Miracle-dz/UniFAR-FTUs huggingface dataset:
Genomic Sequence of Saccharomyces cerevisiae BAW-6, a Yeast Strain Optimal for Brewing Barley Shochu

ABSTRACT Here, we report the draft genome sequence of Saccharomyces cerevisiae strain BAW-6, which is used for the production of barley shochu, a traditional Japanese spirit. This genomic information can be used to elucidate the genetic basis underlying the high alcohol production capacity and citric acid tolerance of shochu yeast.
Genome-Wide Screening Uncovers the Significance of N-Sulfation of Heparan Sulfate as a Host Cell Factor for Chikungunya Virus Infection

ABSTRACT The molecular mechanisms underlying chikungunya virus (CHIKV) infection are poorly characterized. In this study, we analyzed the host factors involved in CHIKV infection using genome-wide screening. Human haploid HAP1 cells, into which an exon-trapping vector was introduced, were challenged with a vesicular stomatitis virus pseudotype bearing the CHIKV E3 to E1 envelope proteins. Analysis of genes enriched in the cells resistant to the pseudotyped virus infection unveiled a critical role of N-sulfation of heparan sulfate (HS) for the infectivity of the clinically isolated CHIKV Thai#16856 strain to HAP1 cells. Knockout of NDST1 that catalyzes N-sulfation of HS greatly decreased the binding and infectivity of CHIKV Thai#16856 strain but not infectivity of Japanese encephalitis virus (JEV) and yellow fever virus (YFV). While glycosaminoglycans were commonly required for the efficient infectivity of CHIKV, JEV, and YFV, as shown by using B3GAT3 knockout cells, the tropism for N-sulfate was specific to CHIKV. Expression of chondroitin sulfate (CS) in NDST1-knockout HAP1 cells did not restore the binding of CHIKV Thai#16856 strain and the infectivity of its pseudotype but restored the infectivity of authentic CHIKV Thai#16856, suggesting that CS functions at later steps after CHIKV binding. Among the genes enriched in this screening, we found that TM9SF2 is critical for N-sulfation of HS and therefore for CHIKV infection because it is involved in the proper localization and stability of NDST1. Determination of the significance of and the relevant proteins to N-sulfation of HS may contribute to understanding mechanisms of CHIKV propagation, cell tropism, and pathogenesis. IMPORTANCE Recent outbreaks of chikungunya fever have increased its clinical importance. Chikungunya virus (CHIKV) utilizes host glycosaminoglycans to bind efficiently to its target cells. However, the substructure in glycosaminoglycans required for CHIKV infection have not been characterized. Here, we unveil that N-sulfate in heparan sulfate is essential for the efficient infection of a clinical CHIKV strain to HAP1 cells and that chondroitin sulfate does not help the CHIKV binding but does play roles at the later steps in HAP1 cells. We show, by comparing previous reports using Chinese hamster ovary cells, along with another observation that enhanced infectivity of CHIKV bearing Arg82 in envelope E2 does not depend on glycosaminoglycans in HAP1 cells, that the infection manner of CHIKV varies among host cells. We also show that TM9SF2 is required for CHIKV infection to HAP1 cells because it is involved in the N-sulfation of heparan sulfate through ensuring NDST1 activity.
The Demands of a Women’s College Soccer Season

The purpose of this study was to use GPS, accelerometers, and session rating of perceived exertion (sRPE) to examine the demands of a Division II women’s soccer team. Data was collected on 25 collegiate Division II women’s soccer players over an entire regular season (17 matches and 24 practices). ZephyrTM BioHarnesses (BHs) were used to collect tri-axial acceleration information and GPS derived variables for all matches and practices. Acceleration data was used to calculate Impulse Load, a measure of mechanical load that includes only locomotor related accelerations. GPS was used to quantify total distance and distance in six speed zones. Internal Training Loads were assessed via sRPE. Mean Impulse Load, total distance, and sRPE during match play was 20,120 ± 8609 N·s, 5.48 ± 2.35 km, and 892.50 ± 358.50, respectively. Mean Impulse Load, total distance, and sRPE during practice was 12,410 ± 4067 N·s, 2.95 ± 0.95 km, and 143.30 ± 123.50, respectively. Several very large to nearly perfect correlations were found between Impulse Load and total distance (r = 0.95; p < 0.001), Impulse Load and sRPE (r = 0.84; p < 0.001), and total distance and sRPE (r = 0.82; p < 0.001). This study details the mechanical demands of Division II women’s soccer match play. This study also demonstrates that Impulse Load is a good indicator of total distance.
Performance Analysis of Wireless Powered Communications With Multiple Antennas

