Miracle-dz/UniFAR-FTUs huggingface dataset:
Modelling the production and species richness of wild mushrooms in pine forests of the Central Pyrenees in northeastern Spain

Multiple-use forestry requires comprehensive planning to maximize the utilization and sustainability of many forest resources whose growth and productivity are interconnected. Forest fungi represent an economically important nonwood forest resource that provides food, medicine, and recreation worldwide. A vast majority of edible and marketed forest mushrooms belong to fungi that grow symbiotically with forest trees. To respond to the need for planning tools for multiple-use forestry, we developed empirical models for predicting the production of wild mushrooms in pine forests in the South-Central Pyrenees using forest stand and site characteristics as predictors. Mushroom production and species richness data from 45 plots were used. A mixed modelling technique was used to account for between-plot and between-year variation in the mushroom production data. The most significant stand structure variable for predicting mushroom yield was stand basal area. The stand basal area associated with maximum mushroom .
Twist regulates Yorkie to guide lineage reprogramming of syncytial alary muscles

The genesis of syncytial muscles is typically considered as a paradigm for an irreversible developmental process. Notably, transdifferentiation of syncytial muscles is naturally occurring during Drosophila development. The ventral longitudinal heart-associated musculature (VLM) arises by a unique mechanism that revokes the differentiated fate from the so-called alary muscles and comprises at least two distinct steps: syncytial muscle cell fragmentation into single myoblasts and direct reprogramming into founder cells of the VLM lineage. Here we provide evidence that the mesodermal master regulator twist plays a key role during this reprogramming process. Acting downstream of Drosophila Tbx1 (Org-1) in the alary muscle lineage, Twist is crucially required for the derepression of the Hippo pathway effector Yki and thus for the initiation of syncytial muscle dedifferentiation and fragmentation. Subsequently, cell-autonomous FGFR-Ras-MAPK signaling in the resulting mono-nucleated myoblasts is maintaining Twist expression, thereby stabilizing nuclear Yki activity and inducing their lineage switch into the founder cells of the VLM.
Nutritional "Omics" Technologies for Elucidating the Role(s) of Bioactive Food Components in Colon Cancer Prevention

The B vitamin folate is essential for one-carbon transfer reactions, including those related to the methylation of DNA or other substrates and nucleotide synthesis. Epidemiologic and experimental studies impli- cate low-folate intakes in elevated risk of colorectal neoplasia and suggest that biologic mechanisms underlying this relation include disturbances in DNA methylation patterns or adverse effects on DNA synthesis and repair. With the completion of the Human Genome Project, a vast amount of data on inherited genetic variability has become available. This genetic information can be used in studies of molecular epidemiology to provide information on multiple aspects of folate metabolism. First, studies linking polymorphisms in folate metabolism to an altered risk of cancer provide evidence for a causal link between this pathway and colorectal carcinogenesis. Second, studies on genetic characteristics can help clarify whether certain individuals may benefit from higher or lower intakes of folate or nutrients relevant to folate metabolism. Third, studies on genetic polymorphisms can generate hypotheses regarding possible biologic mechanisms that connect this pathway to carcinogenesis. Last, genetic variability in folate metabolism may predict survival after a cancer diagnosis, possibly via pharmacogenetic effects. To solve the puzzle of the folate-cancer relation, a transdisciplinary approach is needed that integrates knowledge from epidemiology, clinical studies, experimental nutrition, and mathematical modeling. This review illustrates knowl- edge that can be gained from molecular epidemiology in the context of nutrigenetics, and the questions that this approach can answer or raise. J. Nutr. 135: 2698-2702, 2005.
SCAR: Sentence Compression using Autoencoders for Reconstruction

