Miracle-dz/UniFAR-FTUs huggingface dataset:
PENGARUH JENIS SUBSTRAT YANG BERBEDA TERHADAP SINTASAN DAN PERTUMBUHAN LOBSTER AIR TAWAR (Cherax quadricarinatus

The existence of freshwater crayfish in Indonesia is not well known among the community, even some people think that this type of lobster can only be obtained from catches. Freshwater lobster cultivators are always faced with the classic problem of low survival, especially during seed stages. The role of the water bottom substrate for freshwater crayfish is to support stabilizing water quality (temperature, pH, dissolved oxygen and ammonia levels). If the substrate condition of the habitat is not suitable, it can inhibit growth and even death. The purpose of this study is; to find out the effect of different basic substrates can increase the survival and growth of freshwater lobsters. The research method used a Completely Randomized Design (CRD) with 4 treatments 3 replications and 1 control. Each container is stocked with 2-inch lobster seeds with a density of 10 heads / container. The substrate application for each treatment is: A = Control, B = Land, C = Sand Malang, and D = Gravel. Based on the results of the research that has been done, it can be concluded that the administration of different substrates only shows significant differences in the survival variable, with the highest number of 96,67% in treatment C (Malang sand) and the lowest with 66,00% in treatment A (Control). While the variables of absolute weight, absolute length, and daily growth rate did not show significant differences in all treatments.
PATTIE: Publication access through tiered interaction & exploration

In this work we present Publication Access Through Tiered Interaction & Exploration (PATTIE) – an information foraging, sense-making, and exploratory spatial-semantic information retrieval (IR) system (http://pattie.unc.edu/plos). Non-spatial, spatial IR systems, and some recent studies focused on their principal functions are discussed and compared. To interactively work through a use-case from the biomedical domain, instructions are provided for readers to conduct exploratory searches directly on the PLOS archive based on the software embedded in the online version of this paper (http://vzlib.unc.edu/software/). To carefully evaluate some of the critical parameters of the PATTIE algorithm, and the core functions of the implemented system, a set of experiments were conducted. Along with details on the experimental methods and their rationale, key findings from the experiments are analyzed and presented. Finally, with an eye toward the future of software-embedded scientific papers, their potential benefits for supporting direct engagement with scientific content, replication, and validation are discussed.
Evaluation of Tulane Virus as a Surrogate for the study of Human Norovirus

Among all known causes of acute gastroenteritis, human noroviruses (HuNoV) are the primary cause (68%) of outbreaks and are associated with 78% of illnesses, 46% of hospitalizations, and 86% of deaths. The main obstacle to studying the pathogenesis of HuNoV is the lack of cell culture system and small animal model. Murine norovirus (MNV) and feline calicivirus (FCV) have been utilized as model surrogate viruses to study HuNoV. In this research, a more recent surrogate virus, Tulane virus (TV), was evaluated for physicochemical stability and environmental persistence. The primary goal was to determine the suitability of TV as a surrogate for HuNoV by comparing its environmental persistence and physicochemical stability to previously published results for MNV and FCV. Physicochemical profiles suggest that TV is more stable at 56, 63 and 72°C. When exposed to 60 and 70% ethanol concentrations at room temperature (RT), TV is more tolerant, but at 90% ethanol, TV is less tolerant. Tulane virus is also stable at acidic (2 and 3), neutral (7) and basic (9 and 10) pH levels though after 90 min there was a 2.25-log reduction in TV at pH 10. Last, TV is stable on a solid surface when exposed to 200 and 1000ppm chlorine for 10 min resulting in 0.63and 2.22-log10 reduction, respectively. For environmental persistence, TV can survive in surface water for 28 d with less than 0.3-log10 reduction at RT under diurnal variations. Conversely, TV is not persistence in groundwater in the dark at 4°C with a complete loss of infectivity after day 14. Tulane virus is also stable at RT on non-porous fomite surfaces (acrylic based solid surface and stainless steel surface) with only a 1log10 reduction at day 14. Comparing these observations and data published on TV elsewhere to previously published studies on MNV and FCV, it can be concluded that TV is likely a more conservative surrogate to study HuNoV though experimental differences make direct comparisons difficult.
Genetically Independent Tetranucleotide to Hexanucleotide Core Motif SSR Markers for Identifying Lentinula edodes Cultivars