This paper analytically investigates the performance of a wireless powered communication system, where a source powered by multiple dedicated power beacons communicates with a destination. Specifically, we consider a harvest-then-transmit multiple-input multiple-output communication system, where the source uses all harvested energy for information transmission in each time block. The random placement of terminals is characterized by stochastic geometry tools. Taking into account the effects of imperfect channel state information in wireless energy transfer and wireless information transmission, the ergodic achievable rate of information transmission is derived analytically by considering co-channel interference (CCI) and the noise. In addition, assuming the CCI can be accurately approximated by a Gamma distributed variable, the outage probability of information transmission is investigated. Numerical results validate the analytical results and show the impacts of the antenna number, distribution density, estimation error, and the transmit power of terminals on the system performance.
Phosphorus Diffusion Mechanisms and Deep Incorporation in Polycrystalline and Single-Crystalline CdTe

A key challenge in cadmium telluride (CdTe) semiconductors is obtaining stable and high hole density. Group I elements substituting Cd can form acceptors but easily self-compensate and diffuse quickly. For example, CdTe photovoltaics have relied on copper as a dopant, but this creates stability problems and hole density that has not exceeded 10 15 cm -3 . If hole density can be increased beyond 10 16 cm -3 , CdTe solar technology can exceed multicrystalline silicon performance and provide levelized costs of electricity below conventional energy sources. Group V elements substituting Te offer a solution, but they are very difficult to incorporate. Using time-of-flight secondary-ion mass spectrometry, we examine bulk and grain boundary (GB) diffusion of phosphorous (P) in CdTe in Cd-rich conditions. We find that in addition to slow bulk diffusion and fast GB diffusion, there is a critical fast bulk diffusion component that enables deep P incorporation in CdTe. Detailed first-principles calculations indicate the slow bulk diffusion component is caused by substitutional P diffusion through the Te sublattice, whereas the fast bulk diffusion component is caused by P diffusing through interstitial lattice sites following the combination of a kick-out step and two rotation steps. The latter is limited in magnitude by high formation energy, but is sufficient to manipulate P incorporation. In addition to an increased physical understanding, this result opens up new experimental possibilities for Group V doping in CdTe applications.
Fairness in Multiterminal Data Compression: Decomposition of Shapley Value

We consider the problem of how to attain fairness in the multiterminal data compression problem by a game-theoretic approach and present a decomposition method for obtaining the Shapley value, a fair source coding rate vector in the Slepian-Wolf achievable region. We model a discrete memoryless multiple random source (DMMS) by a coalitional game where the entropy function quantifies the cost incurred by the source coding rates in each coalition. In the typical case for which the game is decomposable, we show that the Shapley value can be obtained separately for each subgame. The complexity of this decomposition method is determined by the maximum size of subgames, which is strictly smaller than the total number of terminals in the DMMS and contributes to a considerable reduction in computational complexity. An experimental result demonstrates large complexity reduction when the number of terminals in the DMMS becomes large.
Physical versus biological control of element incorporation into biogenic carbonate: an in situ experiment in a New Zealand fjord

