Miracle-dz/UniFAR-FTUs huggingface dataset:
Assessment of the Distribution and Abundance of Coastal Sharks in the U.S. Gulf of Mexico and Eastern Seaboard, 1995 and 1996

During 1995 and 1996, the National Marine Fisheries Service (NMFS), conducted pilot studies to develop survey methodology and a sampling strategy for assessment of coastal shark populations in the Gulf of Mexico and western North Atlantic. Longline gear similar to that used in the commercial shark fishery was deployed at randomly selected stations within three depth strata per 60 nautical mile gridf rom Brownsville, Tex. to Cape Ann, Mass. The survey methodology and gear design used in these surveys proved effective for capturing many of the small and large coastal sharks regulated under the auspices of the 1993 Fisheries Management Plan (FMP) for Sharks oft he Atlantic Ocean. Shark catch rates, species composition, and relative abundance documented in these pilot surveys were similar to those reported from observer programs monitoring commercial activities. During 78 survey days, 269 bottom longline sets were completed with 879 sharks captured.
A Novel Arc Fault Detection Method Integrated Random Forest, Improved Multi-scale Permutation Entropy and Wavelet Packet Transform

Arc faults are one of the important causes of electric fires. In order to solve the problem of randomness, diversity, the concealment of series arc faults and to improve the detection accuracy, a novel arc fault detection method integrated random forest (RF), improved multi-scale permutation entropy (IMPE) and wavelet packet transform (WPT) are designed. Firstly, singular value decomposition (SVD) was applied to filter the current signal and then the high-dimensional fault features were constructed by extracting IMPE, the wavelet packet energy and the wavelet packet energy-entropy. Afterward, the high-dimensional fault features were employed to train the RF to realize the arc fault detection of different load types and the experimental results verify the effectiveness of the arc fault detection method designed in this paper. Finally, the comparative experiments demonstrates that the RF shows better performance in arc fault detection compared to the back-propagation neural network (BPNN) and least squares support vector machines (LSSVM), and that the experiments of transient events indicate that RF is able to effectively avoid incorrectly detecting different load types during the start operations and stop operations.
Participation in Undergraduate Research Reduces Equity Gaps in STEM Graduation Rates

Many students who enroll in a public U.S. 4-y college will not graduate. The odds of completing a college degree are even lower for students who have been marginalized in higher education, especially in Science, Technology, Engineering, and Math (STEM) fields. Can undergraduate research increase a student’s likelihood of graduating college and close educational equity gaps in college completion? To answer this question, we use data from six public U.S. universities (N = 120,308 students) and use Propensity Score Matching to generate a comparison group for analyses. We conducted logistic regressions on graduation rates and equity gaps in 4 and 6 y using the matched comparison group and undergraduate researchers in STEM (n = 2727). When being compared with like-peers and controlling for background characteristics and prior academic performance, students who participated in undergraduate research were twice as likely to graduate in 4 y and over 10 times as likely to graduate in 6 y. We also found that equity gaps in 4-y graduation rates for students of color, low-income, and first-generation students were cut in half for undergraduate researchers. At 6 y, these gaps were completely closed for undergraduate researchers. As we seek ways to close education gaps and increase graduation rates, undergraduate research can be a meaningful practice to improve student success.
Environmental awareness and attitude among Iranian students in Malaysian universities

This study focuses on environmental awareness and attitude among Iranian students in Malaysian universities. It evaluates the awareness and attitude of a group of 541 from 14 universities. The figure to 541 is considered the representative of these students and the selection was based on Stratified Random sampling method and G-power soft ware. A set of questionnaire which comprised of 25 questions was applied as instrument for data collection. The results revealed that environmental awareness was overall moderate while environmental attitude was high. The study also found that there was no significant difference observed between sex groups while environmental awareness results indicated that there were significant difference among different levels of education. This trend was in contrast with observation for environment alattitude status. The age groups analysis results revealed significant difference in environmental awareness and attitude. It was also found that the media positively affected the level of environmental awareness and attitude among students. The study concluded that increase on age and level of education would improve the level of awareness and attitude regarding to environmental issues.
Exploring the mechanism of LncRNA CASC15 affecting hepatocellular carcinoma through miRNA

