Miracle-dz/UniFAR-FTUs huggingface dataset:
PDX1, a key factor in pancreatic embryogenesis, can exhibit antimetastatic activity in pancreatic ductal adenocarcinoma

Background: In cancer biology, metastasizing is one of the most poorly studied processes. Pancreatic ductal adenocarcinoma (PDAC) is characterized by early metastasis, which is the leading cause of death. The PDX1 protein is crucial for the development of cancer, and its low levels are characteristic of the most aggressive PDAC tumors. The PDX1 is a mediator of initiation and progression of PDAC. However, further studies are needed to elucidate the role of PDX1 in the cancer metastasis. Purpose: To confirm the hypothesis that PDX1 in PDAC plays suppressor role of epithelial–mesenchymal transition (EMT), and to study its possible ability to inhibit metastasis. Methods: A PDX1-overexpressing PDAC cell line was obtained by lentiviral transduction of PANC-1 cells. PDX1 overexpression was confirmed by RT-PCR and Western blotting. Effects of PDX1 ectopic expression on cell proliferation and motility were determined in PANC-1 cells using MTS, cell cycle analysis, transwell and wound-healing assay. EMT genes expression was analyzed in PDX1-overexpressing and Control PANC-1. Finally, the migration potential of pancreatic cancer cells expressing PDX1 was evaluated using a zebrafish embryo model. Results: The motility of human PDAC cells PANC-1 considerably decreased at ectopic expression of PDX1. The decreased expression of ZEB1, the key factor of EMT, and almost unchanged expression of the genes that characterize the epithelial state suggest a decrease in the EMT ability. Suppression of PDX1 expression by siRNA knockdown restored the PANC1 motility. Conclusion: The results obtained suggest a possible therapeutic use of PDX1 delivery into PDAC patients with a reduced or absent expression of PDX1 in the most aggressive tumors.
Comparative Study of Nutrient Composition of Selected Cereal Grains Available in Jaffna, Sri Lanka

Grains are the seeds of grass-like plants called cereals. Grains contain important nutrient necessary for human health. Consumption of grains and grain foods is encouraged in dietary guidelines around the world because of the significant contribution of the nutrient content of grains. The present work aims to compare the general nutrient composition of selected seventeen grains available in Jaffna, Sri Lanka to consider them as excellent candidates for consumption. Proximate macronutrient content of the seeds of selected grains were estimated by nutrient content analysis according to the standard protocols recommended by the Association of Analytical Chemists (AOAC), the USA at the Department of Botany, University of Jaffna and compared the general nutrient composition among cereal grains. Grain varieties have moisture contents varied from 3.70% to 14.42%, ash contents varied from 0.66% to 5.52%, fat contents ranged from 2.80% to 52.93%, protein contents varied from 7.44% to 48.47%, and carbohydrate contents varied from 12.39% to 68.58%. Black gram has the highest moisture content (14.42%), soya has the highest ash (5.52%) and protein content of 48.47% while sesame has the highest fat content (52.93%). Among the entire samples, soya possesses some desirable nutritional attributes than other grains with respect lower fat and carbohydrate and greater protein (48.47%) and ash content (5.52%).
Potential Adiponectin Receptor Response Modifier Therapeutics

Many human diseases may benefit from adiponectin replacement therapy, but due to pharmacological disadvantages of the intact protein, druggable options focus on peptidic, and small molecule agonists of the adiponectin receptor. Peptide-based adiponectin replacement drug leads are derived from, or resemble, the active site of globular adiponectin. ADP355, the first-in-class such peptide, exhibits low nanomolar cellular activities, and clinically acceptable efficacies in a series of fibrotic and inflammation-derived diseases. The advantage of small molecule therapies, spearheaded by AdipoRon, is oral availability and extension of utility to a series of metabolic conditions. It is exactly the difficulties in the reliability and readout of the in vitro measures and the wealth of in vivo models that make comparison of the various drug classes complicated, if not impossible. While only a fewer number of maladies could take advantage of adiponectin receptor antagonists, the limited number of these available can be very useful tools in target validation studies. Alternative approaches to direct adiponectin signaling control use upstream adiponectin production inducing therapies but currently these offer relatively limited success compared to direct receptor agonists.
Occurrence of Ice-Bonded Sediments in the Mackenzie Trough, Beaufort Sea

