Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of curcumin on canine semen parameters and expression of NOX5 gene in cryopreserved spermatozoa

Canine seminal plasma contains antioxidant enzymes to protect sperm against internally generated ROS. These enzymes are removed from seminal plasma during the process of cryopreservation. The freezing/thawing process can cause some morphological and functional changes via ice crystallization and osmolality imbalance. The present study was conducted to evaluate the effects of curcumin supplementation on sperm total count, motility, progressive motility, viability, morphology, total antioxidant capacity (TAC), DNA integrity and NOX5 gene expression of dog frozen semen. The pooled semen was allocated to fresh (Group 1) and frozen (Group 2) controls, curcumin (2.50 mM) (Group 3) and curcumin (5.00 mM), (Group 4). Sperm parameters including total sperm count, morphology, motility, progressive motility, sperm concentration and DNA integrity in addition to TAC were evaluated in fresh and frozen-thawed semen samples. Real-time RT-PCR was used to investigate NOX5 and GADPH (reference gene) genes expressions. Curcumin at 2.50 mM provided a greater protective effect on the DNA integrity compared to 5.00 mM and control groups. TAC was significantly higher in 2.50 mM group than other groups. NOX5 gene expression in curcumin 2.50 mM was higher than 5.00 mM group. In conclusion, curcumin seems to emolliate sperm parameters and to protect sperm against sperm reactive oxygen stress and increases NOX5 gene expression.
Osteopontin promotes survival of intestinal intraepithelial lymphocytes and protects against colitis

Intestinal intraepithelial lymphocytes (IEL) comprise a diverse population of cells residing in the epithelium at the interface between the intestinal lumen and the sterile environment of the lamina propria. Because of this anatomical location, IEL are considered critical components of intestinal immune responses. Indeed, IEL are involved in many different immunological processes ranging from pathogen control to tissue stability. However, maintenance of IEL homeostasis is incompletely understood. In this report we present evidence that osteopontin, a glycophosphoprotein with diverse roles in biomineralization, cell-mediated immunity, and inflammation, is important for maintaining normal levels of IEL. Mice in which the osteopontin gene (Spp-1) is disrupted present decreased levels of IEL subtypes, such as TCRαβ and TCRγδ IEL in the intestine, an effect not observed for lymphocytes in other immune compartments such as spleen or lamina propria, indicating an epithelium-specific effect. In vitro experiments show that mouse and human IEL survival is improved by culture with recombinant osteopontin. CD44, a ligand for osteopontin, is conspicuously expressed in IEL, including mucosal regulatory T cells. We present in vitro and in vivo evidence supporting a role for the osteopontin-CD44 interaction in IEL and regulatory T cell homeostasis, with implications in the development of intestinal inflammation.
Measuring Mechanodynamics using an Unsupported Epithelial Monolayer Grown at an Air-Water Interface

Actomyosin contraction and relaxation in a monolayer is a fundamental biophysical process in development and homeostasis. Current methods used to characterize the mechanodynamics of monolayers often involve cells grown on solid supports such as glass or gels. The results of these studies are fundamentally influenced by these supporting structures. Here, we describe a new methodology for measuring the mechanodynamics of epithelial monolayers by culturing cells at an air-liquid interface. These model monolayers are grown in the absence of any supporting structures removing cell-substrate effects. This method’s potential was evaluated by observing and quantifying the generation and release of internal stresses upon actomyosin contraction (320±50Pa) and relaxation (190±40Pa) in response to chemical treatments. Although unsupported monolayers exhibited clear major and minor strain axes, they were not correlated to nuclear alignment as observed when the monolayers were grown on soft deformable gels. It was also observed that both gels and glass substrates led to the promotion of long-range cell nuclei alignment not seen in the hanging drop model. This new approach provides us with a picture of basal actomyosin mechanodynamics in a simplified system allowing us to infer how the presence of a substrate impacts contractility and long-range multi-cellular organization and dynamics.
Physiological and Molecular Responses in Rice, Weedy Rice and Barnyardgrass Exposed to Supra-Optimal Temperatures

