Miracle-dz/UniFAR-FTUs huggingface dataset:
What Determines the Distinct Morphology of Species with a Particular Ecology? The Roles of Many-to-One Mapping and Trade-Offs in the Evolution of Frog Ecomorphology and Performance

Organisms inhabiting a specific environment often have distinct morphology, but the factors that affect this fit are unclear when multiple morphological traits affect performance in multiple behaviors. Does the realized morphology of a species reflect a compromise in performance among behaviors (i.e., trade-offs)? Or does many-to-one mapping result in morphological distinctness without compromising performance across behaviors? The importance of these principles in organismal design has rarely been compared at the macroevolutionary scale. Here I study 191 species of frogs from around the world that inhabit different microhabitats, using models of phenotypic evolution to examine how form-function relationships may explain the fit between ecology and morphology. I found three key results. First, despite being distinct in leg morphology, ecomorphs were similar in jumping performance. Second, ecomorphs that regularly swim showed higher swimming performance, which paralleled the higher leg muscle mass in these taxa. Third, many-to-one mapping of form onto function occurred at all but the highest levels of both jumping and swimming performance. The seemingly contradictory first two results were explained by the third: when one behavior occurs in all species while another is restricted to a subset, many-to-one mapping allows species with distinct ecologies to have distinct body forms that reflect their specialized behavior while maintaining similar performance in a more general shared behavior.
Apoptotic markers and antioxidant enzymes have altered expression in cumulus and granulosa cells of young women with poor response to ovarian stimulation

Background: The objective of this study was to evaluate apoptosis and oxidative stress markers in Granulose (GC) and Cumulus Cells (CC) of women with low response to Controlled Ovarian Stimulation (COS) and controls which underwent an IVF treatment. Methods: mRNA concentrations of BCL-2, BAX, caspase-3, caspase-9, Superoxide Dismutase (SOD) and catalase were evaluated in patients (n=30) and donors (n=45) using qRT-PCR analysis on CG and CC. Results: The concentrations of mRNA coding for BCL-2, BAX, caspase-3, and caspase-9 were significantly higher in GC from women with low response compared to women with normal response (p<0.001). In contrast, concentrations of catalase mRNA were significantly increased in normoresponders women (p< 0.05). The levels of catalase mRNA were also significantly higher in CCs from normoresponders women compared to patients with low response (p<0.003), and the levels of BAX mRNA in CC were significantly increased in patients (p<008). Conclusions: In addition, we found a correlation between the expression of genes regulating OS and apoptosis and response to ovarian stimulation, which could mean that an increase in ovarian oxidative stress can reduce the number of oocytes obtained after ovarian stimulation.
Liquid-liquid phase separation and aggregation of the prion protein globular domain modulated by a high-affinity DNA aptamer

Structural conversion of cellular prion protein (PrPC) into scrapie PrP (PrPSc) and subsequent aggregation are key events for the onset of Transmissible Spongiform Encephalopathies (TSEs). Experimental evidences support the role of nucleic acids (NAs) in assisting the protein conversion process. Here, we used the SELEX methodology to identify two 25-mer DNA aptamers against the globular domain of recombinant murine PrP (rPrP90-231), namely A1 and A2. High-affinity binding of A1 and A2 to rPrP was verified by ITC. Aptamers structure was characterized by theoretical predictions, CD, NMR and SAXS, revealing that A1 adopts a hairpin conformation. Aptamer binding caused dynamic aggregation of rPrP90-231, resulting from the ability of rPrP90-231 to undergo liquid-liquid phase separation (LLPS). While free rPrP90-231 phase separated into large droplets, aptamer binding increased the amount but reduced the size of the condensates. Strikingly, a modified A1 aptamer that does not adopt a hairpin structure induced transition to an ordered state, suggestive of amyloid formation on the surface of the droplets. Our results describe for the first time PrP:NA interaction leading to LLPS and modulation of this effect depending on NA structure and binding stoichiometry, shedding light on the role of NAs in PrP misfolding and TSEs.
Causality : statistical perspectives and applications