This study aimed to determine the potential mechanisms through which long noncoding (Lnc) RNA cancer susceptibility candidate 15 (CASC15) affects hepatocellular carcinoma (HCC). We retrieved HCC RNA-seq and clinical information from the UCSC Xena database. The differential expression (DE) of CASC15 was detected. Overall survival was analyzed using Kaplan–Meier (K–M) curves. Molecular function and signaling pathways affected by CASC15 were determined using Gene Set Enrichment Analysis. Associations between CASC15 and the HCC microenvironment were investigated using immuno-infiltration assays. A differential CASC15-miRNA-mRNA network and HCC-specific CASC15-miRNA-mRNA ceRNA network were constructed. The overexpression of CASC15 in HCC tissues was associated with histological grade, clinical stage, pathological T stage, poor survival, more complex immune cell components, and 12 immune checkpoints. We identified 27 DE miRNAs and 270 DE mRNAs in the differential CASC15-miRNA-mRNA network, and 10 key genes that were enriched in 12 cancer-related signaling pathways. Extraction of the HCC-specific CASC15-miRNA-mRNA network revealed that IGF1R, MET, and KRAS were associated with HCC progression and occurrence. Our bioinformatic findings confirmed that CASC15 is a promising prognostic biomarker for HCC, and elevated levels in HCC are associated with the tumor microenvironment. We also constructed a disease-specific CASC15-miRNA-mRNA regulatory ceRNA network that provides a new perspective for the precise indexing of patients with elevated levels of CASC15.
Observation of Electrostatically Driven Surface Adsorption in Mixed Surfactant Systems

We employed heterodyne-detected vibrational sum-frequency generation (HD-VSFG) spectroscopy to obtain a molecular-level understanding of the interaction between the anionic surfactant sodium dodecyl ammonium sulfate (SDS) and the cationic surfactant dodecyltrimethylammonium bromide (DTAB). We observed that these surfactants show a strong cooperative effect on their adsorption to the water–air interface. Even at bulk concentrations 1000 times lower than the critical micelle concentrations of SDS and DTAB, a nearly complete surface surfactant layer is observed when both surfactants are present. This strong enhancement of the surface concentrations of DS– and DTA+ can be quantitatively explained from the favorable Coulomb interaction of the oppositely charged headgroups of DS– and DTA+ and the electrostatic interactions with their counterions. The HD-VSFG results are complemented by a modified Langmuir adsorption model in which we include the free energy associated with the electrostatic interactions of the surfactant ions and their counterions.
USE OF NONLINEAR MEASURES TO COMPARE ATHLETE POSTURAL SWAY DYNAMICS

The purpose of this study was to examine the use of nonlinear analysis as a tool to evaluate postural sway patterns in athletes and physically active non-athletes. Balance is an integral part of many sports but seems to be task specific. Data collection occurred for 30 seconds during eyes open condition on double leg and single left and right leg trials. Analysis of the data using Transfer Entropy (TE) and Fractal Dimension (FD) yielded Ice Hockey and Football players having distinctly different postural dynamic control from each other and physically active non-players in only a couple conditions for TE and multiple conditions for FD. These balance measures support the idea of sports requiring different postural sway dynamics.
Incorporation of a cost of deliberation time in perceptual decision making

Many decisions benefit from the accumulation of evidence obtained sequentially over time. In such circumstances, the decision maker must balance speed against accuracy, and the nature of this tradeoff mediates competing desiderata and costs, especially those associated with the passage of time. A neural mechanism to achieve this balance is to accumulate evidence in suitable units and to terminate the deliberation when enough evidence has accrued. To accommodate time costs, it has been hypothesized that the criterion to terminate a decision may become lax as a function of time. Here we tested this hypothesis by manipulating the cost of time in a perceptual choice-reaction time task. Participants discriminated the direction of motion in a dynamic random-dot display, which varied in difficulty across trials. After each trial, they received feedback in the form of points based on whether they made a correct or erroneous choice. They were instructed to maximize their points per unit of time. Unbeknownst to the participants, halfway through the experiment, we increased the time pressure by canceling a small fraction of trials if they had not made a decision by a provisional deadline. Although the manipulation canceled less than 5% of trials, it induced the participants to make faster decisions while lowering their decision accuracy. The pattern of choices and reaction times were explained by bounded drift-diffusion. In all phases of the experiment, stopping bounds were found to decline as a function of time, consistent with the optimal solution, and this decline was exaggerated in response to the time-cost manipulation.
Cost-benefit analysis of cryogenic electron tomography subtomogram averaging of chaperonin MmCpn at near atomic resolution

Cryogenic electron microscopy single particle reconstruction (cryoEM-SPR) has evolved into a routine approach for determining macromolecule structures to near-atomic resolution. Cryogenic electron tomography subtomogram averaging (cryoET-STA) towards similar resolution, in contrast, is still under active development. CryoET can capture the 3D snapshot of individual macromolecules by stage tilting, offering multiple angular views per particle than the single particle reconstruction approach. Here we use the archaea chaperonin MmCpn as a model macromolecule to investigate the resolution limiting factors of cryoET-STA in terms of cumulative electron dose, ice thickness, subtomogram numbers and tilt angle ranges. By quantitative analysis of these factors against the STA reconstruction resolution, we delineate the feasibility of attaining high resolution structure determination with cryoET-STA. This study provides biophysical guidance for the application of cryoET-STA towards high resolution and the cost against benefit of using cryoET-STA to achieve an efficient outcome at the desired resolution.
Conway-Bromage-Lyndon (CBL): an exact, dynamic representation of k-mer sets

