Miracle-dz/UniFAR-FTUs huggingface dataset:
Human Endometrial Transcriptome and Progesterone Receptor Cistrome Reveal Important Pathways and Epithelial Regulators

The endometrium undergoes highly dynamic modifications in a time and compartment specific manner during each menstrual cycle resulting in receptivity to embryo implantation during a discrete temporal window of implantation (WOI). Attainment of receptivity is strictly governed by the steroid hormone progesterone, which acts via the two isoforms of its nuclear Progesterone Receptor (PGR). In order to define the molecular mechanisms regulated by PGR in uterine receptivity, we conducted RNA-sequencing (RNA-seq) and PGR ChIP-sequencing (ChIP-seq) in endometrial biopsies taken from fertile women during the proliferative (P) and mid-secretory (MS) phases. Overlaying the genes with altered PGR binding and differential expression (DEGs) during the phase transition identified 653 genes, which are involved in inflammatory response signaling, xenobiotic metabolism, epithelial-mesenchymal transition (EMT), cell death regulation, interleukin/STAT signaling, estrogen response, as well as MTORC1 response. RNA-sequencing conducted using epithelium-derived RNA identified 3,052 DEGs in the epithelium, of which 658 were uniquely regulated in the epithelium. Transcription factors IRF8 and MEF2C were selected for validation and found to be regulated in the epithelium during the WOI at the protein level, suggesting potentially important functions that are previously unrecognized. In summary, we present herein data that expands our understanding of progesterone action in human endometrium during the WOI.
The effect of mung bean on improving dietary diversity in women and children in Senegal

Since 2015, a U.S. Agency for International Development (USAID) and Virginia Tech Education and Research in Agriculture (ERA) collaboration has introduced and tested mung bean as a potential crop to alleviate malnutrition and food insecurity in Senegal. This MS thesis describes a study conducted to assess the impact of mung bean on dietary diversity of Senegalese women and children in the Kaolack, Matam and Bakel localities of Senegal. A mixed-methods research approach included individual surveys to determine dietary diversity scores (DDS) and focus groups to assess the perceived impacts of mung bean. The dietary diversity survey was conducted with 194 participants including adult women, ages 15 to 70 years (n=109) and children, ages 0-10 years (n=85). Half (52%) of the population were mung bean consumers. The dietary diversity surveys revealed an average DDS of 5.73 on a scale of one to 10, with 5.83 and 5.62 for mung bean and non-mung bean-consuming groups, respectively. There was a statistically significant difference in DDS between mung bean consuming women and both mung bean and non-mung bean children, and between mung bean and non-mung bean consumers in Bakel; however, there was no significant difference between overall mung bean and non-mung bean groups DDS. Focus groups (n=11) with mung bean consuming women identified perceived agricultural, health, and financial benefits associated with mung bean consumption. These results can increase our understanding of how mung bean may influence policy-relevant issues for the Senegalese population, including agricultural, health and financial outcomes that are not reflected in dietary diversity surveys. The Effect of Mung Bean on Improving Dietary Diversity of Women and Children in Senegal
DELEGATION MODEL FOR CSCW BASED ON RBAC POLICIES AND VISUAL MODELING

Traditional access control of CSCW system is lack of delegation mechanism. For improving it and achieving resource share in the heterogeneous distributed environment, Role-Activity Based Delegation Model for CSCW (abbr. RABDM for CSCW) was presented based on RBAC policies and the important properties of activity, object-oriented visual modeling was also further represented using Unified Modeling Language. The model with time and constraint characters solves the issue of authorization centralization in the actual application of Graphics and Images Collaboration Processing System Based on CSCW, and realizes distributed and dynamic characters. Visual modeling also shortens the gap between the abstract theory model and implementation of the applied system, and benefits designing and development of systems based on the self-contained model. Keyword: access control; computer support cooperative work; role; delegation; constraint rule. * This work is partially supported by National Nature Science Foundation of China (Grant No.60475021), Henan Province Science Fund for Distinguished Young Scholars (Grant No.0412000400).
Calcium induces phytochelatin accumulation to cope with chromium toxicity in rice (Oryza sativa L.)