Sentence compression is the task of shortening a sentence while retaining its meaning. Most methods proposed for this task rely on labeled or paired corpora (containing pairs of verbose and compressed sentences), which is often expensive to collect. To overcome this limitation, we present a novel unsupervised deep learning framework (SCAR) for deletion-based sentence compression. SCAR is primarily composed of two encoder-decoder pairs: a compressor and a reconstructor. The compressor masks the input, and the reconstructor tries to regenerate it. The model is entirely trained on unlabeled data and does not require additional inputs such as explicit syntactic information or optimal compression length. SCAR’s merit lies in the novel Linkage Loss function, which correlates the compressor and its effect on reconstruction, guiding it to drop inferable tokens. SCAR achieves higher ROUGE scores on benchmark datasets than the existing state-of-the-art methods and baselines. We also conduct a user study to demonstrate the application of our model as a text highlighting system. Using our model to underscore salient information facilitates speed-reading and reduces the time required to skim a document.
The Effect of Clinically Controllable Factors on Neural Activation During Dorsal Root Ganglion Stimulation

Dorsal root ganglion stimulation (DRGS) is an effective therapy for chronic pain, though its mechanisms of action are unknown. Currently, we do not understand how clinically controllable parameters (e.g., electrode position, stimulus pulse width) affect the direct neural response to DRGS. Therefore, the goal of this study was to utilize a computational modeling approach to characterize how varying clinically controllable parameters changed neural activation profiles during DRGS.
Pastures seedbank composition in relation to soil nutrient content in areas under goat grazing management (Tenerife)

Seed bank composition is an important part of the plant community that should be analyzed in order to understand the dynamic processes related to the plant community (germination, recruitment, species composition, etc.). We have analyzed the seed bank composition in a pasture community of Tenerife, one of the richest communities of the archipelago with a high environmental and social importance due to the dependence of local population of the maintenance of the pastures and because the unquestionable inheritage value. We analyzed the soils seed bank composition in ten plots (replicated in three seed banks) in the area with different soil nutrient composition. Soil nutrient composition of the plots was also analyzed. Our results revealed that the density of leguminous in the plots can be explained due to P and pH, while grasses can be explained by CIC and pH and th e other group of species (non-grasses and leguminous) by K and EC. The analysis of species composition in relation to the nutrient content of the soils revealed a big heterogeneity. Because there is broad soil variability in the pastures, a high number of species are found. High number of grasses was found in different situations, as in poor soils and very rich soils, and in other groups. This diversity can be very useful in order to manage the pastures for the maintenance of local activity as goat grazing.
Individual and combined effects of disturbance and N addition on understorey vegetation in a subarctic mountain birch forest

Questions: What are the effects of repeated disturbance and N-fertilization on plant community structure in a mountain birch forest? What is the role of enhanced nutrient availability in recovery of understorey vegetation after repeated disturbance? How are responses of soil micro-organisms to disturbance and N-fertilization reflected in nutrient allocation patterns and recovery of understorey vegetation after disturbance? Location: Subarctic mountain birch forest, Finland. Methods: We conducted a fully factorial experiment with annual treatments of disturbance (two levels) and N-fertilization (four levels) during 1998‐2002. We monitored treatment effects on above-ground plant biomass, plant community structure and plant and soil nutrient concentrations. Results: Both disturbance and N-fertilization increased the relative biomass of graminoids. The increase of relative biomass of graminoids in the disturbance treatment was over twice that of the highest N-fertilization level, and Nfertilization further increased their relative biomass after disturbance. As repeated disturbance broke the dominance of evergreen dwarf shrubs, it resulted in a situation where deciduous species, graminoids and herbs dominated the plant community. Although relative biomass of deciduous dwarf shrubs declined with N-fertilization, it did not cause a shift in plant community structure, as evergreen dwarf shrubs remained dominant. Both disturbance and N-fertilization increased the N concentration in vascular plants, whereas microbial biomass N and C were not affected by the treatments. Concentrations of NH4 , dissolved organic N (DON) and dissolved organic C (DOC) increased in the soil after N-fertilization, whereas concentrations of NH4 and DON decreased after disturbance. Conclusions: Disturbances caused by e.g. humans or herbivores contribute more to changes in the understorey vegetation structure than increased levels of N in subarctic vegetation. Fertilization accelerated the recovery potential after repeated disturbance in graminoids. Microbial activities did not limit plant growth.
Ethylene Exposure Duration Affects Postharvest Needle Abscission in Balsam Fir (Abies balsamea L.)