A state of the art volume on statistical causality "Causality: Statistical Perspectives and Applications" presents a wide? ranging collection of seminal contributions by renowned experts in the field, providing a thorough treatment of all aspects of statistical causality. It covers the various formalisms in current use, methods for applying them to specific problems, and the special requirements of a range of examples from medicine, biology and economics to political science. This book: (1) provides a clear account and comparison of formal languages, concepts and models for statistical causality, and (2) addresses examples from medicine, biology, economics and political science to aid the reader's understanding, and (3) is authored by leading experts in their field, and (4) is written in an accessible style. Postgraduates, professional statisticians and researchers in academia and industry will benefit from this book.
Book Reviews : Two-Sided Matching: A Study in Game-Theoretic Modeling and Analysis. BY ALVIN E. ROTH AND MARILDA A. OLIVEIRA SOROMAYER. Cambridge: Cambridge University Press, 1991. Cloth, pp. 265, $54.50

true. First, students can achieve a better matching by highly rating the hospitals reasonably likely to rate them highly. In other words, one can do worse by listing &dquo;fliers. &dquo; Second, the algorithm is designed to be optimal from the perspective of the hospital, not from the perspective of the prospective resident. In fact, from among the set of &dquo;stable&dquo; matches, the one chosen by NIMP is least optimal from the perspective of the students.
PREDICTING BIOMASS AND YIELD AT HARVEST OF SALT-STRESSED TOMATO PLANTS USING UAV IMAGERY

Abstract. Biomass and yield are important variables used for assessing agricultural production. However, these variables are difficult to estimate for individual plants at the farm scale and may be affected by abiotic stressors such as salinity. In this study, the wild tomato species, Solanum pimpinellifolium, was evaluated through field and UAV-based assessment of 600 control and 600 salt-treated plants. The aim of this research was to determine, if UAV-based imagery, collected one, two, four, six, seven and eight weeks before harvest could predict fresh shoot mass, tomato fruit numbers, and yield mass at harvest and if predictions varied for control and salt-treated plants. A Random Forest approach was used to model biomass and yield. The results showed that shape features such as plant area, border length, width and length had the highest importance in the random forest models. A week prior to harvest, the explained variance of fresh shoot mass, number of fruits and yield mass were 86.60%, 59.46% and 61.09%, respectively. The explained variance was reduced as a function of time to harvest. Separate models may be required for predicting yield of salt-stressed plants, whereas the prediction of yield for control plants was less affected if the model included salt-stressed plants. This research demonstrates that it is possible to predict biomass and yield of tomato plants up to four weeks prior to harvest, and potentially earlier in the absence of severe weather events.
Arsenic Species Analysis at Trace Level by High Performance Liquid Chromatography with Inductively Coupled Plasma Mass Spectrometry

A sensitive and accurate simultaneous continuous analysis for six arsenic species including arsenobetaine (AsB), arsenocholine (AsC), monomethylarsonic acid (MMA), dimethylarsinic acid (DMA), arsenite (AsIII), and arsenate (AsV) has been developed by high performance liquid chromatography with inductively coupled plasma mass spectrometry (HPLC-ICP-MS). An anion-exchange column of Hamilton PRP-X100 (Switzerland) was applied for separation of the six arsenic species with gradient elution of 1.25 mmol/L Na2HPO4 and 11.0 mmol/L KH2PO4 as the mobile phase A and 2.5 mmol/L Na2HPO4 and 22.0 mmol/L KH2PO4 as the mobile phase B. The linearity ranges for AsB, AsC, MMA, DMA, AsIII, and AsV were between 0.5 and 50.0 μg/L, and the detection limits of the six arsenic species were all within 0.01–0.35 ng/L. The relative standard deviations (RSDs) were within 2.26–3.68% and the recovery rates of samples ranged from 95 to 103%. The proposed method was applied for the arsenic speciation analysis of sediment pore-water samples, which were taken from the supernatant after centrifugation and filtration.
Context-Aware Information-Based Access Restriction Scheme for Cloud Data