Abstract For the purpose of protecting the rights of Lentinula edodes breeders, we developed a new simple sequence repeat (SSR) marker set consisting only of genetically independent tetranucleotide or longer core motifs. Using available genome sequences for five L. edodes strains, we designed primers for 13 SSR markers that amplified polymorphic sequences in 20 L. edodes cultivars. We evaluated the independence of every possible marker pair based on genotype data. Consequently, eight genetically independent markers were selected. The polymorphic information content values of the markers ranged from 0.269 to 0.764, with an average of 0.409. The markers could distinguish among 20 L. edodes cultivars and produced highly repeatable and reproducible results. The markers developed in this study will enable the precise identification of L. edodes cultivars, and may be useful for protecting breeders’ rights.
A Randomized Controlled Trial Evaluating Lanolin for the Treatment of Nipple Pain Among Breastfeeding Women

It is widely accepted that breast milk is the optimal source of infant nutrition. Despite the World Health Organization (WHO) recommendation of exclusive breastfeeding for the first 6 months of infant life, many women discontinue breastfeeding as a result of perceived difficulties. Nipple pain is a highly prevalent, significant reason for breastfeeding cessation. Among the numerous interventions for nipple pain, the application of lanolin is commonly recommended, with endorsement by Health Canada, The La Leche League, and International Board Certified Lactation Consultants. The few studies that have evaluated the effectiveness of lanolin on nipple pain have lacked methodologic rigor, and are thus not reliable or generalizable. As such, the purpose of this trial was to rigourously evaluate the effect of lanolin for the treatment of nipple pain among breastfeeding women. This single-site randomized controlled trial (RCT) compared the application of lanolin (treatment) to usual postpartum care (not applying lanolin) for the treatment of nipple pain. The primary outcome for this trial was the effect on pain severity, as measured by a numeric rating scale (NRS) at 4 days post-randomization. Of 186 participants, 93 were randomized to the treatment group and 93 to the usual care group. At 4 and 7 days post-randomization there were no statistically significant differences in pain scores between groups. It is noteworthy that by 7 days post-randomization there were clinically relevant decreases in nipple pain in both groups. However, there were no statistically significant differences between groups for other outcomes, including pain measured with the short-form McGill Pain Questionnaire, breastfeeding duration, breastfeeding exclusivity, and breastfeeding self-efficacy. Despite these findings, women in the treatment group were significantly more satisfied receiving lanolin for their nipple pain than those receiving usual care. Since the use of lanolin is no more effective than applying nothing to the nipples for the management of nipple pain, the widespread use of lanolin is questionable. Further research is required on the role of interventions to prevent nipple pain and damage, and the effect of anticipatory guidance on improving breastfeeding outcomes for those experiencing nipple pain in the early postpartum period. %%%%PhD
Hypophysis Size Evolution in Chiroptera