In this paper, we introduce the Conway-Bromage-Lyndon (CBL) structure, a compressed, dynamic and exact method for representing k-mer sets. Originating from Conway and Bromage’s concept, CBL innovatively employs the smallest cyclic rotations of k-mers, akin to Lyndon words, to leverage lexicographic redundancies. In order to support dynamic operations and set operations, we propose a dynamic bit vector structure that draws a parallel with Elias-Fano’s scheme. This structure is encapsulated in a Rust library, demonstrating a balanced blend of construction efficiency, cache locality, and compression. Our findings suggest that CBL outperforms existing dynamic k-mer set methods. Unique to this work, CBL stands out as the only known exact k-mer structure offering in-place set operations. Its different combined abilities position it as a flexible Swiss knife structure for k-mer set management. Availability: https://github.com/imartayan/CBL
Brain white matter pathways of resilience to chronic back pain: a multisite validation

Chronic back pain (CBP) is a global health concern with significant societal and economic burden. While various predictors of back pain chronicity have been proposed, including demographic and psychosocial factors, neuroimaging studies have shown that brain characteristics can serve as robust predictors of CBP. However, large-scale, multisite validation of these predictors is currently lacking. In two independent longitudinal studies, we examined white matter diffusion imaging data and pain characteristics in patients with subacute back pain (SBP) over six- and 12-month periods. Diffusion data from individuals with CBP and healthy controls (HC) were analyzed for comparison. Whole-brain tract-based spatial statistics analyses revealed that a cluster in the right superior longitudinal fasciculus (SLF) tract had larger fractional anisotropy (FA) values in patients who recovered (SBPr) compared to those with persistent pain (SBPp), and predicted changes in pain severity. The SLF FA values accurately classified patients at baseline and follow-up in a third publicly available dataset (Area under the Receiver Operating Curve ∼ 0.70). Notably, patients who recovered had FA values larger than those of HC suggesting a potential role of SLF integrity in resilience to CBP. Structural connectivity-based models also classified SBPp and SBPr patients from the three data sets (validation accuracy 67%). Our results validate the right SLF as a robust predictor of CBP development, with potential for clinical translation. Cognitive and behavioral processes dependent on the right SLF, such as proprioception and visuospatial attention, should be analyzed in subacute stages as they could prove important for back pain chronicity.
NELF coordinates Pol II transcription termination and DNA replication initiation

Regulation of RNA polymerase II (Pol II) transcription is closely associated with cell proliferation. However, it remains unclear how the Pol II transcription program is altered in cancer to favour cell growth. Here, we find that gene expression of NELFCD, a known negative elongation factor, is up-regulated in colorectal tumours. To dissect the direct role of NELF-C on Pol II transcription in such cancer, we employed an auxin-dependent protein degradation system for NELF-C in combination with nascent transcript sequencing technologies. Strikingly, we demonstrated that the acute loss of NELF-C protein globally perturbs Pol II transcription termination and also increases transcription elongation rate, independently of promoter-proximal Pol II pausing. This results in Pol II transcription into DNA replication initiation zones, and may link to failure of the cell cycle transition into S phase. We anticipate that NELF will be a potential therapeutic target to restrict colorectal cancers by promoting transcription-replication conflict. HIGHLIGHTS Expression of NELFCD transcript is up-regulated in colorectal tumors NELF-C protein is mandatory for the transition between G1-S phases during cell cycle NELF-C loss impairs transcription termination independently of Pol II promoter-proximal pausing NELF-C loss leads Pol II to invade DNA replication initiation zones
Age-Related RPE changes in Wildtype C57BL/6J Mice between 2 and 32 Months

Purpose This study provides a systematic evaluation of age-related changes in RPE cell structure and function using a morphometric approach. We aim to better capture nuanced predictive changes in cell heterogeneity that reflect loss of RPE integrity during normal aging. Using C57BL6/J mice ranging from P60-P730, we sought to evaluate how regional changes in RPE shape reflect incremental losses in RPE cell function with advancing age. We hypothesize that tracking global morphological changes in RPE is predictive of functional defects over time. Methods We tested three groups of C57BL/6J mice (young: P60-180; Middle-aged: P365-729; aged: 730+) for function and structural defects using electroretinograms, immunofluorescence, and phagocytosis assays. Results The largest changes in RPE morphology were evident between the young and aged groups, while the middle-aged group exhibited smaller but notable region-specific differences. We observed a 1.9-fold increase in cytoplasmic alpha-catenin expression specifically in the central-medial region of the eye between the young and aged group. There was an 8-fold increase in subretinal, IBA-1-positive immune cell recruitment and a significant decrease in visual function in aged mice compared to young mice. Functional defects in the RPE corroborated by changes in RPE phagocytotic capacity. Conclusions The marked increase of cytoplasmic alpha-catenin expression and subretinal immune cell deposition, and decreased visual output coincide with regional changes in RPE cell morphometrics when stratified by age. These cumulative changes in the RPE morphology showed predictive regional patterns of stress associated with loss of RPE integrity.
Lead in the head: persistent lead poisoning of waterfowl in the Camargue (southern France) ten years after the ban on the use of lead shot in wetlands