To provide secure and efficient access control methods in cloud computing environments, many system models have been proposed that employ attribute-based encryption and proxy re-encryption schemes. Most of these access control schemes are based on the user’s authentication information and access privileges. However, when users request access privileges through non-secure environments such as mobile devices and wireless networks, we need to be able to restrict access requests, depending on the user’s context-aware information. To achieve this, in this paper we propose an access restriction scheme for access to cloud data that is based on context-aware information.1
Hydrophilic and Insoluble Electrospun Cellulose Acetate Fiber-Based Biosensing Platform for 25-Hydroxy Vitamin-D3 Detection

The present work describes the fabrication of a simple, low-cost, eco-friendly, and disposable conducting paper substrate (RCP) decorated with electrospun cellulose acetate fibers (CAEFs) for biosensor application. CAEFs were electrospun under spinning conditions at a voltage of 16 kV, flow rate of 0.2 mL h–1, and tip-to-collector distance of 15 cm. CAEFs were directly collected onto RCP. A scanning electron microscopy study revealed the diameter of CAEFs in the range of 330 ± 3.50 nm. The contact angle of CAEFs was found to be 38.07 ± 5.10°, which indicates a hydrophilic nature of the fibers. Further, the CAEF/RCP electrode was modified with antibody specific to 25-hydroxy vitamin-D3 (AB-25OHD3), followed with bovine serum albumin (BSA) to block nonspecific binding sites for detection of 25-OH vitamin-D3. The BSA/AB-25OHD3/CAEF/RCP immunoelectrode fabrication was confirmed thorough scanning electron microscopy, Fourier transform infrared spectroscopy, contact angle and electrochemical techniques. The chr.
Development of Fault Detection System for Ball Bearing of Induction Motor Using Vibration Signal

ABSTRACT Induction motors are the most important and significant component of any industry. Induction motor faults results in motor failure causing loss of production time and cost of repairing. Vibration analysis is one of the most successful technique used for condition monitoring of rotating machines. This paper describes a new condition monitoring method for induction motors based on vibration signal analysis. A robust bearing fault detection scheme has been developed by time domain feature extraction from vibration signals of healthy and faulty bearings. The statistical parameters such as peak value, RMS value, crest factor, kurtosis, skewness, impulse factor, shape factor, clearance factor, upper bound and lower bound value of histogram are used for feature extraction. Development of Fault Detection System for Ball Bearing of Induction Motor Using Vibration Signal
hypeR: An R Package for Geneset Enrichment Workflows

Summary Geneset enrichment is a popular method for annotating high-throughput sequencing data. Existing tools fall short in providing the flexibility to tackle the varied challenges researchers face in such analyses, particularly when analyzing many signatures across multiple experiments. We present a comprehensive R package for geneset enrichment workflows that offers multiple enrichment, visualization, and sharing methods in addition to novel features such as hierarchical geneset analysis and built-in markdown reporting. hypeR is a one-stop solution to performing geneset enrichment for a wide audience and range of use cases. Availability and implementation The most recent version of the package is available at https://github.com/montilab/hypeR. Supplementary information Comprehensive documentation and tutorials, are available at https://montilab.github. io/hypeR-docs.
Text mining: An analysis of research published under the subject category ‘Information Science Library Science’ in Web of Science Database during 1999-2013

Purpose – The purpose of this paper was to analyse text mining (TM) literature indexed in the Web of Science (WoS) under the “Information Science Library Science” subcategory. More specifically, it analyses the chronological growth of TM literature, and the major countries, institutions, departments and individuals contributing to TM literature. Collaboration in TM research is also analysed. Design/methodology/approach – Bibliographic and citation data required for this research were retrieved from the WoS database. TM being a multidisciplinary field, the search was restricted to “Information Science Library Science” subcategory in the WoS. A comprehensive query statement covering all synonyms of “text mining” was prepared using the Boolean operator “OR”. Microsoft Excel and HistCite software were used for data analysis. Pajek and VoSviewer were used for data visualization. Findings – It was found that USA is the major producer of TM research literature, and the highest number of papers were published in the Journal of The American Medical Informatics. Columbia University ranked first both in number of articles and citations received in the top ten institutes publishing TM literature. It was also observed that six of the top ten subdivisions of institutions are either from medicine or medical informatics or biomedical information. H.C. Chen and C. Friedman were seen to be the most prolific authors. Research limitations/implications – The paper analyses articles on TM published during 1999-2013 in WoS under the subcategory Information Science Library Science’. Originality/value – The paper is based on empirical data exclusively gathered for this research.
A cyclic hybrid method to select a smaller subset of informative genes for cancer classification