We exploit the pronounced and persistent low salinity layer in Doubtful Sound, southwest New Zealand, as a natural experimental system with sharp environmental gradients in which to study physical versus biological control of element incorporation into biogenic carbonate. Mussels Mytilus galloprovincialis transplanted to cages in the low salinity layer and saline layer in inner, mid and outer fjord habitats were used as biological integrators of physico-chemical conditions in each water mass over a period of several months. We used solution inductively coupled plasma mass spectrometry (ICP-MS) to measure the concentrations of 15 elements (Li, B, Mg, P, S, Mn, Fe, Co, Cu, Zn, Rb, Sr, Cd, Ba, Pb) in the experimental shell growth and relate spatial trends to those in salinity and elemental sources. S concentrations were consistently below detection limits while Zn and Rb showed no spatial variability. The majority of elements were subject to environmental control, likely reflecting ambient concentrations and salinity. Sr incorporation showed evidence of strong biological mediation of environmental signals via the crystal shell growth rate. These findings are a valuable addition to the growing body of literature seeking to resolve physical versus biological controls of individual trace element incorporation into biogenic carbonates, and have important consequences for their use as environmental indicators or tracers for ecological studies.
Broadcast Algorithms for Mobile Ad hoc Networks based on Depth-first Traversal

Two deterministic broadcast algorithms are presented for mobile ad hoc networks where the mobile nodes possess collision detection capabilities. The first algorithm, based on a depth-first traversal of the nodes, accomplishes broadcast in O(n log n) time in the worst case. The second algorithm is mobility resilient even when the topology changes very frequently, with O(∆·n log n+n· |M |) time to broadcast in the worst case, where |M | is the length of the message to be broadcasted and ∆ is the maximum node degree.
A comparison of the implant stability among various implant systems: clinical study

PURPOSE To determine the change in stability of single-stage, three different design of implant systems in humans utilizing resonance frequency analysis for early healing period (24 weeks), without loading. MATERIAL AND METHODS Twenty-five patients were included into this study. A total of 45 implants, three different design of implant systems (group A,C,R) were placed in the posterior maxilla or mandible. The specific transducer for each implant system was used. ISQ (implant stability quotient) reading were obtained for each implant at the time of surgery, 3, 6, 8, 10, 12, 24 weeks postoperatively. Data were analyzed for different implant type, bone type, healing time, anatomical locations. RESULTS For each implant system, a two-factor mixed-model ANOVA demonstrated that a significant effect on ISQ values (group A = 0.0022, C = 0.017, R = 0.0018). For each implant system, in a two-factor mixed model ANOVA, and two-sample t-test, the main effect of jaw position (P > .005) on ISQ values were not significant. CONCLUSIONS All the implant groups A, C and R, the change patterns of ISQ over time differed by bone type. Implant stability increased greatly between week 0 and week six and showed slow increase between week six and six months (plateau effect).
Molecular evolution of DNMT1 in vertebrates: Duplications in marsupials followed by positive selection

DNA methylation is mediated by a conserved family of DNA methyltransferases (Dnmts). The human genome encodes five Dnmts: Dnmt1, Dnmt2, Dnmt3a, Dnmt3b and Dnmt3L. Despite their high degree of conservation among different species, genes encoding Dnmts have been duplicated and/or lost in multiple lineages throughout evolution, indicating that the DNA methylation machinery has some potential to undergo evolutionary change. However, little is known about the extent to which this machinery, or the methylome, varies among vertebrates. Here, we study the molecular evolution of Dnmt1, the enzyme responsible for maintenance of DNA methylation patterns after replication, in 79 vertebrate species. Our analyses show that all studied species exhibit a single copy of DNMT1, with the exception of tilapia and marsupials (tammar wallaby, koala, Tasmanian devil and opossum), each of which exhibits two apparently functional DNMT1 copies. Our phylogenetic analyses indicate that DNMT1 duplicated before the divergence of marsupials (i.e., at least ~75 million years ago), thus giving rise to two DNMT1 copies in marsupials (copy 1 and copy 2). In the opossum lineage, copy 2 was lost, and copy 1 recently duplicated again, generating three DNMT1 copies: two putatively functional genes (copy 1a and 1b) and one pseudogene (copy 1ψ). Both marsupial copies (DNMT1 copies 1 and 2) are under purifying selection, and copy 2 exhibits elevated rates of evolution and signatures of positive selection, suggesting a scenario of neofunctionalization. This gene duplication might have resulted in modifications in marsupial methylomes and their dynamics.
Oligo-Alginate with Low Molecular Mass Improves Growth and Physiological Activity of Eucomis autumnalis under Salinity Stress

