Miracle-dz/UniFAR-FTUs huggingface dataset:
Prediction of Short-term Precipitation in Qinghai Lake Based on BiLSTM-Attention Method

The short-term precipitation forecast plays a crucial role in production and life. The prediction accuracy and stability of the traditional model have a large room for improvement. In order to improve this problem, this paper attempts to establish a precipitation prediction method based on deep learning. A short-term precipitation prediction model for Qinghai Lake combined with a bidirectional long-term memory network and attention mechanism. Based on historical precipitation over the past month, average water pressure and average temperature, forecasts are made for precipitation over the next 48 hours. The experimental results show that the prediction model is superior to the traditional prediction method in terms of prediction accuracy, convergence speed and root mean square error and average absolute error, which can effectively improve the accuracy and stability of the short-term precipitation prediction model in local areas.
Clustering Data Stream with Rough Set

In this paper, the upper and lower approximations of rough set are introduced to describe the micro-cluster feature in the procedure of clustering uncertain data stream. The proposed algorithm employs presents the micro-cluster timestamp with the time decay and uses agglomerative clustering method to emerge new cluster in the buffer of outliers. Experimental results show that the proposed algorithm can generate natural clusters and outperforms the existing method in term of accuracy.
A Semi-automatic Technique for Fetus Segmentation in 3D Ultrasound Exams

Ultrasound exams have an important role in obstetrics due to its low cost, low risk, and real-time capabilities. The advent of three-dimensional ultrasonography has made possible the use of the fetal volume as a biometric measurement to monitor its development. The quantification of the fetal volume requires a previous process of segmentation, which consists of the labeling of the sites that belong to the object of interest in a digital image. There is not; however, a standard methodology for fetal volumetry, and most studies rely on manual segmentations. The segmentation of ultrasound images is particularly challenging due to the presence of artifacts as the speckle noise and acoustic shadows, and the fact that the contrast between regions of interest is commonly low. In this study, we have developed and tested a semiautomatic method of fetal segmentation in 3D ultrasound exams. Due to the difficulties as mentioned above, proper ultrasound segmentation methods need to make use of expected characteristics of the specific segmented structures. This thought has guided the development of our methodology that, through a sequence of simple steps, achieved good quantitative results in the segmentation task.
Blockage of HCN Channels with ZD7288 Attenuates Mechanical Hypersensitivity in Rats Model of Diabetic Neuropathy

Background: Diabetes is a chronic condition that affects millions of people worldwide. The disease can have severeimpact on many systems of the human body particularly the nervous system. Indeed, chronic peripheral nerve pain, also known as peripheral neuropathic pain (NP), is the most common complication caused by diabetes. There have existed preclinical researches that were performed using different types of Rodents as models of Chronic Pain. Such studies have proven that hypersensitivity to pain is caused, at least partially, by increased excitability of primary afferent dorsal root ganglion (DRG) neurons that send the sensory information from the periphery to the brain. However, the mechanism of this hyperexcitability is yet to be known. Aims: The primary aim of the continuing work is to examine the hypothesis that Hyperpolarization-activated Cyclic Nucleotide gated (HCN) channels (that are known to regulate excitability of the neurons) are involved in the pathophysiology of diabetic neuropathic pain (DNP). Methods and Results: To examine this hypothesis, we used a rat model of diabetic neuropathy by 60 mg/kg, i.p., of (streptozotocin (STZ), a toxin of pancreatic β-cells that release insulin) and tested the effects of blocking the HCN channels with a selective blocker, ZD7288, on two pain behaviours (mechanical hypersensitivity/allodynia, and heat hypersensitivity/hyperalgesia) in these STZ treated rats. The results showed that intraplantar administration of ZD7288 (100 μM) reduced mechanical allodynia but not heat hyperalgesia. Conclusions: The results are in agreement with previous investigations which used other models of chronic pain and suggest that HCN channels may be a good target for developing new analgesics (pain killers) for chronic pain.
Relationships between Species Communities as Determined by Analysis of Data from Multiple Surveys of Pleasant Bay, Cape Cod, MA

