Miracle-dz/UniFAR-FTUs huggingface dataset:
The role of floral traits in community assembly process at high elevations in Lesser Himalaya

Ecological theory postulates that plant trait research should consider multiple traits related to different organs and/or ontogenetic stages as such traits represent different ecological niche axes. Particularly, floral traits have been suggested to play an important role in assembling plant communities along environmental gradients as they determine the reproductive success, one of the key functions in plants. Yet, the predictive power of floral traits in community assembly research remains largely unverified empirically. We analyzed the predictive power of six floral traits of 139 herbaceous species for inferring community assembly process in twenty-one sites located along an elevation gradient in Lesser Himalaya ranging from 2,000 to 4,000 meters above sea level. The floral trait variability along the gradient was analyzed using community-weighted trait mean (CWM) values and functional diversities (FD) calculated for each of the study communities. The CWM values for onset of flowering and flower display area increased significantly with increasing elevation, whereas specific flower area showed an opposite pattern. In combination with convergence in onset of flowering and specific area (i.e., lower FD values in high elevation sites), these patterns suggest that abiotic filtering and plant-pollinator interactions affected the floral trait composition of the communities studied. Increasing low-temperature stress towards high-elevation sites selected for late-flowering species that produce resource-intensive flowers with larger display areas. Low pollinator abundancy and activity in high elevation, could also explain why these traits were selected in the study communities. Delayed flowering with increasing elevations might facilitate the phenological overlap of plants and their pollinators, as pollinator activity at higher elevation peaks in the second half of the vegetation period. The dominance of species with low specific flower area and larger display area in high elevation communities were attributed to the increased flower longevity and attraction of pollinators, respectively, to maximize pollination success under pollinator scarcity. Synthesis. Our study provides empirical support of the recent argument that floral traits contribute considerably to the assembly of plant communities along environmental gradients. Thus, such traits should be included into community assembly research agenda as they represent key growth and survival ecological functions.
Using Biometric Data to Measure and Predict Emotional Engagement of Video Games

Measurement and prediction of engagement in video games are very important because these are indicators to guide the development of game applications. Existing methods to predict game engagement are mostly based on subjective evaluations. This paper presents results correlating subjective and biometric data to show the potential of using biometric measures for assessment and prediction of engagement. Using three different games, we measured the biometric responses of participants and analyzed the responses using statistical and data mining methods. We compared the results with those obtained using subjective evaluations. Our results show that biometric measurements do correlate with subjective measures and better predict the self-reported engagement of a game.
Discovery of compounds that inhibit SARS-CoV-2 Mac1-ADP-ribose binding by high-throughput screening

The emergence of several zoonotic viruses in the last twenty years, especially the pandemic outbreak of SARS-CoV-2, has exposed a dearth of antiviral drug therapies for viruses with pandemic potential. Developing a diverse drug portfolio will be critical for our ability to rapidly respond to novel coronaviruses (CoVs) and other viruses with pandemic potential. Here we focus on the SARS-CoV-2 conserved macrodomain (Mac1), a small domain of non-structural protein 3 (nsp3). Mac1 is an ADP-ribosylhydrolase that cleaves mono-ADP-ribose (MAR) from target proteins, protects the virus from the anti-viral effects of host ADP-ribosyltransferases, and is critical for the replication and pathogenesis of CoVs. In this study, a luminescent-based high-throughput assay was used to screen ∼38,000 small molecules for those that could inhibit Mac1-ADP-ribose binding. We identified 5 compounds amongst 3 chemotypes that inhibit SARS-CoV-2 Mac1-ADP-ribose binding in multiple assays with IC50 values less than 100µM, inhibit ADP-ribosylhydrolase activity, and have evidence of direct Mac1 binding. These chemotypes are strong candidates for further derivatization into highly effective Mac1 inhibitors.
Structural motifs for subtype-specific pH-sensitive gating of vertebrate otopetrin proton channels