Needle loss after harvest is a major problem for Atlantic Canada's Christmas tree and greenery industry. Ethylene is a signal for abscission in balsam fir, but preliminary studies have suggested that the role of ethylene may be influenced by length of exposure. Short-term and long-term ethylene exposure experiments were conducted. Branches were exposed to ethylene for 24 h (short-term) or continuously (long-term) at concentrations of 0 to 1000 ppm. The response variables measured were needle retention duration (NRD), average water use (AWU), and xylem pressure potential (XPP). Short- term exposure to any concentration of ethylene delayed needle abscission by 30 to 40 days. In contrast, long-term exposure to all concentrations of ethylene accelerated abscission, most evident by a 21-day decrease in NRD at 1000 ppm ethylene. There was a 60% decrease in NRD, 160% decrease (more negative) in XPP, and 80% increase in AWU as a result of long-term exposure to ethylene. Overall, our results demonstrate an opposite effect of short-term and long-term ethylene exposure, which suggests that short- term exposure to ethylene might help to precondition balsam fir and delay needle abscission during postharvest handling. Balsam fir is a tree typically found in eastern to central Canada and northeastern United States (Burns and Honkala, 1990). Balsam fir is also the principal Christmas tree species grown in Atlantic Canada (a region that includes the provinces of Nova Scotia, New Brunswick, Prince Edward Island, and Newfoundland). Over three million trees are harvested annually from Atlantic Canada, val- ued at $72 million. Of these trees, over 80% of all balsam fir are shipped to the United States (CTCNS, 2009). Balsam fir trees are preferred by consumers for their unique fragrance, color, and needle density (Burns and Honkala, 1990). To meet demands, balsam fir harvest begins in mid-October, although trees are expected to remain in good condition until the end of December. Unfortunately, balsam fir trees suffer from inferior needle retention compared with many other species used as Christmas trees. It has been estimated that as many as one in three balsam fir trees harvested in October will not last until the end of December (MacDonald and Lada, 2008). Postharvest needle loss between October and December is threatening the Christmas tree industry, largely as a result of decreasing tolerance from consumers toward needle loss and increased competition from artificial trees (Davis, 1996). Identifying the physiological mechanism of needle abscission in balsam fir has been difficult as a result of complications from several other factors. For example, there is considerable genetic variation in needle re- tention characteristics. An experiment by MacDonald and Lada (2008) screened 197
Mmu_circ_003795 regulates osteoblast differentiation and mineralization in MC3T3-E1 and MDPC23 by targeting COL15A1

Circular RNAs (circRNAs) are a class of non-coding RNAs that exhibit important regulatory roles in various biological processes. However, the role of circRNAs and their potential role in osteoblast differentiation and mineralization is unclear. The aim of the present study was to investigate the expression of mmu_circ_003795 and its effect on collagen type XV α 1 chain (COL15A1). First, it was identified that the expression levels of mmu_circ_003795 and osteopontin (OPN) were upregulated in the induced cells. Silencing of mmu_circ_003795 reduced the gene and protein levels of COL15A1 and OPN, whereas the expression level of mmu-microRNA (miR)-1249-5p was upregulated. In addition, after 7 or 14 days of induction, alkaline phosphatase and Alizarin Red-S staining were decreased in the mmu_circRNA_003795 inhibitory group compared with the negative control group. In conclusion, mmu_circ_003795 may regulate osteoblast differentiation and mineralization in MC3T3-E1 and MDPC23 cells via mmu-miR-1249-5p by targeting COL15A1.
“Truly holistic?” Differences in documenting physical and psychosocial needs and hope in Portuguese palliative patients