Abstract Pleasant Bay, MA, is a 8741-ha (21,600-acre) coastal lagoon with extensive eelgrass, shellfish, and salt marsh habitats and is subject to predictable variations in inlet formation resulting in shifting tides and access to the ocean. Here we describe methods to link data from independent surveys (benthic habitat assessment and fishery-independent trawl/dredge sampling) to create linkages across the ecosystem in order to guide future monitoring and management efforts. The integration of water parameters, grain size, and surficial benthic analysis to create habitat categories allowed us to explain 45% of microinvertebrate distribution. Microinvertebrate communities had significant correlations to fish and macroinvertebrate communities, strengthening the usefulness of microinvertebrate surveys. Habitat categories containing Zostera marina (Common Eeelgrass) had higher species diversity and abundances of fishes and macroinvertebrates than other habitats. The links between habitat, communities of microinvertebrates, macroinvertebrates, and fish indicate a connected ecosystem.
Using CMECS to Create Benthic Habitat Maps for Pleasant Bay, Cape Cod, Massachusetts

Abstract Benthic habitat maps are an important part of ecosystem-based management as they document biotic and abiotic resources. Integrating multiple ecosystem and environmental components is challenging, and the ability to do this is highly dependent on the methodology employed. The US Coastal and Marine Ecological Classification Standard (CMECS) uses a standardized set of classifications in a hierarchal structure to create benthic habitat maps. This study used acoustic surveys and benthic samples from Pleasant Bay, Cape Cod, MA, to develop benthic habitat maps and test relationships between biotic and abiotic variables. The collected data comprise a critical baseline record of biological and physical characteristics and will inform future management decisions as well as guide future studies of coastal resources in Pleasant Bay.
Epidemiological Investigation and Etiological Analysis of a Cutaneous Anthrax Epidemic Caused by Butchering Sick Cattle in Guizhou, China

A suspected human cutaneous anthrax epidemic caused by butchering sick cattle occurred in Zhijin County of Guizhou Province, Southwest of China, in 2016. Epidemiological investigation and etiological analysis were performed to provide a scientific basis for the source tracking of the epidemic. The epidemic was epidemiologically investigated, and skin blister samples collected from patients and soil samples collected from the butchering spots were used for Bacillus anthracis isolation. The suspicious B. anthracis isolates were identified using conventional methods and PCR, followed by genotyping using multiple-locus variable-number tandem repeats (VNTRs) analysis (MLVA-15) and canonical single-nucleotide polymorphism (canSNP). The genetic relationship of epidemic strains and isolates collected from other regions was analyzed. Epidemiological investigation results showed that the patients may be infected by B. anthracis during butchering sick cattle. Two suspected B. anthracis strains were isolated from blood samples and blister fluids, respectively. Conventional methods identified the two suspected isolates as B. anthracis, while PCR results showed that anti-protective antigen (PA) and capsule (CAP) gene were positive in the two isolates. MLVA-15 showed that the MLVA profiles of the two isolates were 9-20-12-53-16-2-8-8-8-4-4-4-4-10-4, which is different from the MLVA profiles of representative strains from other regions. CanSNP analysis showed that the two strains belonged to cluster A.Br. 001/002. Clustering analysis and minimum spanning tree (MST) demonstrated that the two isolates were clustered with strains previously isolated from Guizhou Province. The results indicated that B. anthracis was the pathogen for this epidemic, and the patients were infected during butchering the sick. The genetic characteristics and the relationship of the B. anthracis isolates to strains from other regions indicated that the epidemic was a local occurrence.
Hypoxia Tolerance of 10 Euphausiid Species in Relation to Vertical Temperature and Oxygen Gradients