Otopetrin (OTOP) channels are proton-selective ion channels conserved among vertebrates and invertebrates and with no structural similarity to other ion channels. There are three vertebrate OTOP channels (OTOP1, OTOP2, and OTOP3), of which one (OTOP1), functions as a sour taste receptor. Whether OTOP channels are gated by, as well as permeating, protons was not known. Here, by comparing functional properties of the three vertebrate proton channels with patch-clamp recording and cytosolic pH microfluorimetry, we provide evidence that each is gated by external protons. OTOP1 and OTOP3 are both activated by extracellular protons, with a sharp threshold of pHe <6.0 and 5.5 respectively, while OTOP2 is negatively gated by protons, and more conductive at alkaline extracellular pH (>pH 9.0). Strikingly, we found that we could change pH-sensitive gating of OTOP2 and OTOP3 channels by swapping extracellular linkers that connect transmembrane domains. Swaps of linkers within the N domain changed the relative conductance at alkaline pH, while swaps within the C domain tended to change the rates of OTOP3 current activation. We conclude that members of the OTOP channel family are proton-gated (acid-sensitive) proton channels and that the gating apparatus is distributed across multiple extracellular regions within both the N and C domains of the channels. In addition to the taste system, OTOP channels are found in the vestibular and digestive systems, where pH sensitivity may be tuned to specific functions.
Identification of protein aggregates in the aging vertebrate brain with prion-like and phase separation properties

Protein aggregation, which can sometimes spread in a prion-like manner, is a hallmark of neurodegenerative diseases. However, whether prion-like aggregates form during normal brain aging remains unknown. Here we use quantitative proteomics in the African turquoise killifish to identify protein aggregates that accumulate in old vertebrate brains. These aggregates are enriched for prion-like RNA binding proteins, notably the ATP-dependent RNA helicase DDX5. We validate that DDX5 forms mislocalized cytoplasmic aggregates in the brains of old killifish and mice. Interestingly, DDX5’s prion-like domain allows these aggregates to propagate across many generations in yeast. In vitro, DDX5 phase separates into condensates. Mutations that abolish DDX5 prion propagation also impair the protein’s ability to phase separate. DDX5 condensates exhibit enhanced enzymatic activity, but they can mature into inactive, solid aggregates. Our findings suggest that protein aggregates with prion-like properties form during normal brain aging, which could have implications for the age-dependency of cognitive decline.
Inducible CRISPR/Cas9 Allows for Multiplexed and Rapidly Segregated Single-Target Genome Editing in Synechocystis Sp. PCC 6803

Establishing various synthetic biology tools is crucial for the development of cyanobacteria for biotechnology use, especially tools that allow for precise and markerless genome editing in a time-efficient manner. Here we describe a riboswitch-inducible CRISPR/Cas9 system, contained on one single replicative vector, for the model cyanobacteria Synechocystis sp. PCC 6803. A theophylline-responsive riboswitch allowed tight control of Cas9 expression, which enabled reliable transformation of the CRISPR/Cas9 vector into Synechocystis. Induction of the CRISPR/Cas9 mediated various types of genomic edits, specifically deletions and insertions of varying size. The editing efficiency varied depending on the target and intended edit; smaller edits overall performed better, reaching e.g. 100% for insertion of a FLAG-tag onto rbcL. Importantly, the single-vector CRISPR/Cas9 system described herein was also shown to mediate multiplexed editing of up to three targets in parallel in Synechocystis. All single-target and several double-target mutants were also fully segregated after the first round of induction, adding to the usefulness of this system. Further, a vector curing system that is separately induced by nickel and contained on the CRISPR/Cas9 vector itself, improved curing efficiencies by roughly 4-fold, enabling the final mutants to become truly markerless.
dSeqSb: A systems biology approach to decipher dynamics of host-pathogen interactions using temporal dual RNA-seq data