ABSTRACT: The global temperature to rise 0.3 to 4.8 oC to century. Supra-optimal temperatures can affect plants at different organizational levels, causing morphological, physiological, biochemical and gene expression alterations. Rice, weedy rice, and barnyardgrass may to response differently when subjected to supra-optimal temperatures. Thus, the aimed at determining the physiological response and expression of the genes APX2, HSP24.15 e HSP71.10 in rice, weedy rice, and barnyardgrass when in to supra-optimal temperatures. A greenhouse experiment was conducted in randomized complete desing with four repetitions, with a factorial combination of temperature x plantas, where: factor A consisted of two temperatures (25 oC and 40 oC); and factor B of three plants [rice (Oryza sativa cv. Puitá INTA-CL), weedy rice (Oryza spp.), and barnyardgrass (Echinochloa spp.)]. The 40 oC temperature, in general, caused a reduction in the photosynthesis parameters and in the protein content, and increased the oxidative stress in C3 plants; no damage was observed in the C4 plant subjected to this temperature. In response to the supra-optimal temperatures, rice and weedy rice increased of APX and SOD activity and the expression of OsAPX2, OsHSP24.15 and OsHSP71.10 genes. Barnyardgrass exposed to supra-optimal temperature do not modify the activity of its antioxidant system and increased the OsHSP71.10 gene expression.
NG2 glia are required for maintaining microglia homeostatic state

Microglia play vital roles in the health and diseases of the central nervous system. Loss of microglia homeostatic state is a key feature of brain aging and neurodegeneration. However, the mechanisms underlying the maintenance of distinct microglia states are largely unclear. Here we show that NG2 glia, also known as oligodendrocyte precursor cells, are essential for maintaining the homeostatic microglia state. We developed a highly efficient and selective NG2 glia depletion method using small-molecule inhibitors of platelet-derived growth factor signaling in cultured brain slices. We found that loss of NG2 glia abolished the homeostatic microglia signature without affecting the disease-associated microglia profiles. Similar findings were also observed in vivo by genetically ablating NG2 glia in the adult mouse brain. These data suggest that NG2 glia exert a crucial influence onto microglia cellular states that are relevant to brain aging and neurodegenerative diseases. In addition, our results provide a powerful, convenient and selective tool for the investigation of NG2 glia function. Main points Postnatal NG2 glia maintenance obligatorily depends on continuous PDGF signaling. A highly efficient, selective and versatile NG2 glia depletion method is established. Loss of NG2 glia abolishes the homeostatic microglia signature both in vitro and in vivo.
Simulated and experimental estimates of hydrodynamic drag from bio‐logging tags

Drag force acting on swimming marine mammals is difficult to measure directly. Researchers often use simple modeling and kinematic measurements from animals, or computational fluid dynamics (CFD) simulations to estimate drag. However, studies that compare these methods are lacking. Here, computational simulation and physical experiments were used to estimate drag forces on gliding bottlenose dolphins ( Tursiops truncatus ). To facilitate comparison, variable drag loading ( no-tag, tag, tag + 4, tag + 8 ) was used to increase force in both simulations and experiments. During the experiments, two dol-phins were trained to perform controlled glides with variable loading. CFD simulations of dolphin/tag geometry in steady flow (1 – 6 m/s) were used to model drag forces. We expect both techniques will capture relative changes created by experimental conditions, but absolute forces predicted by the methods will differ. CFD estimates were within a calculated 90% confidence interval of the experimental results for all but the tag condition. Relative drag increase predicted by the simulation vs. experiment, respectively, differed by between 21% and 31%: tag , 4% vs. 33%; tag + 4 , 47% vs. 68%; and tag + 8 , 108% vs. 77%. The results from this work provide a direct comparison of computational and experimental estimates of drag, and provide a framework to quantify uncertainty.
Description of a New Species of Ponyfish (Teleostei: Leiognathidae: Equulitini: Photolateralis) from the Gulf of Oman