The hypophysis influences biological functions in mammals at various levels, and its volumetric variation in Chiroptera is recently well known. We explored the relation of the hypophysis size as a whole (Hyp) and its separate components, adenohypophysis (Adh) and neurohypophysis (Neh), from 96 species of bats (Yinpterochiroptera and Yangochiroptera), with social (roosting association), reproductive (testes mass, mating system, female promiscuity), body size (body mass) and foraging (diet) variables (when available for the sampled species), through ANCOVA and linear regressions analyses. We also explored the phylogenetic legacy of the volumetric changes of Hyp, Adh and Neh over a well-resolved phylogenetic tree, through Phylogenetically independent contrasts analysis, phylogenetic signal, and character optimizations. Hyp, Adh, Neh volumes and testes mass showed significant relation with body mass. When body mass effect was excluded, Hyp, Adh and Neh showed no significant relation with testes mass nor significant differences within roosting association, mating system and female promiscuity variables. However, Hyp, Adh and Neh volumes showed a pattern with diet, probably related to the regulatory role of the hypophysis at the endogenous protein metabolism in Mammals. The significant phylogenetic effect at linear regressions of Hyp, Adh and Neh volumes against body mass suggests the hypophysis volume and the body mass has coevolved, which was also supported by the significant phylogenetic signal and the optimizations considering body mass. Optimizations excluding body mass also showed significant phylogenetic signal, demonstrating that the volumetric changes bear phylogenetic information beyond body size. Our results suggest that the hypophysis size variations in bats are rather explained by phylogenetic legacy, as phylogenetic inertia linked to the ecology of the ancestors of the different clades, than current ecological aspects related to the natural history of the extant species.
Effect of cutting size on rooting ability and first year growth of Pinus thunbergii in nursery containers

ABSTRACT To improve the productivity of rooted cuttings in pine wilt disease-resistant Pinus thunbergii, the effect of cutting size on rooting ability and first year growth was studied. Sprouts collected as cuttings from four genetically different clones were assigned to various size combinations (five or six classes by diameter and four by length). One year after insertion, rooting percentages and height of rooted cuttings were measured and GLMM and LMM analyses applied to assess the effect of cutting size. Small diameter cuttings showed high rooting ability and lesser height, whereas large diameter cuttings showed low rooting ability and greater height. Therefore, results suggest there is an optimum intermediate diameter to maximise the productivity of rooted cuttings. Longer cuttings showed greater height but cutting length did not affect rooting ability. Rooting ability and first year growth differed among clones, suggesting that the optimum diameter for high productivity differs among clones, and highlighting the importance of selecting suitable clones to improve productivity.
Prostaglandins regulate invasive, collective border cell migration

While prostaglandins (PGs), short-range lipid signals, regulate cell migration, their mechanisms of action are poorly understood in collective migration. To address this, we use Drosophila border cell migration during Stage 9 of oogenesis. The border cells delaminate from the epithelium, and migrate collectively and invasively between the nurse cells. Pxt is the Drosophila cyclooxygenase-like enzyme responsible for all PG synthesis. Loss of Pxt results in both a significant delay in border cell migration during Stage 9 and an increase in cluster length compared to wild-type controls. Contributing to these phenotypes is altered integrin localization. Integrins are enriched on the border cell membranes, and this enrichment is lost in pxt mutants. Active integrins require interaction with the actin cytoskeleton. As we previously found PGs regulate the actin bundler Fascin and Fascin is required for border cell migration, we hypothesized PGs regulate Fascin to control integrins. Supporting this, loss of Fascin results in a pxt-like integrin localization, and dominant genetic interaction studies reveal that co-reduction of Pxt and Fascin results in delayed and elongated border cell clusters. Together these data lead to the model that PG signaling controls Fascin, and thereby integrins, to mediate on-time border cell migration and maintain cluster cohesion.
The neural signature of numerosity by separating numerical and continuous magnitude extraction in visual cortex with frequency-tagged EEG

