–specific responses to acute cocaine experience in a rat model system. Using this transcriptional map, we identified an immediate early gene expression program that is up-regulated following cocaine experience in vivo and dopamine receptor activation in vitro. Multiplexed induction of this gene program with a large-scale CRISPR-dCas9 activation strategy initiated a secondary synapse-centric transcriptional profile, altered striatal physiology in vitro, and enhanced cocaine sensitization in vivo. Together, these results define the transcriptional response to cocaine with cellular precision and demonstrate that drug-responsive gene programs can potentiate both physiological and behavioral adaptations to drugs of abuse.
Genetic analysis workshop IV: Insulin dependent diabetes mellitus ‐ summary

The Insulin Dependent Diabetes Mellitus (IDDM) study was one of the topics of Genetic Analysis Workshop IV (GAW IV) discussed October 7 - 8 at a pre-workshop meeting and presented October 9, 1985 at the American Society of Human Genetics meeting in Salt Lake City. The aim of the study was to have different groups analyze an identical body of real data in order to compare their analytical methods and the results based on their different approaches. This summary describes the available datasets and presents the main results of the nine participating groups. The detailed descriptions of analytical methods and results are presented in the individual papers following this overview. Although differing analytical methods were used there were no discrepancies regarding the interpretation of the data. Whereas the presented gametic associations were well established before, the real gain of this workshop was the unanimous result that the recessive 2-allele-model with incomplete penetrance had to be rejected and at least a 3-allele-model with differing susceptibility alleles and differing penetrances for heterozygotes and homozygotes had to be postulated for the transmission of IDDM.
Cytoskeletal organization in isolated plant cells under geometry control

Significance The cytoskeleton, a network of polymers including microtubules and actin, supports many functions in cells. In plants, the cytoskeleton orientation is an important parameter dictating the direction of cell growth. While light, hormonal, or mechanical signals can affect the cytoskeleton organization, the role of cell geometry remains to be clarified. With a microwell-based approach, we confined plant cells lacking walls in different geometries and found that the cytoskeletons align with the long axis in cells in rectangular wells. Basic geometrical rules of the microtubules are computationally modeled in three dimensions and reveal the role of severing proteins in the shape response, which was observed experimentally. These findings demonstrate how cell geometry feeds back on cytoskeletal organization in plant cells. The cytoskeleton plays a key role in establishing robust cell shape. In animals, it is well established that cell shape can also influence cytoskeletal organization. Cytoskeletal proteins are well conserved between animal and plant kingdoms; nevertheless, because plant cells exhibit major structural differences to animal cells, the question arises whether the plant cytoskeleton also responds to geometrical cues. Recent numerical simulations predicted that a geometry-based rule is sufficient to explain the microtubule (MT) organization observed in cells. Due to their high flexural rigidity and persistence length of the order of a few millimeters, MTs are rigid over cellular dimensions and are thus expected to align along their long axis if constrained in specific geometries. This hypothesis remains to be tested in cellulo. Here, we explore the relative contribution of geometry to the final organization of actin and MT cytoskeletons in single plant cells of Arabidopsis thaliana. We show that the cytoskeleton aligns with the long axis of the cells. We find that actin organization relies on MTs but not the opposite. We develop a model of self-organizing MTs in three dimensions, which predicts the importance of MT severing, which we confirm experimentally. This work is a first step toward assessing quantitatively how cellular geometry contributes to the control of cytoskeletal organization in living plant cells.
Type IV CRISPR–Cas systems are highly diverse and involved in competition between plasmids

CRISPR-Cas systems provide prokaryotes with adaptive immune functions against viruses and other genetic parasites by leveraging small non-coding RNAs for nuclease-dependent degradation of their nucleic acid targets. In contrast to all other types of CRISPR-Cas systems, the mechanisms and biological roles of type IV systems have remained largely overlooked. Here, we describe a previously uncharted diversity of type IV gene cassettes, distributed across diverse prokaryotic genome backgrounds, and propose their classification into subtypes and variants. Congruent with recent findings, type IV modules were primarily found on plasmid-like elements. Remarkably, via a comprehensive analysis of their CRISPR spacer content, these systems were found to exhibit a strong bias towards the targeting of other plasmids. Our data indicate that the functions of type IV systems have diverged from those of other host-related CRISPR-Cas immune systems to adopt a yet unrecognised role in mediating conflicts between plasmids that compete to monopolize their hosts. Furthermore, we find evidence for cross-talk between certain type IV and type I CRISPR-Cas systems that co-exist intracellularly, thus providing an answer to the enigmatic absence of adaptation modules in these systems. Collectively, our results lead to the expansion and reclassification of type IV systems and provide novel insights into the biological function and evolution of these elusive systems.
Spatial ecology, phenological variability and moulting patterns of the Endangered Atlantic petrel Pterodroma incerta