A new species belonging to the leiognathid genus Photolateralis, collected from the coastal waters of Oman, is described herein. Photolateralis is unique among leiognathid genera in possessing a species-specific translucent midlateral flank stripe that may be comprised of either multiple independent translucent windows (P. stercorarius, P. moretoniensis, and the new species) or a continuous translucent lateral band (P. antongil). Photolateralis polyfenestrus, new species, is distinguished from congeners by the presence of a short, composite midlateral stripe comprised of three small, rounded translucent windows (vs. numerous windows in both P. stercorarius and P. moretoniensis, or a continuous translucent stripe in P. antongil), and that is confined to the midflank (vs. extending a majority of the length of the flank in congeners). The new species is further distinguished from both P. moretoniensis and P. antongil by a shallower body, and from both P. stercorarius and P. moretoniensis by a pigmentation pattern above the lateral midline comprised primarily of larger rounded blotches (vs. smaller sinuous lines and markings comprising a vermiculated pattern). Photolateralis polyfenestrus is characterized by a lower jaw that is deep and convex in lateral view (vs. mostly straight in congeners, excluding P. antongil), and that forms an angle of between 60°–70° to horizontal (vs. less than 45° in congeners, excluding P. antongil). The only other species of Photolateralis reported from the Western Indian Ocean is P. antongil, to date only known from the coastal waters of Madagascar, whereas both P. stercorarius and P. moretoniensis have ranges restricted to the western Pacific and extending into the eastern Indian Ocean.
CONTROL OF THE ROOT ROT DISEASES OF WHEAT USING FUNGICIDES ALONE AND IN COMBINATIONS WITH SELENIUM

Five fungicides (tebuconazole, fludioxonil, iprodione, azoxystrobin and flutolanil) were evaluated separately or in mixtures with the antioxidant (selenium) against Fusarium graminearum and Rhizoctonia solani which causing root rot diseases of wheat. Depend upon EC50 values of the tested fungicides, the in vitro studies showed that the descending order of fungicidal activity against F.graminearum growth was as follows;fludioxonil> tebuconazole > iprodione > azoxystrobin > flutolanil, while it was flutolanil >fludioxonil> tebuconazole > iprodione > azoxystrobin against R. solani growth.The two fungi tolerated high concentration of selenium. Interestingly, the fungitoxic activities of the tested fungicides were greatly increased by adding selenium to the fungicide- amended medium. In greenhouse trials, the fungicides were applied at rates of 1.5 and 3.0 g /kg seeds, while selenium was applied at 10 and 20 μg / ml (as seed treatments) alone or in combinations with fungicides for controlling root rot diseases. The results showed that all fungicides treatments significantly reduced diseases incidence and increased emergence and plant stands. Generally the addition of the antioxidant (Se) at 20μg / ml to the higher rate (3.0 g/kg seeds) of each fungicide caused significant reduction of the pre- and post- emergence damping off and subsequently increased plant survivals. However, the addition of Se to the low rate of each fungicide gave satisfactory fungicidal action as well as minimizing the environmental pollution.
Data-driven characterization of molecular phenotypes across heterogeneous sample collections