Biopolymers have become increasingly popular as biostimulators of plant growth. One of them, oligo-alginate, is a molecule that regulates plant biological processes and may be used in horticultural practice as a plant growth regulator. Biostimulators are mainly used to improve plant tolerance to abiotic stresses, including salinity. The aim of the study was to assess the effects of salinity and oligo-alginate of various molecular masses on the growth and physiological activity of Eucomis autumnalis. The species is an ornamental and medicinal plant that has been used for a long time in the traditional medicine of South Africa. The bulbs of E. autumnalis were coated using depolymerized sodium alginate of molecular mass 32,000; 42,000, and 64,000 g mol−1. All of these oligo-alginates fractions stimulated plant growth, and the effect was the strongest for the fraction of 32,000 g mol−1. This fraction was then selected for the second stage of the study, when plants were exposed to salt stress evoked by the presence of 100 mM NaCl. We found that the oligo-alginate coating mitigated the negative effects of salinity. Plants treated with the oligomer and watered with NaCl showed smaller reduction in the weight of the above-ground parts and bulbs, pigment content and antioxidant activity as compared with those not treated with the oligo-alginate. The study demonstrated for the first time that low molecular mass oligo-alginate may be used as plant biostimulator that limits negative effects of salinity in E. autumnalis.
Different extracellular domains of the neural cell adhesion molecule (N- CAM) are involved in different functions

The neural cell adhesion molecule (N-CAM) engages in diverse functional roles in neural cell interactions. Its extracellular part consists of five Ig-like domains and two fibronectin type III homologous (type III) repeats. To investigate the functional properties of the different structural domains of the molecule in cell interactions and signal transduction to the cell interior, we have synthesized, in a bacterial expression system, the individual domains and tandem sets of individual domains as protein fragments. These protein fragments were tested for their capacity to influence adhesion and spreading of neuronal cell bodies, promote neurite outgrowth, and influence cellular migration patterns from cerebellar microexplants in vitro. Ig-like domains I and II and the combined type III repeats I-II were most efficient for adhesion of neuronal cell bodies, when coated as substrates. Neurite outgrowth was best on the substrate-coated combined type III repeats I- II, followed by the combined Ig-like domains I-V and Ig-like domain I. Spreading of neuronal cell bodies was best on substrate-coated combined type III repeats I-II, followed by Ig-like domain I and the combined Ig- like domains I-V. The cellular migration pattern from cerebellar microexplant cultures plated on a mixture of laminin and poly-L-lysine was modified by Ig-like domains I, III, and IV, while Ig-like domains II and V and the combined type III repeats I-II did not show significant modifications, when added as soluble fragments. Outgrowth of astrocytic processes from the explant core was influenced only by Ig- like domain I. Metabolism of inositol phosphates was strongly increased by Ig-like domain I and less by the Ig-like domains II, III, IV, and V, and not influenced by the combined type III repeats I-II. Intracellular concentrations of Ca2+ and pH values were increased only by the Ig-like domains I and II. Intracellular levels of cAMP and GMP were not influenced by any protein fragment. These experiments indicate that different domains of N-CAM subserve different functional roles in cell recognition and signal transduction, and are functionally competent without nervous system-derived carbohydrate structures.
A standardized Hippophae extract (SBL-1) counters neuronal tissue injuries and changes in neurotransmitters: implications in radiation protection