The Arctic continental shelves experienced subsea permafrost degradation because of the long-term warming and sea level rise since the Last Glacial Maximum (LGM), when the sea level was ~100 m lower than its present level. However, the current status of the subsea permafrost limit is not yet clearly defined due to a lack of evidence. New subbottom profiling and subsurface temperatures were acquired to examine the subsea permafrost limit on the eastern slope of the Mackenzie Trough during Korean Icebreaker R/V Araon expeditions in the summer of 2013 and 2014. We found anomalous subbottom acoustic features indicating ice-bonded sediments where cold bottom water and a subsurface with subzero temperature exists. The cold bottom water belongs to the Arctic halocline. We conclude that with help from cold Arctic halocline, ice-bonded sediments can exist at shallow water depths of <100 m. We argue that they are relict subsea permafrost from the LGM, but further investigation is required to clarify their origin. Our conclusion implies that ice-bonded sediments can occur at shallow water depths over the Arctic continental shelves and that their fate depends on the temperature change in seawater.
Gene expression profiles complement the analysis of genomic modifiers of the clinical onset of Huntington disease

Huntington disease (HD) is a neurodegenerative disorder that is caused by a CAG repeat expansion in the HTT gene. In an attempt to identify genomic modifiers that contribute towards the age of onset of HD, we performed a transcriptome wide association study assessing heritable differences in genetically determined expression in diverse tissues, employing genome wide data from over 4,000 patients. This identified genes that showed evidence for colocalization and replication, with downstream functional validation being performed in isogenic HD stem cells and patient brains. Enrichment analyses detected associations with various biologically-relevant gene sets and striatal coexpression modules that are mediated by CAG length. Further, cortical coexpression modules that are relevant for HD onset were also associated with cognitive decline and HD-related traits in a longitudinal cohort. In summary, the combination of population-scale gene expression information with HD patient genomic data identified novel modifier genes for the disorder.
Present status of isolation and culture of pre-antral follicles in buffalo species (Bubalus bubalis): A review

Buffalo ovaries have an inherently lower number of primordial, preantraland antral follicles as compared to cattle. Culture of preantral follicles in buffalo is an alternative source for the in vitro production of embryos. Culture of preantral follicles had been done in many species like bovine, ovine, caprine, swine and canine. Effective isolation protocols for buffalo preantral follicles employing mechanical and enzymatic methods were standardized during the last decade. It needs further investigations. It can be helpful for understanding the mechanism of folliculogenesis and different substances that affect the ovarian function.
Heat dissipation capacity influences reproductive performance in an aerial insectivore

ABSTRACT Climatic warming is predicted to increase the frequency of extreme weather events, which may reduce an individual's capacity for sustained activity because of thermal limits. We tested whether the risk of overheating may limit parental provisioning of an aerial insectivorous bird in population decline. For many seasonally breeding birds, parents are thought to operate close to an energetic ceiling during the 2–3 week chick-rearing period. The factors determining the ceiling remain unknown, although it may be set by an individual's capacity to dissipate body heat (the heat dissipation limitation hypothesis). Over two breeding seasons we experimentally trimmed the ventral feathers of female tree swallows (Tachycineta bicolor) to provide a thermal window. We then monitored maternal and paternal provisioning rates, nestling growth rates and fledging success. We found the effect of our experimental treatment was context dependent. Females with an enhanced capacity to dissipate heat fed their nestlings at higher rates than controls when conditions were hot, but the reverse was true under cool conditions. Control females and their mates both reduced foraging under hot conditions. In contrast, male partners of trimmed females maintained a constant feeding rate across temperatures, suggesting attempts to match the feeding rate of their partners. On average, nestlings of trimmed females were heavier than controls, but did not have a higher probability of fledging. We suggest that removal of a thermal constraint allowed females to increase provisioning rates, but additionally provided nestlings with a thermal advantage via increased heat transfer during maternal brooding. Our data provide support for the heat dissipation limitation hypothesis and suggest that depending on temperature, heat dissipation capacity can influence reproductive success in aerial insectivores. Highlighted Article: Empirical evidence that the ability to dissipate body heat constrains offspring feeding behaviour in a breeding bird, the tree swallow.
Reaching around obstacles accounts for uncertainty in coordinate transformations