Abstract Existing large gene expression data repositories hold enormous potential to elucidate disease mechanisms, characterize changes in cellular pathways, and to stratify patients based on molecular profiles. To achieve this goal, integrative resources and tools are needed that allow comparison of results across datasets and data types. We propose an intuitive approach for data-driven stratifications of molecular profiles and benchmark our methodology using the dimensionality reduction algorithm t-distributed stochastic neighbor embedding (t-SNE) with multi-study and multi-platform data on hematological malignancies. Our approach enables assessing the contribution of biological versus technical variation to sample clustering, direct incorporation of additional datasets to the same low dimensional representation, comparison of molecular disease subtypes identified from separate t-SNE representations, and characterization of the obtained clusters based on pathway databases and additional data. In this manner, we performed an integrative analysis across multi-omics acute myeloid leukemia studies. Our approach indicated new molecular subtypes with differential survival and drug responsiveness among samples lacking fusion genes, including a novel myelodysplastic syndrome-like cluster and a cluster characterized with CEBPA mutations and differential activity of the S-adenosylmethionine-dependent DNA methylation pathway. In summary, integration across multiple studies can help to identify novel molecular disease subtypes and generate insight into disease biology.
PKD2 is an essential ion channel subunit in the primary cilium of the renal collecting duct epithelium

Mutations in either Pkd1 or Pkd2 result in Autosomal Dominant Polycystic Kidney Disease (ADPKD). Although PKD2 is proposed to be an ion channel subunit, recordings of PKD2 ion channels conflict in their properties. Using a new ADPKD mouse model, we observe primary cilia are abnormally long in cells associated with cysts. Using primary cultures of collecting duct epithelial cells, we show that PKD2, but not PKD1, is a required subunit for primary cilia ion channel. The ciliary PKD2 channel conducts potassium and sodium ions, but little calcium. We also demonstrate that PKD2 is not constitutively active in the plasma membrane, but PKD2 channels are functional in primary cilia and are sensitized by high cilioplasmic [Ca2+]. We introduce a novel method for measuring PKD2 channels heterologously expressed in primary cilia of HEK-293 cells, which will have utility characterizing Pkd2 variants that cause ADPKD in their native ciliary membrane.
Apparent total tract digestibility of nutrients and the digestible and metabolizable energy values of five unconventional feedstuffs fed to growing pigs

ABSTRACT This study was conducted to determine the nutrient profiles, the apparent total tract digestibility (ATTD) of nutrients and the digestible energy (DE) and the metabolizable energy (ME) values of five unconventional feedstuffs: highland barley (HB), buckwheat (BKW), glutinous broomcorn millet (GBM), non-glutinous broomcorn millet (NBM) and Chinese naked oat (CNO) fed to growing pigs. Thirty-six crossbred barrows were allotted to six dietary treatments in a completely randomized design including a corn-soybean meal basal diet and five test diets containing unconventional ingredients. The ATTD of nutrients and energy as well as the DE and ME values of the five ingredients were calculated using the difference method. Among the five unconventional feedstuffs, GBM had the greatest ATTD of dry matter (DM) and CP, and NBM had the greatest ATTD of organic matter (OM), ether extract (EE), and acid detergent fibre (ADF), while HB had the lowest ATTD of OM, DM, CP, and ADF. On DM basis, the DE and ME values for HB, BKW, GBM, NBM and CNO were 15.97–17.87 MJ/kg and 15.38–17.34 MJ/kg, respectively. From the nutritional point of view, those five unconventional feedstuffs especially the broomcorn millets could be potential replacements of corn in growing pig diets.
The effects of sample plot selection strategy and the number of sample plots on inoptimality losses in forest management planning based on airborne laser scanning data

In forest management planning, errors in predicted stand attributes might lead to suboptimal decisions that result in decreased net present value (NPV). Forest inventory data will have higher value if the amount of suboptimal decisions can be decreased. Therefore, the value of information can be measured through the decrease in inoptimality losses, which are the NPV differences between the optimal and suboptimal decisions. In this study, four alternative sample plot selection strategies with different numbers of sample plots were compared in terms of expected mean inoptimality losses. Stand-level mean inoptimality losses varied between €41.1·ha–1 and €80.7·ha−1, depending on the sample plot selection strategy and the number of sample plots used as training data in the k-nearest neighbors imputation method. Mean inoptimality losses decreased substantially when the number of sample plots increased from 25 to 100, and the decreasing trend continued until 500 sample plots. Total inoptimality losses can decrease by approximately €1 million in an inventory area of 100 000 ha when the number of sample plots is increased from 100 to 500. The measurement of more sample plots can be justified as long as the field measurement costs do not exceed the decrease in inoptimality losses.
Multi‐trophic β‐diversity mediates the effect of environmental gradients on the turnover of multiple ecosystem functions