ABSTRACT Heavy metal chromium (Cr) is considered to be a serious environmental contaminant due to its toxic effect on living organisms. To mitigate and reduce the negative impacts of Cr in rice plant, the effect of exogenous supplementary calcium was evaluated as it functions as a signaling molecule at cellular level. In this study, growth parameters, protein content, and membrane stability were found to be restored due to calcium under Cr stress. Further, Atomic absorption spectrophotometric analysis revealed that calcium inhibits Cr translocation from root to shoot in rice seedlings. This event was addressed by the enhanced accumulation of phytochelatin that leads to vacuolar sequestration of Cr in roots. Furthermore, increased activity of Catalase, Peroxidase, and Glutathione reductase along with elevated glutathione also assures that calcium enhances antioxidant defense mechanism to cope with Cr toxicity.
Full-featured, real-time database searching platform enables fast and accurate multiplexed quantitative proteomics

Multiplexed quantitative analyses of complex proteomes enable deep biological insight. While a multitude of workflows have been developed for multiplexed analyses, the most quantitatively accurate method (SPS-MS3) suffers from long acquisition duty cycles. We built a new, real-time database search (RTS) platform, Orbiter, to combat the SPS-MS3 method’s longer duty cycles. RTS with Orbiter enables the elimination of SPS-MS3 scans if no peptide matches to a given spectrum. With Orbiter’s online proteomic analytical pipeline, which includes RTS and false discovery rate analysis, it was possible to process a single spectrum database search in less than 10 milliseconds. The result is a fast, functional means to identify peptide spectral matches using Comet, filter these matches, and more efficiently quantify proteins of interest. Importantly, the use of Comet for peptide spectral matching allowed for a fully featured search, including analysis of post-translational modifications, with well-known and extensively validated scoring. These data could then be used to trigger subsequent scans in an adaptive and flexible manner. In this work we tested the utility of this adaptive data acquisition platform to improve the efficiency and accuracy of multiplexed quantitative experiments. We found that RTS enabled a 2-fold increase in mass spectrometric data acquisition efficiency. Orbiter’s RTS was able to quantify more than 8000 proteins across 10 proteomes in half the time of an SPS-MS3 analysis (18 hours for RTS, 36 hours for SPS-MS3).
Beauty Is Our Business: A Birthday Salute to Edsger W.Dijkstra

More than anything else, this book is a tribute to Edsger W. Dijkstra, on the occasion of his sixtieth birthday, by just a few of those fortunate enough to be influenced by him and his work and to be called his friend or relation, his master, colleague, or pupil. This book contains fifty-four technical contributions in different areas of endeavor, although many of them deal with an area of particular concern to Dijkstra: programming. Each contribution is relatively short and could be digested in one sitting. Together, they form a nice cross section of the discipline of programming at the beginning of the nineties. While many know of Dijkstra's technical contributions, they may not be aware of his ultimate goal, the mastery of complexity in mathematics and computing science. He has forcefully argued that beauty and elegance are essential to this mastery. The title of this book, chosen to reflect his ultimate goal, comes from a sentence in an article of his on some beautiful arguments using mathematical induction: ". when we recognize the battle against chaos, mess, and unmastered complexity as one of computing sci- ence's major callings, we must admit that 'Beauty Is Our Business'. "
Variation in pollinator potential to carry a blueberry fungal pathogen and assessment of transfer efficiency in two managed bee species

Plant diseases are ubiquitous in agricultural systems and are major sources of economic loss. Vaccinium corymbosum, or highbush blueberry, is an economically important crop affected by an insect-vectored, fungal pathogen, Monilinia vaccinii-corymbosi, or mummy berry disease. Highbush blueberry yield is maximized through outcrossed pollination; however, the pathogen is vectored by pollinators. We used field collections and molecular techniques to identify floral visitors to highbush blueberry and quantify levels of pathogen spores carried by each visiting species. We also conducted a cage trial using single flower visits to determine differences in vectoring efficiency between two managed pollinators, Apis mellifera and Bombus impatiens. We found that bees, flies, and wasps were all common visitors, and that all bee species and several fly and wasp species carried the pathogen. Of the bee species, A. mellifera most often tested positive for the pathogen, while Dolichovespula maculata (Bald-faced Hornet) tested positive most among wasps and Mallota posticata among flies. Considering only individuals that tested positive, mummyberry levels per individual were highest in D. maculata and Andrena bees, and relatively low in flies. In cage trials, we found no differences between A. mellifera and B. impatiens in pathogen load or transfer efficiency, suggesting that these managed species are equally capable of vectoring mummyberry during a single visit to a blighted stem and then a flower. This research demonstrates the variety of floral visitors that carry mummyberry and that two common commercial pollinator species have similar potential to vector mummyberry to blueberry flowers during a single visit.
Magnetic-alignment of polymer macro-nanodiscs enables residual dipolar couplings based high-resolution structural studies by NMR.