Abstract Context: Effects of a radioprotective, standardized leaf extract (code SBL-1) from traditional medicinal plant, sea buckthorn [Hippophae rhamnoides L. (Elaeagnaceae)], on neurotransmitters and brain injuries in rats showing radiation-induced conditioned taste aversion (CTA), are not known. Understanding CTA in rats is important because its process is considered parallel to nausea and vomiting in humans. Objective: This study investigated the levels of neurotransmitters, antioxidant defences and histological changes in rats showing radiation CTA, and their modification by SBL-1. Materials and methods: The inbred male Sprague-Dawley rats (age 65 days, weighing 190 ± 10 g) were used. Saccharin-preferring rats were selected using standard procedure and divided into groups. Group I (untreated control) was administered sterile water, group II was 60Co-γ-irradiated (2 Gy), and group III was administered SBL-1 before irradiation. Observations were recorded up to day 5. Results: Irradiation (2 Gy) caused (i) non-recoverable CTA (≥ 64.7 ± 5.0%); (ii) degenerative changes in cerebral cortex, amygdala and hippocampus; (iii) increases in brain dopamine (DA, 63.4%), norepinephrine (NE, 157%), epinephrine (E, 233%), plasma NE (103%) and E (160%); and (iv) decreases in brain superoxide dismutase (67%), catalase (60%) and glutathione (51%). SBL-1 treatment (12 mg/kg body weight) 30 min before irradiation (i) countered brain injuries, (ii) reduced CTA (38.7 ± 3.0%, day 1) and (iii) normalized brain DA, NE, E, superoxide dismutase, catalase and CTA from day 3 onwards. Discussion and conclusion: Radiation CTA was coupled with brain injuries, disturbances in neurotransmitters and antioxidant defences. SBL-1 pretreatment countered these disturbances, indicating neuroprotective action.
Multispectral demosaicing using intensity-based spectral correlation

Single-sensor color cameras, which classically use a color filter array (CFA) to sample RGB channels, have recently been extended to the multispectral domain. To sample more than three wavelength bands, such systems use a multispectral filter array (MSFA) that provides a raw image in which a single channel level is available at each pixel. A demosaicing procedure is then needed to estimate a multispectral image with full spectral resolution. In this paper, we propose a new demosaicing method that takes spectral and spatial correlations into account by estimating the level for each channel. Experimental results show that it provides estimated images of better quality than classical methods.
What exactly is ‘N’ in cell culture and animal experiments?

Biologists establish the existence of experimental effects by applying treatments or interventions to biological entities or units, such as people, animals, slice preparations, or cells. When done appropriately, independent replication of the entity-intervention pair contributes to the sample size (N) and forms the basis of statistical inference. However, sometimes the appropriate entity-intervention pair may not be obvious, and the wrong choice can make an experiment worthless. We surveyed a random sample of published animal experiments from 2011 to 2016 where interventions were applied to parents but effects examined in the offspring, as regulatory authorities have provided clear guidelines on replication with such designs. We found that only 22% of studies (95% CI = 17% to 29%) replicated the correct entity-intervention pair and thus made valid statistical inferences. Approximately half of the studies (46%, 95% CI = 38% to 53%) had pseudoreplication while 32% (95% CI = 26% to 39%) provided insufficient information to make a judgement. Pseudoreplication artificially inflates the sample size, leading to more false positive results and inflating the apparent evidence supporting a scientific claim. It is hard for science to advance when so many experiments are poorly designed and analysed. We argue that distinguishing between biological units, experimental units, and observational units clarifies where replication should occur, describe the criteria for genuine replication, and provide guidelines for designing and analysing in vitro, ex vivo, and in vivo experiments.
State aware test case regeneration for improving web application test suite coverage and fault detection

This paper introduces two test cases regeneration approaches for web applications, one uses standard Def-Use testing but for state variables, the other uses a novel value-aware dataflow approach. Our overall approach is to combine requests from a test suite to form client-side request sequences, based on dataflow analysis of server-side session variables and database tables. We implemented our approach as a tool SART (State Aware Regeneration Tool) and used it to evaluate our proposed approaches on 4 real world web applications. Our results show that for all 4 applications, both server-side coverage and fault detection were statistically significantly improved. Even on relatively high quality test suites our algorithms improve average coverage by 14.74% and fault detection by 9.19%.