Abstract Objective Palliative care (PC) aims to improve patients' and families' quality of life through an approach that relieves physical, psychosocial, and spiritual suffering, although the latter continues to be under-assessed and under-treated. This study aimed to describe the prevalence of physical, psychosocial, and hope assessments documented by a PC team in the first PC consultation. Method The retrospective descriptive analysis of all first PC consultations registered in our anonymized database (December 2018–January 2020), searching for written documentation regarding (1) Edmonton Symptom Assessment Scale (ESAS) physical subscale (pain, tiredness, nausea, drowsiness, appetite, shortness of breath, constipation, insomnia, and well-being), (2) the single question “Are you depressed? ” (SQD), (3) the question “Do you feel anxious? ” (SQA), (4) feeling a burden, (5) hope-related concerns, (6) the dignity question (DQ), and (7) will to live (WtL). Results Of the 174 total of patients anonymously registered in our database, 141 PC home patients were considered for analysis; 63% were male, average age was 70 years, the majority had malignancies (82%), with a mean performance status of 52%. Evidence of written documentation was (1) ESAS pain (96%), tiredness (89%), nausea (89%), drowsiness (79%), appetite (89%), shortness of breath (82%), constipation (74%), insomnia (72%), and well-being (52%); (2) the SQD (39%); (3) the SQA (11%); (4) burden (26%); (5) hope (11%); (6) the DQ (33%); and (7) WtL (33%). Significant differences were found between the frequencies of all documented items of the ESAS physical subscale (29%), and all documented psychosocial items (SQD + SQA + burden + DQ) (1%), hope (11%), and WtL (33%) (p = 0.0000; p = 0.0005; p = 0.0181, respectively). Significance of results There were differences between documentation of psychosocial, hope, and physical assessments after the first PC consultation, with the latter being much more frequent. Further research using multicenter data is now required to help identify barriers in assessing and documenting non-physical domains of end-of-life experience.
Using PRMSE to evaluate automated scoring systems in the presence of label noise

The effect of noisy labels on the performance of NLP systems has been studied extensively for system training. In this paper, we focus on the effect that noisy labels have on system evaluation. Using automated scoring as an example, we demonstrate that the quality of human ratings used for system evaluation have a substantial impact on traditional performance metrics, making it impossible to compare system evaluations on labels with different quality. We propose that a new metric, PRMSE, developed within the educational measurement community, can help address this issue, and provide practical guidelines on using PRMSE.
Soft tissue discrimination with contrast agents using micro-CT scanning

The use of high resolution, three-dimensional visualization has been receiving growing interest within life sciences, with non-invasive imaging tools becoming more readily accessible. Although initially useful for visualizing mineralized tissues, recent developments are promising for studying soft tissues as well. Especially for micro-CT scanning, several X-ray contrast enhancers are performant in sufficiently contrasting soft tissue organ systems by a different attenuation strength of X-rays. Overall visualization of soft tissue organs has proven to be possible, although the tissue-specific capacities of these enhancers remain unclear. In this study, we tested several contrast agents for their usefulness to discriminate between tissue types and organs, using three model organisms (mouse, zebrafish and Xenopus ). Specimens were stained with osmium tetroxide (OsO4), phosphomolybdic acid (PMA) and phosphotungstic acid (PTA), and were scanned using high resolution microtomography. The contrasting potentials between tissue types and organs are described based on volume renderings and virtual sections. In general, PTA and PMA appeared to allow better discrimination. Especially epithelial structures, cell-dense brain regions, liver, lung and blood could be easily distinguished. The PMA yielded the best results, allowing discrimination even at the level of cell layers. Our results show that those staining techniques combined with micro-CT imaging have good potential for use in future research in life sciences.
Influenza-associated Fulminant Myocarditis Complicated by Guillain-Barré Syndrome

We herein report the case of a 47-year-old woman who was admitted with weakness and numbness of the limbs and dyspnea after being infected with influenza virus A. She had a history of Guillain-Barré syndrome (GBS) 7 years prior to this presentation. On admission, she was in shock, and transthoracic echocardiography showed severely reduced left-ventricular function. She was diagnosed with fulminant myocarditis by an endomyocardial biopsy, which was complicated by GBS. Venoarterial extracorporeal membrane oxygenation was required to manage the cardiogenic shock. After her condition improved, immunoadsorption for GBS was performed, and the motor and sensory disorders gradually improved.
Experimental evaluation of stiffness predictions of multiaxial flax fibre composites by classical laminate theory