Lead pollution remains a worldwide environmental and health issue with persistent detrimental effects on human and wildlife. Despite having been identified as an issue for wildlife a long time ago, the use of lead shot for hunting in wetlands was banned only in 2006 in France. Here, we took advantage of a long-term monitoring of waterfowl lead shot contamination in the Camargue (southern France) to (1) assess the local effectiveness of the French regulation in reducing waterfowl contamination and to (2) assess local compliance regarding the use of nontoxic shots in wetlands from 2007 onwards. We collected waterfowl gizzard from 38 hunters in the Camargue during 20 hunting seasons (1998 to 2017) for a total of 2306 gizzards from 28 different species. From 2008 to 2019, we also systematically collected the cartridge casings at three sites of communal wetland hunting. Ratio of lead vs nontoxic cartridges found in the field allowed monitoring hunter compliance with the new regulation. Despite a ten-year long ban on lead shot our results do not show any significant reduction in waterfowl exposure to lead through shot ingestion in the Camargue over the 20-year monitoring period. Indeed, gizzards of harvested waterfowl were as likely to contain at least one lead shot before the ban as after with a mean prevalence of 12% over the 13 species considered across the study period. Cartridge casings showed the persistence of use of lead shots by hunters in the Camargue wetlands despite a slow increase in the use of nontoxic cartridges. This unequivocally indicates that the law is far from being strictly applied, pointing to an insufficient policy enforcement. Our results support the need for a complete ban of lead ammunition for both wetland and terrestrial wildfowl which will facilitate policy enforcement and compliance.
Community context influences the conjugation efficiency of E. coli

In urinary tract infections different bacteria can live in a polymicrobial community, it is unknown how such community members affect the conjugation rate of uropathogenic Escherichia coli. We investigated the influence of the polymicrobial urinary tract infection (UTI) community context on the conjugation rate of E. coli isolates in artificial urine medium. Pairwise conjugation rate experiments were conducted between a donor E. coli strain containing pOXA-48 and six uropathogenic E. coli isolates in the presence and absence of five community members to elucidate their effect on the rate of conjugation. We found that the basal conjugation rates in the absence of community members are genotype dependent. Interestingly, bacterial interactions have an overall positive effect on E. coli conjugation rates. Particularly Gram-positive enterococcal species were found to enhance the conjugation rates of most uropathogenic E. coli isolates. We hypothesize that the nature and co-culture of the interactions is important for these increased conjugation rates in AUM.
Mitochondrial Ca2+ efflux controls neuronal metabolism and long-term memory across species

While impairing neuronal metabolism limits brain performance, it remains poorly understood whether enhancing metabolism in neurons, in contrast, could boost brain function. We find that reducing the expression of the mitochondrial H+/Ca2+ exchanger Letm1 results in increased Ca2+ retention in the mitochondrial matrix of firing neurons, which overactivates neuronal metabolism in flies and rodents. We find that upscaled metabolic states in active neurons of central memory circuits of flies and mice enable storing long-term memories in training paradigms in which wild-type counterparts of both species fail to remember. Our findings unveil an evolutionarily conserved mechanism that controls mitochondrial metabolism in active neurons and prove its crucial role in governing higher brain functions, such as long-term memory formation. Highlights - Letm1 controls activity-driven mitochondrial Ca2+ efflux in neurons - Increased mitochondrial Ca2+ retention during activity overactivates neuronal metabolism - Activity-driven upscaling of neuronal metabolism facilitates long-term olfactory memory in flies and mice
Automated generation of tactile maps

ABSTRACT The Support Centre for Students with Special Needs at Masaryk University (the Teiresias Centre) in Brno, Czech Republic asked the team at the Department of Geography at the Faculty of Science to develop a technological procedure for the preparation of tactile maps from available sources of data. Most users would be blind and visually impaired students of Masaryk University. A set of scripts in Python language was prepared for the ArcGIS environment. The scripts prepare the source data, modify the layers, generate the layout of map sheets and export map sheets. The grid of map sheets covers the whole area of Brno City. Printed map sheets are combinable into larger areas. The scale of each map sheet is 1:2500.