Microarray data are expected to be useful for cancer classification. The main problem that needs to be addressed is the selection of a smaller subset of genes from the thousands of genes in the data that contributes to a cancer disease. This selection process is difficult due to many irrelevant genes, noisy data, and the availability of the small number of samples compared to the huge number of genes (higher-dimensional data). Hence, this paper aims to select a smaller subset of informative genes that is the most relevant for the cancer classification. To achieve the aim, a cyclic hybrid method has been proposed. Five real microarray data sets are used to test the effectiveness of the method. Experimental results show that the performance of the proposed method is superior to other experimental methods and related previous works in terms of classification accuracy and the number of selected genes. In addition, a scatter gene graph and a list of informative genes in the best gene subsets are also presented for biological usage.
Phosphatidylcholine Biosynthesis in Mitis Group Streptococci via Host Metabolite Scavenging

We lack fundamental information about the composition of the cellular membrane even for the best-studied pathogens of critical significance for human health. The mitis group streptococci are closely linked to humans in health and disease, but their membrane biology is poorly understood. Here, we demonstrate that these streptococci scavenge major human metabolites and use them to synthesize the membrane phospholipid PC. Our work is significant because it identifies a mechanism by which the major human pathogen S. pneumoniae and the primary human oral colonizers S. mitis and S. oralis remodel their membranes in response to host metabolites. ABSTRACT The mitis group streptococci include the major human pathogen Streptococcus pneumoniae and the opportunistic pathogens Streptococcus mitis and Streptococcus oralis, which are human oral cavity colonizers and agents of bacteremia and infective endocarditis in immunocompromised patients. Bacterial membrane lipids play crucial roles in microbe-host interactions; for many pathogens, however, the composition of the membrane is poorly understood. In this study, we characterized the lipidomes of selected species of mitis group streptococci and investigated the mechanistic basis for biosynthesis of the phospholipid phosphatidylcholine (PC). PC is a major lipid in eukaryotic cellular membranes, but it is considered to be comparatively rare in bacterial taxa. Using liquid chromatography-mass spectrometry in conjunction with stable isotope tracing, we determined that mitis group streptococci synthesize PC via a rare host-metabolite-scavenging pathway, the glycerophosphocholine (GPC) pathway, which is largely uncharacterized in bacteria. Our work demonstrates that mitis group streptococci, including S. pneumoniae, remodel their membranes in response to the major human metabolites GPC and lysophosphatidylcholine. IMPORTANCE We lack fundamental information about the composition of the cellular membrane even for the best-studied pathogens of critical significance for human health. The mitis group streptococci are closely linked to humans in health and disease, but their membrane biology is poorly understood. Here, we demonstrate that these streptococci scavenge major human metabolites and use them to synthesize the membrane phospholipid PC. Our work is significant because it identifies a mechanism by which the major human pathogen S. pneumoniae and the primary human oral colonizers S. mitis and S. oralis remodel their membranes in response to host metabolites.
CLUSTERING WITH CLUSTER-LEVEL CONSTRAINTS

The task of clustering is to group data objects into clusters which exhibit internal cohesion and external isolation. The generated clusters provide useful knowledge to support decision making in many applications. However, clustering methods may fail to discover satisfactory results due to the lack of user involvement, especially in the form of supplying background knowledge about target domains and application needs. Normally, background knowledge can be captured by three types of constraints, Le. , instance-level constraints, cluster-level constraints, and model-level constraints. In this thesis, we study how cluster-level constraints are used to capture the background knowledge and users' special requirements in several real life clustering tasks, e.g., catalog segmentation, community identification, and privacy preservation etc. We design appropriate clustering models that integrate those constraints. We analyze the complexity of the proposed models, develop efficient clustering algorithms, and evaluate the clustering results on synthetic and real data sets.
The multimodulus blind equalization algorithm