Insights into the year-round movements and behaviour of seabirds are essential to better understand their ecology and to evaluate possible threats at sea. The Atlantic petrel Pterodroma incerta is an Endangered gadfly petrel endemic to the South Atlantic Ocean, with virtually the entire population breeding on Gough Island (Tristan da Cunha archipelago). We describe adult phenology, habitat preferences and at-sea activity patterns for each phenological phase of the annual cycle and refine current knowledge about its distribution, by using light-level geolocators on 13 adults over 1−3 consecutive years. We also ascertained moulting pattern through stable isotope analysis (SIA) of nitrogen and carbon in feathers from 8 carcasses. On average, adults started their post-breeding migration on 25 December, taking 10 d to reach their non-breeding areas on the South American shelf slope. The pre-breeding migration started around 11 April and took 5 d. From phenological data, we found evidence of carry-over effects between successive breeding periods. The year-round distribution generally coincided with the potential distribution obtained from habitat modelling, except during the non-breeding and pre-laying exodus periods, when birds only used the western areas of the South Atlantic. Moulting occurred during the nonbreeding period, when birds spent more time on the water, and results from SIA helped us to distinguish feathers grown around Gough Island from those grown in the non-breeding area. Overall, our results bring important new insights into the spatial ecology of this Endangered seabird, which should help improve conservation strategies in the South Atlantic Ocean.
Taxonomic revision of South African Memecylon (Melastomataceae—Olisbeoideae), including three new species

Earlier works recognised two South African species Memecylon bachmannii and M. natalense within M. sect. Buxifolia, but recent molecular analyses have revealed that M. natalense as previously circumscribed is not monophyletic and includes several geographically outlying populations warranting treatment as distinct taxa. In this revision we recognise five endemic South African species of which M. bachmannii and M. natalense are both maintained but with narrower circumscriptions, and M. kosiense, M. soutpansbergense and M. australissimum are newly described. Memecylon kosiense is localised in north-eastern KwaZulu-Natal (Maputaland) and is closely related to M. incisilobum of southern Mozambique. Memecylon soutpansbergense, from Limpopo Province, was previously confused with M. natalense but is clearly distinguished on vegetative characters. Memecylon australissimum occurs in the Eastern Cape (Hluleka and Dwesa-Cwebe nature reserves) and has relatively small leaves like those of M. natalense, but the floral bracteoles are persistent and the fruit is ovoid as in M. bachmannii. We further designate a lectotype for M. natalense, provide an updated key to the South African species of Memecylon, and provisionally assess the status of each species in accordance with International Union for Conservation of Nature criteria.
Effects of dietary extruded linseed (Linum usitatissimum L.) on performance and meat quality in Podolian young bulls

This study compared effects of a diet containing 3% extruded linseed (EL) ( Linum usitatissimum L.) with a control diet (C) on growth, carcass traits, and meat quality in young Podolian bulls. After 208 days on feed, the bulls were slaughtered at 18 months of age. Samples of Longissimus lumborum (Ll) were analysed to assess their physical and chemical parameters and intramuscular fatty acid composition. Average daily gain, feed intake and feed efficiency were not affected by treatments. Bulls fed EL (n = 6) had significantly greater final (612 kg versus 593 kg) and slaughter weights (583 kg versus 563 kg) than those fed C (n = 6). Compared with C, EL significantly increased percentages of lean from the pelvic limb (71.9% versus 69.3%) and of bone from the lumbar region (30.0 versus 27.1%). Meat pH recorded at slaughter was significantly greater for C than EL (6.7 versus 6.4). Diet did not affect meat colour, chemical composition and shear force of either the raw or cooked meat. Total amounts of saturated, monounsaturated and polyunsaturated fatty acids were not influenced by the diets. Concentrations of linoleic acid (C18:2 n-6) (3.30 versus 4.08) and total n-6 fatty acids (3.83 versus 4.73) were reduced by EL, while EL significantly enhanced linolenic acid (C18:3 n-3) (0.45 vs 0.20) and total n-3 fatty acids (1.64 versus 1.18) in the meat compared with C. Thus, dietary supplementation with 3% EL improved the amount of n-3 fatty acids in the meat from young Podolian bulls without affecting their performance. Keywords: carcass traits, fatty acids, feed efficiency, growth, meat colour
Versatility of reproductive modes and ploidy level interactions in Sorbus s.l. (Malinae, Rosaceae)