When reaching to a visual target, humans need to transform the spatial target representation into the coordinate system of their moving arm. It has been shown that increased demands in such coordinate transformations, for instance when the head is rolled toward one shoulder, lead to higher movement variability and influence movement decisions. However, it is unknown whether the brain incorporates such added variability to adjust movements when it is necessary. We designed an obstacle avoidance task in which participants had to reach to a visual target without colliding with an obstacle. We introduced different coordinate transformation demands by varying head roll (straight, 30° clockwise and 30° counterclockwise). In agreement with previous studies, we observed that the reaching variability increased when the head was tilted. In addition, participants systematically changed their obstacle avoidance behavior with head roll. In particular, they changed the preferred direction of passing the obstacle and increased the error margins indicated by stronger movement curvature. Indeed, participants’ reaching movements did not differ in the number of collisions between the head roll and the head straight conditions. These results suggest that the brain takes the added movement variability during head roll into account and compensates for it by adjusting the reaching trajectories.
Recurrent Neural Networks in Forecasting S&P 500 Index

The objective of this research is to predict the movements of the S&P 500 index using variations of the recurrent neural network. The variations considered are the simple recurrent neural network, the long short term memory and the gated recurrent unit. In addition to these networks, we discuss the error correction neural network which takes into account shocks typical of the financial market. In predicting the S&P 500 index, we considered 14 economic variables, 4 levels of hidden neurons of the networks and 5 levels of epoch. From these features, relevant features were selected using experimental design. The selection of an experiment with the right features is chosen based on its accuracy score and its Graphical Processing Unit (GPU) time. The chosen experiments (for each neural network) are used to predict the upward and downward movements of the S&P 500 index. Using the prediction of the S&P 500 index and a proposed strategy, we trade the S&P 500 index for selected periods. The profit generated is compared with the buy and hold strategy.
Role of the Btk-PLCγ2 Signaling Pathway in the Bone Destruction of Apical Periodontitis

Chronic apical periodontitis is characterized by alveolar bone absorption in the apical region and is the result of the participation of various inflammatory mediators. Studies have shown that the Bruton tyrosine kinase- (Btk-) phospholipase Cγ2 (PLCγ2) signaling pathway plays an important role in bone absorption, but it is unknown whether it plays a role in apical periodontitis bone destruction. Therefore, this study verified the role of Btk and PLCγ2 in bone resorption of apical periodontitis by in vivo and in vitro experiments. In the in vivo experiment, a mice model of apical periodontitis was established; apical bone resorption was confirmed by the numbers of osteoclasts and HE staining. Btk, PLCγ2, and nuclear factor of activated T-cells 1 (NFATc-1) were detected by immunohistochemical staining. In the in vitro experiment, lipopolysaccharides (LPS) were used to stimulate osteoclast precursor cell RAW264.7 to establish an inflammatory microenvironment and detect osteoclast differentiation. By silencing Btk, the expression of Btk, PLCγ2, and NFATc-1 was detected by real-time qPCR and Western blot, and osteoclastogenesis was detected by enzyme histochemical staining to further confirm the role of Btk in bone resorption. It was found that the expression of Btk, PLCγ2, and NFATc-1 changed significantly with the progression of inflammation and bone destruction, indicating that Btk and PLCγ2 may be involved in the progression of inflammation in apical periodontitis and bone absorption. In vitro experiments confirmed that the differentiation of osteoclasts and the expression of PLCγ2 and NFATc-1 were significantly inhibited after silencing Btk expression, but osteoclast precursor cells could be differentiated due to the proinflammatory factor lipopolysaccharide. This study demonstrates that Btk and PLCγ2 are key factors involved in the apical inflammatory response and bone destruction.
Breeding dairy cattle for improved feed efficiency: an overview.