Experimentally measured residual dipolar couplings (RDCs) are highly valuable for atomic-resolution structural and dynamic studies of molecular systems ranging from small molecules to large proteins by solution NMR spectroscopy. Here we demonstrate the first use of magnetic-alignment behavior of lyotropic liquid crystalline polymer macro-nanodiscs (> 20 nm in diameter) as a novel alignment medium for the measurement of RDCs using high resolution NMR. The easy preparation of macro-nanodiscs, high stability against pH and in presence of divalent metal ions, and high homogeneity will render a robust approach to investigate a wide range of molecular systems including natural products, proteins and RNA.
THE INFLUENCE OF BASE TEMPERATURE ON SWEET SORGHUM PRODUCTION IN HUNGARY

In order to reach the goal determined by the 2009/28/EU directive sorghum production for energy purposes can be an adequate method. Efficient sorghum production is based on the consideration of the climatic aspects. An advantage of sorghum is appearing in the field of drought tolerance. The foundation of sorghum’s great drought tolerance is the high heat demand which must be fulfilled. The heat demand varies from 8 °C to 15 °C, so that based on the meteorological data recorded in the period of 1997-2016 the Effective Heat Unit varied between 627 °C and 2097 °C. Base temperature has a remarkable impact on the length of the vegetation period as well. Depending on this value the potential length of the vegetation period can vary from 123 days to 153 days. The sugar accumulation curve of a sorghum hybrid is also an important aspect of efficient bioethanol production where length of the vegetation period is an essential factor.
Genetic control of transition from juvenile to mature wood with respect to microfibril angle (MFA) in Norway spruce (Picea abies) and lodgepole pine (Pinus contorta)

Genetic control of microfibril angle (MFA) transition from juvenile to mature was evaluated in Norway spruce and lodgepole pine. Increment cores were collected at breast height from 5,618 trees in two 21-year-old Norway spruce progeny trials in southern Sweden, and from 823 trees in two 34-35 – year-old lodgepole pine progeny trials in northern Sweden. Radial variations in MFA from pith to bark were measured for each core using SilviScan. To estimate MFA transition from juvenile to mature, a threshold level of MFA 20° was considered and six different regression functions were fitted to the MFA profile of each tree after exclusion of outliers, following three steps. The narrow-sense heritability estimates (h2) obtained for MFA transition were highest based on the slope function, ranging from 0.21 to 0.23 for Norway spruce and from 0.34 to 0.53 for lodgepole pine, while h2 were mostly non-significant based on the logistic function, under all exclusion methods. Results of this study indicate that it is possible to select for an earlier MFA transition from juvenile to mature in Norway spruce and lodgepole pine selective breeding programs, as the genetic gains (∆G) obtained in direct selection of this trait were very high in both species.
Water Use and Leaf Nutrient Status for Terraced Cherimoya Trees in a Subtropical Mediterranean Environment

Water scarcity in many semi-arid agricultural areas, in particular for the Mediterranean basin, is promoting changes in irrigated agriculture, with alternative strategies being introduced for water-use optimization. The coast of Granada and Malaga (Southeast Spain) is an economically important area for subtropical fruit cultivation. This intensively irrigated agriculture is characterized by requiring extra amounts of water and the adoption of sustainable practices to improve agricultural water management. A two-season experiment was conducted to assess (1) the water use in terraced cherimoya (Annona cherimola Mill. cv. Fino de Jete) orchards under conventional and organic production systems with drainage lysimeters, and (2) the impact on fruit yield and nutritional effects between the two considered production systems. Crop coefficient (Kc) values for cherimoya were 0.60–0.66, 0.64–0.71, and 0.48–0.62 at flowering, fruit set, and fruit growth, respectively. Fruit yield was similar in both systems, ranging from 47.1 for conventional to 44.1 kg tree−1 for organic farming, averaging 13.2 and 12.3 t·ha−1, respectively. No differences between these systems were observed in terms of leaf nutrient status, with variations in the N, P, and K contents during the different phenological stages. The N, P, and K lessen during flowering and fruit growth; the highest levels of these nutrients were fixed at harvest. These patterns were the opposite in Ca and Mg, ascribable to the antagonism between K and both Ca and Mg. Thus, these findings highlight the need to establish the optimal use of irrigation water with respect to crop requirements, thereby encouraging sustainable subtropical farming in terraces.
Stereoscopic Rendering in a Head Mounted Display Elicits Higher Functional Connectivity During Virtual Reality