Much effort has been devoted to better understanding the effects of environment and biodiversity on ecosystem functioning. However, few studies have moved beyond measuring biodiversity as species richness of a single group and/or focusing on a single ecosystem function. While there is a growing recognition that along environmental gradients, the compositional turnover of multiple trophic groups influences not only productivity but multiple ecosystem functions, we do not know yet which components of multi‐trophic β‐diversity influence which ecosystem functions. Here, we captured the biodiversity found in soils using environmental DNA to study total soil multi‐trophic β‐diversity (between all taxa regardless of their trophic group association), horizontal β‐diversities (β‐diversities within trophic groups) and vertical β‐diversity (β‐diversity across trophic groups) along a 1,000 m elevational gradient in the French Alps. Using path analyses, we quantified how these β‐diversity components mediate the effects of environmental turnover on the turnover of multiple ecosystem functions (i.e. productivity, N‐cycling, N‐leaching) and overall multifunctionality. While we found a strong direct effect of soil properties on the turnover of multiple ecosystem functions, we also found an indirect effect of climate and soil properties through multi‐trophic β‐diversity. More specifically, only total multi‐trophic β‐diversity and the horizontal β‐diversity of saprophytic fungi were strongly related to the turnover of multifunctionality and, to a lower extent, the turnover of productivity and N‐cycling. Our results suggest that decomposition processes and resulting nutrient availability are key to understand how ecosystem functions change along soil properties and climatic gradients in alpine ecosystems. By demonstrating how saprophytic fungi and their associated trophic groups can offset the direct responses of multiple ecosystem functions to environmental change, our study highlights the paramount importance of multi‐trophic diversity for better understanding ecosystem multifunctionality in a changing world. A free Plain Language Summary can be found within the Supporting Information of this article.
Transcriptional Architecture of Synaptic Communication Delineates Cortical GABAergic Neuron Identity

Understanding the organizational logic of neural circuits requires deciphering the biological basis of neuron type diversity and identity, but there is no consensus on defining a neuron type. We analyzed single cell transcriptomes of anatomically and physiologically characterized cortical ground truth populations and conducted a computational genomic screen for transcription profiles that distinguish them. We discovered that cardinal GABAergic neuron types are delineated by a transcriptional architecture that encodes their synaptic communication patterns. This architecture comprises 6 categories of ~40 gene families including cell adhesion molecules, transmitter-modulator receptors, ion channels, signaling proteins, neuropeptides and vesicular release components, and transcription factors. Combinatorial expression of select members across families shapes a multi-layered molecular scaffold along cell membrane that may customize synaptic connectivity patterns and input-output signaling properties. This molecular genetic framework of neuronal identity integrates cell phenotypes along multiple axes and provides a foundation for discovering and classifying neuron types.
Time preferences are reliable across time-horizons and verbal vs. experiential tasks

Individual differences in delay-discounting correlate with important real world outcomes, e.g. education, income, drug use, & criminality. As such, delay-discounting has been extensively studied by economists, psychologists and neuroscientists to reveal its behavioral and biological mechanisms in both human and non-human animal models. However, two major methodological differences hinder comparing results across species. Human studies present long time-horizon options verbally, whereas animal studies employ experiential cues and short delays. To bridge these divides, we developed a novel language-free experiential task inspired by animal decision-making studies. We find that subjects’ time-preferences are reliable across both verbal/experiential differences and also second/day differences. When we examined whether discount factors shifted or scaled across the tasks, we found a surprisingly strong effect of temporal context. Taken together, this indicates that subjects have a stable, but context-dependent, time-preference that can be reliably assessed using different methods; thereby, providing a foundation to bridge studies of time-preferences across species.