This paper presents a new blind equalization algorithm called the multimodulus algorithm (MMA). This algorithm is particularly well suited to applications using two-dimensional transmission schemes such as carrierless AM/PM (CAP) and quadrature amplitude modulation (QAM). The paper also discusses some of the advantages provided by MMA when compared to traditional blind equalization algorithms, such as the reduced constellation algorithm (RCA) and the constant modulus algorithm (CMA).
Mps1 releases Mad1 from nuclear pores to ensure a robust mitotic checkpoint and accurate chromosome segregation

The strength of the Spindle Assembly Checkpoint (SAC) depends on the amount of the Mad1-C-Mad2 heterotetramer at kinetochores but also on its binding to Megator/Tpr at nuclear pore complexes (NPCs) during interphase. However, the molecular underpinnings controlling the spatiotemporal redistribution of Mad1-C-Mad2 as cells progress into mitosis remain elusive. Here, we show that Mps1-mediated phosphorylation of Megator/Tpr abolishes its interaction with Mad1 in vitro and in Drosophila cells. Timely activation of Mps1 during prophase triggers Mad1 release from NPCs, which we find to be required for competent kinetochore recruitment of Mad1-C-Mad2 and robust checkpoint response. Importantly, preventing Mad1 binding to Megator/Tpr rescues the fidelity of chromosome segregation and aneuploidy in larval neuroblasts of Drosophila mps1-null mutants. Our findings demonstrate that the subcellular localization of Mad1 is stringently coordinated with cell cycle progression by kinetochore-extrinsic activity of Mps1. This ensures that both NPCs in interphase and kinetochores in mitosis can generate anaphase inhibitors to efficiently preserve genomic stability.
Peptidoglycan associated cyclic lipopeptide disrupts viral infectivity

Enteric viruses exploit bacterial components including lipopolysaccharides (LPS) and peptidoglycan (PG) to facilitate infection in humans. With origins in the bat enteric system, we wondered if severe acute respiratory syndrome-coronavirus (SARS-CoV) or Middle East respiratory syndrome-CoV (MERS-CoV) also use bacterial components to modulate infectivity. To test this question, we incubated CoVs with LPS and PG and evaluated infectivity finding no change following LPS treatment. However, PG from B. subtilis reduced infection >10,000-fold while PG from other bacterial species failed to recapitulate this. Treatment with an alcohol solvent transferred inhibitory activity to the wash and mass spectrometry revealed surfactin, a cyclic lipopeptide antibiotic, as the inhibitory compound. This antibiotic had robust dose- and temperature-dependent inhibition of CoV infectivity. Mechanistic studies indicated that surfactin disrupts CoV virion integrity and surfactin treatment of the virus inoculum ablated infection in vivo. Finally, similar cyclic lipopeptides had no effect on CoV infectivity and the inhibitory effect of surfactin extended broadly to enveloped viruses including influenza, Ebola, Zika, Nipah, Chikungunya, Una, Mayaro, Dugbe, and Crimean-Congo hemorrhagic fever viruses. Overall, our results indicate that peptidoglycan-associated surfactin has broad virucidal activity and suggest bacteria byproducts may negatively modulate virus infection. Importance In this manuscript, we considered a role for bacteria in shaping coronavirus infection. Taking cues from studies of enteric viruses, we initially investigated how bacterial surface components might improve CoV infection. Instead, we found that peptidoglycan-associated surfactin is a potent viricidal compound that disrupts virion integrity with broad activity against enveloped viruses. Our results indicate that interactions with commensal bacterial may improve or disrupt viral infections highlighting the importance of understanding these microbial interactions and their implications for viral pathogenesis and treatment.