Significance Approximating large quantities has been identified as a building block of mathematical cognition. Despite its importance from both a fundamental and an educational perspective, the mechanism behind this ability is still not fully understood. The remaining gap comes from the fact that a set is not only characterized by its number of objects but additionally by nonnumerical features naturally correlating with numerosity (e.g., a more numerous set occupies a larger surface). The current frequency-tagging EEG paradigm isolates specific responses to number and to nonnumerical dimensions. We demonstrate that when numerosity and the other dimensions are totally decorrelated in stimulus sequences, changes of each are automatically discriminated in early visual cortex, highlighting the status of numerosity as a primary visual feature. The ability to handle approximate quantities, or number sense, has been recurrently linked to mathematical skills, although the nature of the mechanism allowing to extract numerical information (i.e., numerosity) from environmental stimuli is still debated. A set of objects is indeed not only characterized by its numerosity but also by other features, such as the summed area occupied by the elements, which often covary with numerosity. These intrinsic relations between numerosity and nonnumerical magnitudes led some authors to argue that numerosity is not independently processed but extracted through a weighting of continuous magnitudes. This view cannot be properly tested through classic behavioral and neuroimaging approaches due to these intrinsic correlations. The current study used a frequency-tagging EEG approach to separately measure responses to numerosity as well as to continuous magnitudes. We recorded occipital responses to numerosity, total area, and convex hull changes but not to density and dot size. We additionally applied a model predicting primary visual cortex responses to the set of stimuli. The model output was closely aligned with our electrophysiological data, since it predicted discrimination only for numerosity, total area, and convex hull. Our findings thus demonstrate that numerosity can be independently processed at an early stage in the visual cortex, even when completely isolated from other magnitude changes. The similar implicit discrimination for numerosity as for some continuous magnitudes, which correspond to basic visual percepts, shows that both can be extracted independently, hence substantiating the nature of numerosity as a primary feature of the visual scene.
Spatial transitions in tree cover are associated with soil hydrology, but not with grass biomass, fire frequency, or herbivore biomass in Serengeti savannahs

Although there is a well‐known association between tree cover and soil texture in savannahs, the hydrological drivers of tree cover variation have not been systematically explored, particularly in parallel with factors such as fire, herbivory, and tree–grass interactions. The relationship between hydrological factors and tree cover is important for resolving the relative contribution of bottom‐up versus top‐down factors in structuring savannah vegetation. We quantified soil moisture dynamics across eight 1‐km transects spanning tree cover gradients from open to woody savannah in Serengeti National Park in Tanzania using soil moisture sensors coupled with dataloggers. We mapped tree cover at two spatial scales through supervised classification of high‐resolution satellite imagery. We simultaneously produced water retention curves in open and woody habitats within each transect to compare soil hydrological properties and to convert volumetric water content (θ) from dataloggers to plant‐available water over the course of an annual cycle. We also quantified grass biomass at 100 locations per transect, estimated fire frequency from MODIS satellite data, and quantified herbivore occupancy with paired camera traps situated in open and woody habitats within each transect. We found a positive relationship between tree cover and soil moisture drainage rate, and found that open habitats had more negative water potentials than woody habitats for a given value of θ. In contrast, we found no evidence for a consistent relationship between grass biomass or fire frequency and tree cover. We found evidence for higher browser occupancy in woody than open habitats, but no habitat effects on herbivores as a group (browsers plus grazers), suggesting that herbivory is unlikely to be the dominant factor explaining variation in tree cover. Synthesis. Our results suggest that variation in tree cover is partly driven by hydrological (edaphic) factors unrelated to fire, herbivory, tree–grass interactions or mean annual precipitation at these spatial scales in Serengeti. We contrast our findings with previous work attributing tree cover shifts in Serengeti to precipitation gradients.
SALTClass: classifying clinical short notes using background knowledge from unlabeled data

Background With the increasing use of unstructured text in electronic health records, extracting useful related information has become a necessity. Text classification can be applied to extract patients’ medical history from clinical notes. However, the sparsity in clinical short notes, that is, excessively small word counts in the text, can lead to large classification errors. Previous studies demonstrated that natural language processing (NLP) can be useful in the text classification of clinical outcomes. We propose incorporating the knowledge from unlabeled data, as this may alleviate the problem of short noisy sparse text. Results The software package SALTClass (short and long text classifier) is a machine learning NLP toolkit. It uses seven clustering algorithms, namely, latent Dirichlet allocation, K-Means, MiniBatchK-Means, BIRCH, MeanShift, DBScan, and GMM. Smoothing methods are applied to the resulting cluster information to enrich the representation of sparse text. For the subsequent prediction step, SALTClass can be used on either the original document-term matrix or in an enrichment pipeline. To this end, ten different supervised classifiers have also been integrated into SALTClass. We demonstrate the effectiveness of the SALTClass NLP toolkit in the identification of patients’ family history in a Dutch clinical cardiovascular text corpus from University Medical Center Utrecht, the Netherlands. Conclusions The considerable amount of unstructured short text in healthcare applications, particularly in clinical cardiovascular notes, has created an urgent need for tools that can parse specific information from text reports. Using machine learning algorithms for enriching short text can improve the representation for further applications. Availability SALTClass can be downloaded as a Python package from Python Package Index (PyPI) website at https://pypi.org/project/saltclass and from GitHub at https://github.com/bagheria/saltclass.
Interleukin-2 druggability is modulated by global conformational transitions controlled by a helical capping switch