Virtual reality (VR) simulates real world scenarios by creating a presence in users. Such immersive scenarios lead to more similar behaviour to that displayed in real world settings, which may facilitate the transfer of knowledge and skills acquired in VR to real world situations. VR has already been used in education, psychotherapy, rehabilitation and it is an appealing choice for training intervention. The aim was to investigate to what extend VR technology can be used in a magnetic resonance imaging scanner(MRI), addressing the question of whether brain connectivity differs between VR and screen via mirror projection presentations. Moreover, we investigate whether stereoscopic goggle stimulation, where eyes receive different input, would elicit more brain connectivity than stimulation where both eyes receive the same input (monoscopic). To our knowledge, there is no previous research addressing this question. Multiple analyses were performed to cover different aspects of brain connectivity: fractional low frequency fluctuation, independent component analysis, seed-based functional connectivity and graph analysis. In goggles (mono and stereoscopic) vs. screen, we found connectivity differences in cerebellum and postcentral gyrus and in visual and frontal inferior cortex in visual/default-mode networks. Considering specific areas, we found higher connectivity between superior frontal cortex and temporal lobe, as well as inferior parietal cortex with calcarine and lingual. Furthermore, superior frontal cortex and insula/putamen were more strongly connected in stereoscopic, in line with our hypothesis. We assume that conditions eliciting most connectivity should be suited for long-term interventions as extended training under these conditions could permanently improve functional/structural connectivity.
Dialyzable Leukocyte Extract (Transferon™) Administration in Sepsis: Experience from a Single Referral Pediatric Intensive Care Unit

Immunomodulatory agents have been proposed as therapeutic candidates to improve outcomes in sepsis. Transferon™, a dialyzable leukocyte extract (DLE), has been supported in Mexico as an immunomodulatory adjuvant in anti-infectious therapy. Here we present a retrospective study describing the experience of a referral pediatric intensive care unit (PICU) with Transferon™ in sepsis. We studied clinical and laboratory data from 123 patients with sepsis (15 in the DLE group and 108 in the control group) that were admitted to PICU during the period between January 2010 and December 2016. Transferon™ DLE use was associated with lower C reactive protein (CRP), increase in total lymphocyte counts (TLC), and decrease in total neutrophil count (TNC) 72 hours after Transferon™ DLE administration. The control group did not present any significant difference in CRP values and had lower TLC after 72 hours of admission. There was no difference in PICU length of stay between control and Transferon™ DLE group. Transferon™ DLE administration was associated with a higher survival rate at the end of PICU stay. This study shows a possible immunomodulatory effect of Transferon™ on pediatric sepsis patients.
Mitochondrial ubiquinone-mediated longevity is marked by reduced cytoplasmic protein translation

Mutations in the clk-1 gene impair mitochondrial ubiquinone biosynthesis and extend the lifespan of C. elegans. We demonstrate here that this life extension is linked to the repression of cytoplasmic protein translation. Clk-1 mutations inhibit polyribosome formation similarly to daf-2 mutations that dampen insulin signaling. Comparisons of total versus polysomal RNAs in clk-1 mutants reveal a reduction in the translational efficiencies of mRNAs coding for elements of the translation machinery and an increase in those coding for the oxidative phosphorylation and autophagy pathways. Knocking down the transcription initiation factor TAF-4, a protein that becomes sequestered in the cytoplasm during early embryogenesis to induce transcriptional silencing, ameliorates the clk-1 inhibition of polyribosome formation. These results underscore a prominent role for the repression of cytoplasmic protein translation in eukaryotic lifespan extension, and suggest that mutations impairing mitochondrial function are able to exploit this repression similarly to reductions of insulin signaling. Moreover, this report reveals an unexpected role for TAF-4 as a repressor of polyribosome formation when ubiquinone biosynthesis is compromised.
Two spatially distinct Kinesin-14 Pkl1 and Klp2 generate collaborative inward forces against Kinesin-5 Cut7 in S. pombe