This study focuses on the frequency of reproductive modes and the role of reproductive mode variation in diversification of the genus Sorbus s.l. and evolutionary success of individual taxa. Our sampling covers all four ploidies known in Sorbus and includes stabilized taxa and recently formed biotypes. We infer reproductive modes of 3660 seeds using the flow cytometric seed screen method; we also calculated ploidy of contributing pollen. Sorbus shows high variability in reproduction pathways (sexuality, apomixis, formation of BIII hybrids, haploid parthenogenesis). Diploids are sexual, whereas polyploids show predominantly pseudogamous apomixis. In half of the polyploids studied, several reproductive modes were present and even intra-individual variation was detected. Diploids, tetraploids and pentaploids are pollinated by conspecific pollen, whereas triploids are largely, but not fully, dependent on the pollen of other species. In pseudogamous seeds, fertilization of the central cell by both sperms is a dominant pathway of endosperm origin. Flow cytometry of pollen did not detect unreduced pollen at any ploidy. The principal mechanisms of diversification in Sorbus are residual sexuality in apomicts, production of triploid taxa from diploid–tetraploid crosses and production of BIII hybrids. Evolutionary success of Sorbus taxa is largely dependent on the breeding system and is determined by self-(in)compatibility and the interplay between stabilizing apomixis and variation-generating sexuality.
Mechanosensitive junction remodelling promotes robust epithelial morphogenesis

Morphogenesis of epithelial tissues requires tight spatiotemporal coordination of cell shape changes. In vivo, many tissue-scale shape changes are driven by pulsatile contractions of intercellular junctions, which are rectified to produce irreversible deformations. The functional role of this pulsatory ratchet and its mechanistic basis remain unknown. Here we combine theory and biophysical experiments to show that mechanosensitive tension remodelling of epithelial cell junctions promotes robust epithelial shape changes via ratcheting. Using optogenetic control of actomyosin contractility, we find that epithelial junctions show elastic behaviour under low contractile stress, returning to their original lengths after contraction, but undergo irreversible deformation under higher magnitudes of contractile stress. Existing vertex-based models for the epithelium are unable to capture these results, with cell junctions displaying purely elastic or fluid-like behaviours, depending on the choice of model parameters. To describe the experimental results, we propose a modified vertex model with two essential ingredients for junction mechanics: thresholded tension remodelling and continuous strain relaxation. First, a critical strain threshold for tension remodelling triggers irreversible junction length changes for sufficiently strong contractions, making the system robust to small fluctuations in contractile activity. Second, continuous strain relaxation allows for mechanical memory removal, enabling frequency-dependent modulation of cell shape changes via mechanical ratcheting. Taken together, the combination of mechanosensitive tension remodelling and junctional strain relaxation provides a robust mechanism for large-scale morphogenesis.
Boletus Edulis Mushroom Flour-Based Wheat Bread as Innovative Fortified Bakery Product

Mushroom powder was added to bread in different proportions, namely: 3%, 6% and 9%, in order to improve the nutritional properties of bread. Thus, the new products, had increased contents of protein from 6.60% to 7.79% and fat from 0.78% to 1.43%. Moreover, the content of polyphenols also increased from 39.88 to 84.46 mg GAE/100 g, and the antioxidant activity increased from 16.81% to 27.91%. According to the sensory analysis, performed by means of the hedonic test, the most appreciated bread was that fortified with 6% of mushroom powder. In terms of texture profile, the sample with 6% of mushroom powder recorded the best results. Nowadays, this product has a positive impact on the consumers, who take a growing interest in functional products, that are rich in active compounds. Bread enriched with more than 3 % mushroom powder is a product with high nutritional value.
Non Genetec Parameters and Repeatability for Milk Traits Goat in Northern Iraq