April 22-24, 2019 Tri-State Dairy Nutrition Conference Breeding Dairy Cattle for Improved Feed Efficiency: An Overview Luiz F. Brito1,2, Hinayah R. Oliveira1,2, Tatiane C.S. Chud2, Dave J. Seymour2,3, Filippo Miglior2,4, and Flavio S. Schenkel2,4 1Department of Animal Sciences, Purdue University 2Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada 3Centre for Nutrition Modelling, Department of Animal Biosciences, University of Guelph 4These authors share last co-authorship
Identification of key rearing factors to manage cattle carcass fatness and conformation scores during the fattening period

Abstract The fatness and conformation scores characterise the payment of cattle carcasses in the EUROP system. The management of these carcass traits is important for stakeholders of the meat chain. The aim of this study was to identify rearing factors, applied during the fattening period, influencing the fatness and conformation scores of the carcasses, in two categories of animals (cull cows and young bulls). A data set of individual cattle data (233 cull cows and 565 young bulls) from different experiments was used. It included eleven rearing factors characterising the fattening period. From carcass data, clusters of fatness and conformation scores were defined. To identify the rearing factors with a leverage on carcass traits according to the category of animal, four robust prediction models were developed using logistic regression to predict these clusters. According to the results of the models established, to achieve the fatness score rehearsed by stakeholders, cull cows should ingest less dry matter (DM) and have a shorter fattening period, whereas young bulls should be more efficient, ingest more DM and be slaughtered heavier. To improve the carcass conformation score, the cull cows should ingest more net energy and begin their fattening heavier. For the young bulls, the three rearing factors identified for the fatness score allowed to improve the conformation score. This study showed also that the jointly management of these both carcass traits is possible, nevertheless it is necessary to adapt the applied fattening practices according to the category of animal. Highlights Used rearing factors to predict the fat score and conformation of bovine carcasses. Logistic regression is well adapted to predict fat score and conformation of bovine carcasses. The prediction models of the fat score and conformation are robust.
Impact of Anthropogenic Organic Matter on the Distribution Patterns of Sediment Microbial Community from the Yangtze River, China

Abstract How microbes respond to substantial and increasing anthropogenic disturbance remains an open question in river systems. We tested the hypothesis that the source and distribution of anthropogenic organic matter (OM) were significant factors affecting the spatial variation of the microbial community composition of the Yangtze River sediments. Bulk geochemical proxies and lignin phenols suggested a general decrease of terrestrial C3 plants or soil OM input from the middle to the lower reaches. Fecal sterols inferred higher sewage contamination levels in the middle reaches. Polycyclic aromatic hydrocarbons (PAHs) distribution indicated a dominant biomass and coal combustion signal in the middle reaches, whereas a mixed source including petroleum combustion in the lower reaches. Phylogenetic analysis revealed a large portion of Methanobacteria and Verrucomicrobia enriched in the middle reaches, whereas OM-degrading bacteria, including Flavobacteria, Acidobacteria, and Alphaproteobacteria were dominant in the lower reaches. Quantitative PCR analyses and multivariate analysis further demonstrated that sources and distribution of OM had combined effects in shaping alpha and beta-diversity of sediment microbial communities. Sewage discharge and incomplete OM combustion, respectively, were associated with Methylococcaceae, Chloroflexi, and Bacteroidetes groups. This study provides a foundation for further understanding of the river sediment microbial composition, considering the continued increase of anthropogenic influences.
Extracellular vesicles released in the apoplast of germinating seeds contain almost exclusively a fungal glucanase inhibitor