Infection triggers a dynamic cascade of reciprocal events between host and pathogen wherein the host activates complex mechanisms to recognise and kill pathogens while the pathogen adjusts its virulence and fitness to avoid eradication by the host. The interaction between the pathogen and the host results in large-scale changes in gene expression in both organisms. Dual RNA-seq, the simultaneous detection of host and pathogen transcripts, has become a leading approach to unravel complex molecular interactions between the host and the pathogen and is particularly informative for intracellular organisms. The amount of in vitro and in vivo dual RNA-seq data is rapidly growing which demands computational pipelines to effectively analyse such data. In particular, holistic, systems-level, and temporal analyses of dual RNA-seq data are essential to enable further insights into the host-pathogen transcriptional dynamics and potential interactions. Here, we developed an integrative network-driven bioinformatics pipeline, dRNASb, a systems biology-based computational pipeline to analyse temporal transcriptional clusters, incorporate molecular interaction networks (e.g., protein-protein interactions), identify topologically and functionally key transcripts in host and pathogen, and associate host and pathogen temporal transcriptome to decipher potential between-species interactions. The pipeline is applicable to various dual RNA-seq data from different species and experimental conditions. As a case study, we applied dRNASb to analyse temporal dual RNA-seq data of Salmonella-infected human cells, which enabled us to uncover genes contributing to the infection process and their potential functions and to identify potential host-pathogen interactions between host and pathogen genes. Overall, dRNASb has the potential to identify key genes involved in bacterial growth or host defence mechanisms for future uses as therapeutic targets.
Four drug metabolism-related subgroups of pancreatic adenocarcinoma in prognosis, immune infiltration, and gene mutation

Abstract We aimed to screen the drug metabolism-related subgroups of pancreatic adenocarcinoma (PAAD) and to study the prognosis, clinical features, immune infiltration, and gene mutation differences of different subtypes in PAAD patients. All 181 cases of PAAD samples and clinical characteristics data were downloaded from The Cancer Genome Atlas (TCGA). After matching the drug metabolism-related genes downloaded from PMID 33202946 with the TCGA dataset, the drug metabolism-related genes were initially obtained. Besides, univariate Cox regression analysis was used to screen the drug metabolism genes related to the prognosis of PAAD. Moreover, the construction of the protein–protein interaction (PPI) network and gene ontology were performed. The four subgroups of PAAD obtained from unsupervised clustering analysis were systematically analyzed, including prognostic, GSVA, immune infiltration, and gene mutation analysis. A total of 83 drug metabolism genes related to the prognosis of PAAD were obtained and enriched in 16 pathways. The PPI network was composed of 248 relationship pairs. Four subgroups that can identify different subtypes of PPAD were obtained, and there were significant differences in survival and clinical characteristics, mutation types, and immune infiltration abundance between subgroups. A total of 17 different pathways among the four subgroups involved in cell cycle, response to stimulants such as drugs, and transmembrane transport. In this study, the four subgroups related to the drug metabolism of PAAD were comprehensively analyzed, and the important role of drug metabolism-related genes in the immune infiltration and prognosis of PAAD were emphasized.
Body Muscle Mass Metabolic Data Analysis in Association with Crohn’s Disease Activity

Abstract Malnutrition is a common complication of Crohn’s disease (CD) patients and it is correlated with alterations of the body composition and disease activity. Our prospective pilot study included hospitalised CD patients, age ≥ 18 years. Patients were assessed using the Nutritional Risk Score (NRS2002), the Malnutrition Universal Screening Tool (MUST), and body bioelectrical impedance analysis. Twenty-three hospitalised patients (median age 36.5, interquartile range (IQR): 28.5–51.5 years) were enrolled; the median CD activity index was 128 (IQR = 6.0–207.0). The study group comprised 48% (n = 11) patients with low CD activity and 52% (n = 12) with high disease activity. According to NRS2002 and MUST, 70% (n = 16) CD patients had malnutrition risk and were in need of nutritional support. The median BMI was lower for the CD group (21.10 [IQR = 19.2–23.3]) than for the control group (23.4 [IQR = 21.5–25.8]) (p = 0.014). In terms of deviation from standard weight, 39% (n = 9) of CD patients showed reduced % body fat. Reduced muscle mass was observed in 48% (n = 11) of CD patients. CD patients with high disease activity had a noticeably increased risk of malnutrition. Identification of the reduction in soft lean muscle mass in CD patients can be used as an anticipatory indicator of disease activity.
Transient elastohydrodynamic lubrication analysis of spur gears running-in considering effects of solid particles and surface roughness