A total of 439, 436 and 437 records of average daily milk yield (ADMY), milk yield after weaning (MYAW) and total milk yield (TMY) respectively were analyzed. Data used in this study obtained from mountain does at private project in Raselain Village/ Akre Region/ Duhok governorate. The data related to two milking seasons (2016-2017) and (2017-2018). The animals were allowed to graze natural pasture and stubble, straw and ground oak acorns were providing whenever required. Does were flushed 2 weeks prior to mating and kidding season. The flock was placed on a regular health program. Does were milked by hand at biweekly intervals starting from the first week post kidding till the does are dried off. ADMY was calculated by multiplying test day milk yield * 2. While TMY calculated by multiplying ADMY by lactation period. Statistical analysis of data was carried out by using GLM procedure within SAS programme. This model includes effects of doe's age, year and season of kidding, birth's type and sex and weight of doe at kidding on milk traits. Effect of doe added to above model as a random effect to estimate their repeatability using Restricted Maximum Likelihood method. Overall means for ADMY, MYAW and TMY were 0.727, 54.49 and 129.32 kg respectively. Results showed that the age of does had significantly higher effect (P< 0.01) on all studied traits of milk. Does aged 4.5 years produce significantly higher ADMY (0.772 kg), and accordingly TMY (136.88kg), while higher MYAW recorded for does aged 3.5 years beside 4.5 years. The effectiveness of year was significant (P< 0.01) on all milk yield traits. Also season of kidding affect all studied milk traits significantly (P< 0.01), whereas the does kidding in winter had significantly higher ADMY, MYAW and TMY than those kidding in spring season. The effects of type of birth and sex of kids were significant on all milk traits. Does with female twins produced significantly more ADMY comparing with does having male or female singles only. Does with female twins and male and female twins produced significantly much MYAW. Does with female twins yield significantly higher TMY when compared to those in the other groups, on the same time there were no significant differences in TMY of does with male twin and does with male and female twin. There was no significant effect of doe weight at kidding on all studied traits and the regression coefficients were positive for ADMY (0.0003 kg/kg), and TMY (0.085 kg/kg) while the regression was negative for MYAW (- 0.0024 kg/kg). Repeatability estimates of ADMY, MYAW and TMY were 0.24, 0.31 and 0.27 respectively. It sum: due to the effectiveness of the fixed factors on the studied traits, hence adjusting records is necessary. The estimates of repeatability indicate that selection of does as well their kids depending on their milk production will improve the productivity in the next year.
Meat and sensory quality of major muscles from Angus, Charolais, and Angus crossbred steers with high and low residual feed intake

Abstract: Effects of residual feed intake (RFI) and genetic group on growth, carcass, and meat quality characteristics of bovine longissimus lumborum (LL), triceps brachii (TB), semimembranosus (SM), and gluteus medius (GM) muscles were investigated using 72 purebred Angus, purebred Charolais, and Angus crossbred steers (n = 24 per genetic group) classified as either high (inefficient) or low (efficient) RFI (n = 12 high and low RFI steers within genetic group). There was no RFI effect (P > 0.05) on growth, carcass, and meat quality measurements except high RFI steers had the highest dry matter intake (P < 0.05), and low RFI TB was rated as having reduced beef flavour intensity and sustained juiciness (P < 0.05). Purebred Angus and Charolais LL and GM had lower shear force values (P < 0.05) than Angus crossbreds and ageing reduced mean shear force values except in TB. For TB, SM, and GM, Angus crossbred steers had the highest mean beef flavour intensity scores, and Charolais SM and TB were less tender than those of Angus crossbred (P < 0.05). Overall, RFI did not influence most meat quality traits; therefore, low RFI animals may contribute to reducing feed costs or environmental impact without compromising meat quality and palatability.
ESTIMATION OF GENETIC VARIABILITY AND DIVERGENCE IN SOME SELECTED LINES OF PEARL MILLET

The objective of this study was to estimate the genetic variability , heritability , genotypic and phenotypic coefficients of variations , genetic advance , range , genotypic and phenotypic variances and to study the genetic divergence by using multivariate analysis for yield and yield components in forty selected lines of pearl millet during 2012 and 2013 summer seasons at Sakha Agriculture Research Station . Analysis of variance manifested highly significant differences among all selected lines for all the studied traits. The phenotypic coefficient of variation (PCV) was higher than the genotypic coefficient of variation (GCV). Heritability in broad sense ranged from 11.12%for fresh leaf/ stem ratio to 86.87% for stem diameter. High estimates of bread sense heritability were found in all the studied traits, except dry matter and fresh leaf/stem ratio which, were medium and low, respectably. The environmental variance ranged from 13.13% for stem diameter to 88.88% for fresh leaf / stem ratio. The results also cleared that the genetic advance ranged from 0.91% for fresh leaf / stem ratio to 24.72% for total fresh forage yield. The results cleared that the ascendant order of the importance of evaluated traits were, the first factor accounted 41.78% (number of tillers, plant height, total dry forage yield and total fresh forage yield) while, the second factor accounted 59.62% (dry matter, stem diameter and fresh leaf /stem ratio) of the multivariate variance. The forty selected lines were grouped into eight clusters based on dissimilarity coefficients. Thus, the pearl millet breeder would use these selected lines from divergent cluster for hybridization in order to isolate useful recombinants in the segregating generations.