Despite the good mechanical properties of natural fibre composites, their use in load-bearing components is still limited, which may be due to lack of knowledge and confidence in calculating the performance of the composites by mechanical models. The present study is providing an experimental evaluation of stiffness predictions of multiaxial flax fibre composite by classical laminate theory (CLT). The experimental base is (i) multiaxial flax fibre composites fabricated with two types of biaxial non-crimp fabrics, having a nominal yarn orientation of ±45°, and (ii) uniaxial flax fibre composites fabricated with the same flax yarn as used in the fabrics. The fabricated composites are characterised by volumetric composition, yarn orientation and tensile properties. A fast and easy operational Fast Fibre Orientation (FFO) method is developed to determine the actual yarn orientation in fabrics and composites. It is demonstrated that the FFO method is a robust method, giving repeatable results for yarn orientations, and it can be used both on fabrics and composites. CLT predictions of stiffness of the multiaxial flax fibre composites are shown to be in good agreement with the measured stiffnesses of the composites in three testing directions (0°, 45°, and 90°). The use of the actual yarn orientations measured by the FFO method, instead of the nominal yarn orientations of ±45°, is shown to result in improved CLT predictions of stiffness with a mean deviation between predictions and measurements on 0.2 GPa. Altogether, it is demonstrated that stiffness of multiaxial flax fibre composites can be accurately predicted by CLT, without any fitting constants, based on independently determined stiffness parameters of the related uniaxial flax fibre composite, and based on measured yarn orientations in the flax fibre fabric.
The pre‐B cell receptor and its ligands – it takes two to tango

DFG Training Program GK592, Nikolaus Fiebiger Center for Molecular Medicine, University ofErlangen and Nurnberg, GermanyThe development of early precursor B cells is governed by the surface-bound pre-B cell receptorconsisting of the immunoglobulin µ heavy chain, the surrogate light chain components λ5andVpreB, and the signal transducing subunits immunglobulin α/immunglobulin β. The pre-B cell re-ceptor controls clonal expansion, survival and efficient differentiation of functional B lymphoid pre-cursors; however, it is still controversial how signals from this receptor are initiated. Recent studieswith Abelson murine leukemia virus (Abl-MuLV)-transformed pre-B cell lines suggest that the N-terminal non-immunoglobulin portion of λ5, the so-called unique tail, is required to initiate cell-autonomous signals by mediating self-aggregation of the pre-B cell receptor (pre-BCR). Strikinglyhowever, the λ5 unique tail also controls the interaction with two different groups of stroma cell-derived pre-BCR ligands, namely heparan sulfate glycosaminoglycans and surface-associated ga-lectin-1. Even though these findings are not mutually exclusive, they refresh the discussion aboutpotential modes of pre-BCR signal initiation. In this review, we discuss recent key findings andpropose an integrative model for ligand dependent and independent initiation of pre-BCR signalsduring selection of functional B cell precursors.
The Effect of Chronic Methamphetamine Treatment on Schizophrenia Endophenotypes in Heterozygous Reelin Mice: Implications for Schizophrenia

Reelin has been implicated in the development of schizophrenia but the mechanisms involved in this interaction remain unclear. Chronic methamphetamine (Meth) use may cause dopaminergic sensitisation and psychosis and has been proposed to affect brain dopamine systems similarly to changes seen in schizophrenia. We compared the long-term effect of chronic Meth treatment between heterozygous reelin mice (HRM) and wildtype controls (WT) with the aim of better understanding the role of reelin in schizophrenia. Meth pretreatment induced sensitisation to the effect of an acute Meth challenge on locomotor activity, but it had no effect on baseline PPI or sociability and social preference. In all behavioural models, HRM did not significantly differ from WT at baseline, except spontaneous exploratory locomotor activity which was higher in HRM than WT, and sociability which was enhanced in HRM. Locomotor hyperactivity sensitisation was not significantly different between HRM and WT. Chronic Meth treatment reduced spontaneous locomotor activity to the level of WT. No deficits in PPI or social behaviour were induced by chronic Meth pretreatment in either strain. In conclusion, these data do not support a role of reelin in schizophrenia, at least not in HRM and in the methamphetamine sensitisation model.