Extracellular vesicles (EVs) are small, membrane-enclosed structures released from a cell into the surrounding environment. EVs play an important role in intercellular communication by transporting proteins and RNA. Plant EVs seem to mediate the transport of proteins to the extracellular compartment (apoplast) and could account for the so-called unconventional secretion pathway, where proteins lacking a signal peptide secreted in extracellular fluids Thus, EVs participate in defense responses, acting as carriers of active proteins through the apoplast (Regente et al., 2017). γ-Conglutin from the leguminous plant Lupinus albus has been considered for a long time a storage protein, but recent studies definitely ruled out this function evidencing a multifaceted involvement in plant defence mechanisms triggered by pathogens attacks (Scarafoni et al. , 2010). γ-Conglutin shares structural similarities with members of a large family of glucanase inhibitors widely distributed across the plant kingdom, such as the xyloglucan-specific endo--1,4-glucanase inhibitors (XEGIPs) (Qin et al., 2003, Scarafoni et al., 2016). γConglutin was localized in the apoplasts of germinating seeds while the storage vacuoles appeared void of the protein. How γ-conglutin reaches the extracellular regions is still matter of debate. The present work aimed to investigate if γ-conglutin is secreted outside the cotyledonary cells during the very first moments of seed germination is conveyed by EVs. The results obtained by a combination of vacuum infiltration, 1Dand 2D-gel electrophoresis, ultracentrifugation fractionation and immunoblotting techniques, indicate that after 16 hours from the germination onset γ-conglutin is the most represented protein in apoplast and that it is confined in vesicular material. The hypothesis that the seed-stored protein is released outside the cells through an unconventional secretory vesicles-based pathway, as it occurs for sunflower seed agglutinin 1 and other seed proteins, is suggestive and needs further focused investigations.
Charakterisierung des Reproduktionssystems von Potentilla puberula Krašan und methodische Etablierung der Kreuzungstechnik

Im Rahmen dieser Arbeit wurde der Reprodutionsmodus unterschiedlicher Zytotypen in der polyploiden Art Potentilla puberula Krasan untersucht. Im ersten Teil der Arbeit wurden Pflanzen des sexuellen, tetraploiden Zytotyps miteinander gekreuzt. Die Charakterisierung des Reproduktionsystems ergab obligate Xenogamie. Das Ergebnis belegt das Vorliegen eines funktionierenden, genetischen Selbstinkompatibilitatskomplexes fur Pflanzen dieses Typs. Kontrar dazu bricht (mit Ausnahme des heptaploiden Zytotyps) in den hoherploiden, apomiktischen Individuen, die im zweiten Teil der Arbeit untereinander gekreuzt wurden, der Selbstinkompatibilitatkomplex mit steigendem Ploidieniveau zusammen. So waren die Pflanzen mit grosem Genom imstande, auch bei Selbstbestaubung entwicklungsfahige Fruchtchen zu bilden. Bei den untersuchten Individuen von P. puberula scheint der Reproduktionserfolg nicht vom Pollen jeweils anderer, in der Population vorkommender Zytotypen abhangig zu sein, sondern die Pflanzen zeigen tendenziell einen hoheren Reproduktionserfolg nach Fremdbestaubung mit Pollen des eigenen Zytotyps. Einzige Ausnahme stellt der pentaploide Zytotyp dar, welcher uber eine vergleichsweise schlechte Pollenqualitat verfugt (Milosevic & Dobes, unveroffentlichte Daten).
Parameters and determinants of responses to selection in antibody libraries

Antibody repertoires contain binders to nearly any target antigen. The sequences of these antibodies differ mostly at few sites located on the surface of a scaffold that itself consists of much less varied amino acids. What is the impact of this scaffold on the response to selection of a repertoire? To gauge this impact, we carried out quantitative phage display experiments with three antibody libraries based on distinct scaffolds harboring the same diversity at randomized sites, which we selected for binding to four arbitrary targets. We first show that the response to selection of an antibody library is captured by a simple and measurable parameter with direct physical and information-theoretic interpretations. Second, we identify a major determinant of this parameter which is encoded in the scaffold, its degree of evolutionary maturation. Antibodies undergo an accelerated evolutionary process, called affinity maturation, to improve their affinity to a given target antigen as part of the adaptive immune response. We find that libraries of antibodies built around such maturated scaffolds have a lower response to selection to other arbitrary targets than libraries built around naïve scaffolds of germline origin. Our results are a first step towards quantifying and controlling the evolutionary potential of biomolecules.