Purpose – This paper aims to investigate the mechanism of spur gears running-in and to solve the lubrication problems of teeth running-in. Design/methodology/approach – The elastohydrodynamic lubrication (EHL) model considering solid particles was established by applying multi-grid and multiple-grid integration methods to the numerical solution. Findings – In the region where debris settle, transient pressure increases sharply, and a noticeable increase in the running-in load causes a remarkable increase in both the centre and maximum pressures and a slight increase in the minimum film thickness. Roughness wavelength makes a considerable difference to the minimum film thickness at double-to-single tooth transient. A considerable increase in rotation velocity can cause a remarkable reduction in both the centre and maximum pressures but an amazing increase in the minimum film thickness. The effects of roughness amplitude on the maximum pressure are considerably distinct. Research limitations/implications – .
LOOKing for multi-word expressions in American Sign Language

Abstract Usage-based linguistics postulates that multi-word expressions constitute a substantial part of language structure and use, and are formed through repeated chunking and stored as exemplar wholes. They are also re-used to produce new sequences by means of schematization. While there is extensive research on multi-word expressions in many spoken languages, little is known about the status of multi-word expressions in the mainstream U.S. variety of American Sign Language (ASL). This paper investigates recurring multi-word expressions, or sequences of multiple signs, that involve a high-frequency sign of visual perception glossed as look and the family of ‘look’ signs. The look sign exhibits two broad functions: look/‘vision’ references literal or metaphorical vision and look/‘reaction’ signals a person’s reaction to a visual stimulus. Data analysis reveals that there are recurring sequences in distinct syntactic environments associated with the two functions of look, suggesting that look is in the process of grammaticalization from a verb of visual perception to a stance verb. The sequences demonstrate the emergence of linguistic structure from repeated use through the domain-general cognitive process of chunking in ASL.
Quality of Different Coloured Tomatoes Depending on the Growing Season

Abstract Tomatoes have been widely used in nutrition, as well as in nutritional medicine. Red tomatoes are used for the treatment of anaemia, they contain the antioxidant lycopene, and the high concentration of organic acids promotes digestion. Yellow tomatoes have valuable amounts of ß-carotene, the pigment that gives orange and yellow tomatoes their colour, and helps to neutralise free radicals that may damage cells. The size of brown tomatoes is smaller than an average tomato, but they are sweeter, due to higher concentration of fructose. Cherry tomatoes are among the smallest tomatoes commercially available, but they are known for being rich in carotenoids, lycopene and phenolic compounds. The aim of the study was to evaluate how the concentration of biologically active substances differs depending on the tomato growing season. The study examined four varieties of tomatoes (Bolzano F1 — yellow, Chocomate F1— brown, Encore F1 — red, Strabena F1— red cherry) grown in an industrial greenhouse “Mežvidi” (Latvia) using additional light. The concentration of biologically active substances (lycopene, ß-carotene, total phenolic compounds, and soluble solids) was determined in two vegetation periods — autumn (November) and spring (March). The obtained results showed that tomatoes harvested in autumn contained more biologically active substances than in spring, as many biological processes in plants occur more rapidly at the beginning rather than in the middle or at the end of the vegetation season. Therefore, the concentration of secondary metabolites in tomatoes is higher at the end of the season. In autumn, cherry tomatoes Strabena contained the highest amount of pigments, total phenols, and soluble solids, and therefore the taste index of this variety also was the highest. In spring, pigment concentration was significantly lower (on average by 20–30%), and phenols and soluble solids concentration (oBrix) was not significantly lower — on average by 2–4%. Of the large-fruit tomatoes, at the beginning of vegetation season (autumn), the highest amounts of pigments were in red tomatoes (Encore) — lycopene concentration 4.63 ± 0.04 mg·100 g−1; yellow tomatoes Bolzano were rich in phenolic compounds — 128.46 ± 3.25 GAE mg·100−1, and brown tomatoes Chocomate had the highest soluble solids concentration — 4.48 ± 0.05 oBrix. In spring, the concentration of biologically active substances was lower on average by 10–15%, regardless of the colour and variety of the tomato.
Memory of split-belt walking endures weeks in young children and younger adults but less so in older adults