Significance An extensive body of work has revealed that the conformational plasticity of IL-2 plays an important role in targeting the IL-2 receptor signaling axis in both agonist and antagonist mode; however, a more detailed understanding of such processes is needed for actionable value in drug development. Using mouse IL-2 as a model, our current body of work combines methyl-based chemical exchange NMR spectroscopy (CPMG and CEST) with thermodynamic measurements and immunoassays to characterize a global conformational transition to a sparsely populated autoinhibited conformational state, together with its functional significance. Targeting this minor state through mutations and small molecules can be exploited to fine tune the affinity and selectivity for different IL-2 binding partners, toward engineering novel cytokine functions. Interleukin-2 (IL-2) is a small α-helical cytokine that regulates immune cell homeostasis through its recruitment to a high-affinity heterotrimeric receptor complex (IL-2Rα/IL-2Rβ/γc). IL-2 has been shown to have therapeutic efficacy for immune diseases by preferentially expanding distinct T cell compartments, and several regulatory T cell (Treg)-biasing anti–IL-2 antibodies have been developed for combination therapies. The conformational plasticity of IL-2 plays an important role in its biological actions by modulating the strength of receptor and drug interactions. Through an NMR analysis of milliseconds-timescale dynamics of free mouse IL-2 (mIL-2), we identify a global transition to a sparse conformation which is regulated by an α-helical capping “switch” at the loop between the A and B helices (AB loop). Binding to either an anti-mouse IL-2 monoclonal antibody (mAb) or a small molecule inhibitor near the loop induces a measurable response at the core of the structure, while locking the switch to a single conformation through a designed point mutation leads to a global quenching of core dynamics accompanied by a pronounced effect in mAb binding. By elucidating key details of the long-range allosteric communication between the receptor binding surfaces and the core of the IL-2 structure, our results offer a direct blueprint for designing precision therapeutics targeting a continuum of conformational states.
Passenger mutations confound phenotypes of SARM1-deficient mice

The Toll/IL-1R domain-containing adaptor protein SARM1 is expressed primarily in the brain, where it mediates axonal degeneration. Additional roles for SARM1 in a number of other processes including TLR-signaling, viral infection, chemokine expression, and expression of the proapoptotic protein XAF1 have also been described. Much of the supporting evidence for SARM1 function has been generated by comparing WT C57BL/6 (B6) mice to SARM1-deficient mice backcrossed to the B6 background. Here we show that the Sarm1 gene lies in a gene-rich region encompassing XAF1, and the MIP and MCP chemokine family loci among other genes. Because gene-targeting of SARM1-deficient strains was done with 129 ES cells and these genes are too close to segregate, they remain 129 in sequence. As this could account for phenotypes attributed to SARM1, we generated new knockout mouse strains on a pure B6 background using CRISPR. Experiments in these new strains confirmed the role of SARM1 in axonal degeneration and susceptibility to WNV infection, but not in susceptibility to VSV or LACV infection, or chemokine or Xaf1 expression. Notably, the Xaf1 gene shows sequence variation between B6 and 129, resulting in coding changes and novel splice variants. Given its known role in apoptosis, XAF1 variants may account for some phenotypes described in previously made SARM1-deficient strains. RNAseq in the new strains reveal changes in the mitochondrial electron transport chain and ribosomal proteins, suggesting possible downstream targets of SARM1. Re-evaluation of described phenotypes in these new strains will be critical for defining the function of SARM1.