Kinesin motors play central roles in bipolar spindle assembly. In many eukaryotes, spindle pole separation is driven by Kinesin-5 that generates outward force. This outward force is balanced by antagonistic inward force elicited by Kinesin-14 and/or Dynein. In fission yeast, two Kinesin-14s, Pkl1 and Klp2, play an opposing role against Kinesin-5/Cut7. However, how these two Kinesin-14s coordinate individual activities remains elusive. Here we show that while deletion of either pkl1 or klp2 rescues temperature sensitive cut7 mutants, only pkl1 deletion can bypass the lethality caused by cut7 deletion. Pkl1 is tethered to the spindle pole body, while Klp2 is localized along the spindle microtubule. Forced targeting of Klp2 to the spindle pole body, however, compensates for Pkl1 functions, indicating that cellular localizations, rather than individual motor specificities, differentiate between the two Kinesin-14s. Interestingly, human Kinesin-14/HSET can replace either Pkl1 or Klp2. Moreover, overproducing HSET induces monopolar spindles, reminiscent of the phenotype of Cut7 inactivation. Taken together, this study has uncovered the biological mechanism of how two different Kinesin-14s exert their antagonistic roles against Kinesin-5 in a spatially distinct manner. SUMMARY STATEMENT Proper force-balance generated by Kinesin-5 and Kinesin-14 is crucial for spindle bipolarity. Two fission yeast Kinesin-14s localize to different structures, thereby collaboratively producing inward forces against Kinesin-5-mediated outward force. Abbreviations used GBP GFP-binding protein MWP complex Msd1-Wdr8-Pkl1 complex SPB spindle pole body ts temperature sensitive γ-TuC the γ-tubulin complex
PHYTOPHTHORA CACTORUM (LEBERT & COHN) J. SCHRÖT AS CAUSAL AGENT OF DIEBACK OF CHESTNUT AND APPLE TREES IN MACEDONIA

From 2013–2017, 11 chestnut populations and 16 apple orchards/plantations in Macedonia were examined for health; soil, root and bark samples were collected from trees expressing symptoms regarded as Phytophthora specific. Using leaf baits of Prunus laurocerasus and selective V8 Agar (PARPNH), 19 pure Phytophthora sp. cultures were isolated and identified as P. cactorum by ITS sequencing. Sixteen isolates were from apple trees and 3 from chestnut trees. Phylogenetic analyses suggested slight distance between P. cactorum isolates originating from chestnut trees compared to those from apple orchards. Assessment of pathogenicity using chestnuts twigs showed no differences be-tween P. cactorum isolates from the two tree host species.
The genomic basis of evolved virus resistance is dependent on environmental resources

Parasites impose strong selection on their hosts, but the level of resistance evolved may be constrained by the availability of resources. However, studies identifying the genomic basis of such resource mediated selection are rare, particularly in non-model organisms. Here, we investigated the role of nutrition in the evolution of resistance to a DNA virus (PiGV), and associated trade-offs, in a lepidopteran pest species (Plodia interpunctella). Through selection experiments and whole genome sequencing we identify putative mechanisms of resistance that depend on the nutritional environment during selection. We find that the evolution of resistance is specific to diet, with adaptation to a low nutrition diet constraining resistance when challenged with the pathogen on a high nutrition diet. Resistance in a low nutrition environment is negatively correlated with growth rate, consistent with an established trade-off between immunity and development. Whole genome resequencing of the host shows that resistance mechanisms are highly polygenic and suggests evidence for trade-offs at the genetic level. Critically when populations evolve in high resource conditions, resistance is linked to metabolic and immune pathways, however it is more closely associated with cytoskeleton organisation when selected under low nutrition. Our results emphasise the importance of resources on the evolution of resistance.