Adults and children modify how they move to accommodate persistent changes in their surroundings, called motor adaptation. Walking-related motor adaption can be seen when one walks on a treadmill with two belts running at different speeds, a split-belt treadmill, where a new walking pattern is slowly adopted with practice. This has been suggested as a way to improve left-right symmetry in walking after a stroke. Central to using split-belt walking for rehabilitation is whether the adapted motor pattern is retained over days and weeks, and whether this motor memory is a function of the person’s age. When first exposed to split-belt walking, the walking is asymmetric (initial error), resembling a limp. With subsequent exposure, the error is smaller than the initial error, indicating the adaptation was remembered. Here, we explored the persistence of this memory over 24 hours, one week, and two weeks, in young children (3-6 yr old), younger adults (20-30 yr old) and older adults (50-70 yr old). We found that the motor memory declines with the interval duration, but was still evident up to 2 weeks after initial exposure. Retention of the motor memory in children and younger adults was better than older adults. Further, forgetting between trials was seen on the first day of split-belt walking especially in children and older adults, but this forgetting diminished with repeated trials. The results indicate that long-term memory of motor adaptation on the split-belt treadmill is affected by age, but it may be possible to enhance the memory by more frequent and repeated exposure. This suggests that when using split-belt adaptation in rehabilitation, the sessions should ideally be less than one week apart.
Sentimental Analysis on Big Data – On case of Financial Document Text Mining to Predict Sub-Index Trend

This research analyzed the potential emotion by sentimental analysis in large volume of financial text documents about Taiwan electronic industry to predict the stock trend. In recent researches about sentimental analysis, supervised method was proven to be able to reach high accuracy, but the training set of supervised method should be classified by manpower and couldn't discover the unknown category. So this research put forward a solution which mixed supervised and unsupervised methods. First, we introduce unsupervised method to find out the topics of documents. Then we calculated the sentimental index to judge the document's emotional direction. After that, we find out which theme documents' sentiment index are leading indicators in Taiwan electronic sub-index (TE). Finally, we used supervised method by integrating the sentimental index of leading indicators with other 24 indirect sentimental indexes to build the prediction model of TE. By result, we found that LDA model has better cluster performance than TFIDF-Kmeans model, and also has higher accuracy than NPMI-Concor model on classification. By comparing sentimental index with MACD, we proved that the trend of sentimental index and TE to each other is more similar than MACD line and TE to each other. We also discovered that the sentiment indexes from enterprise operation and macro-economics topics are leading indicators and found that the prediction model of TE which includes the sentiment index is better than which only includes the technical indicators.
Map7D2 and Map7D1 facilitate microtubule stabilization through distinct mechanisms in neuronal cells

The microtubule-associated proteins Map7D2 and Map7D1, which belong to the MAP7 family, stabilize microtubules through distinct mechanisms for the control of cell motility and neurite outgrowth. Microtubule (MT) dynamics are modulated through the coordinated action of various MT-associated proteins (MAPs). However, the regulatory mechanisms underlying MT dynamics remain unclear. We show that the MAP7 family protein Map7D2 stabilizes MTs to control cell motility and neurite outgrowth. Map7D2 directly bound to MTs through its N-terminal half and stabilized MTs in vitro. Map7D2 localized prominently to the centrosome and partially on MTs in mouse N1-E115 neuronal cells, which expresses two of the four MAP7 family members, Map7D2 and Map7D1. Map7D2 loss decreased the resistance to the MT-destabilizing agent nocodazole without affecting acetylated/detyrosinated stable MTs, suggesting that Map7D2 stabilizes MTs via direct binding. In addition, Map7D2 loss increased the rate of random cell migration and neurite outgrowth, presumably by disturbing the balance between MT stabilization and destabilization. Map7D1 exhibited similar subcellular localization and gene knockdown phenotypes to Map7D2. However, in contrast to Map7D2, Map7D1 was required for the maintenance of acetylated stable MTs. Taken together, our data suggest that Map7D2 and Map7D1 facilitate MT stabilization through distinct mechanisms in cell motility and neurite outgrowth.