Oxygen Minimum Zones prevail in most of the world’s oceans and are particularly extensive in Eastern Boundary Upwelling Ecosystems such as the Humboldt and the Benguela upwelling systems. In these regions, euphausiids are an important trophic link between primary producers and higher trophic levels. The species are known as pronounced diel vertical migrators, thus facing different levels of oxygen and temperature within a 24 h cycle. Declining oxygen levels may lead to vertically constrained habitats in euphausiids, which consequently will affect several trophic levels in the food web of the respective ecosystem. By using the regulation index (RI), the present study aimed at investigating the hypoxia tolerances of different euphausiid species from Atlantic, Pacific as well as from Polar regions. RI was calculated from 141 data sets and used to differentiate between respiration strategies using median and quartile (Q) values: low degree of oxyregulation (0.25 < RI median < 0.5); high degree of oxyregulation (0.5 < RI median < 1; Q1 > 0.25 or Q3 > 0.75); and metabolic suppression (RI median, Q1 and Q3 < 0). RI values of the polar (Euphausia superba, Thysanoessa inermis) and sub-tropical (Euphausia hanseni, Nyctiphanes capensis, and Nematoscelis megalops) species indicate a high degree of oxyregulation, whereas almost perfect oxyconformity (RI median ≈ 0; Q1 < 0 and Q3 > 0) was identified for the neritic temperate species Thysanoessa spinifera and the tropical species Euphausia lamelligera. RI values of Euphausia distinguenda and the Humboldt species Euphausia mucronata qualified these as metabolic suppressors. RI showed a significant impact of temperature on the respiration strategy of E. hanseni from oxyregulation to metabolic suppression. The species’ estimated hypoxia tolerances and the degree of oxyconformity vs. oxyregulation were linked to diel vertical migration behavior and the temperature experienced during migration. The results highlight that the euphausiid species investigated have evolved various strategies to deal with different levels of oxygen, ranging from species showing a high degree of oxyconformity to strong oxyregulation. Neritic species may be more affected by hypoxia, as these are often short-distance-migrators and only adapted to a narrow range of environmental conditions.
Genetic Diversity of Circulating Foot and Mouth Disease Virus in Uganda Cross-Sectional Study During 2014–2017

Citation: Velazquez-Salinas L, Mwiine FN, Ahmed Z, Ochwo S, Munsey A, Lutwama JJ, Perez AM, VanderWaal K and Rieder E (2020) Genetic Diversity of Circulating Foot and Mouth Disease Virus in Uganda Cross-Sectional Study During 2014–2017. Front. Vet. Sci. 7:162. doi: 10.3389/fvets.2020. 00162 Genetic Diversity of Circulating Foot and Mouth Disease Virus in Uganda Cross-Sectional Study During 2014–2017
MASQC: Next Generation Sequencing Assists Third Generation Sequencing for Quality Control in N6-Methyladenine DNA Identification

DNA N6-methyladenine (6mA) modification has been discovered as the most prevalent DNA modification in prokaryotes and eukaryotes, involving gene expression, DNA replication and repair, and host-pathogen interactions. Single-molecule real-time sequencing (SMRT-seq) can detect 6mA events in prokaryotic and eukaryotic genomes at the single-nucleotide level. However, there are no strict and economical quality control methods for high false-positive 6mA events in eukaryotic genomes. Therefore, by analyzing the distribution of 6mA in eukaryotic and prokaryotes, we proposed a method named MASQC (MeDIP-seq assists SMRT-seq for quality control in 6mA identification), which can identify 6mA events without doing the whole genome amplification (WGA) sequencing. The proposed MASQC method was assessed on two eukaryotic genomes and six bacterial genomes, our results demonstrate that MASQC performs well in quality control of false positive 6mA identification for both eukaryotic and prokaryotic genomes.
Amniotic Membrane Preparation Crucially Affects Its Broad-Spectrum Activity Against Uropathogenic Bacteria

Urinary tract infections are among the most common bacterial infections in humans. Moreover, they are highly recurrent and increasingly often resistant to antibiotics. The antimicrobial properties of the amniotic membrane (AM), the innermost layer of fetal membranes, have been briefly reported in the literature, however, the results of published studies are often inconsistent and unclear; moreover, its effect on uropathogenic bacteria has not yet been investigated. Further, there is no data in the literature about the effect of AM preparation and storage on its antimicrobial properties. To examine the impact of several preparation procedures on the antimicrobial properties of AM, we prepared patches and homogenates of fresh (fAM) and cryopreserved (cAM) human AM and tested them on 14 selected Gram-positive and Gram-negative uropathogenic bacteria. By employing novel antimicrobial efficiency assays we showed that fAM and cAM homogenates have broad-spectrum antimicrobial activity against all here tested uropathogenic bacteria, except for Serratia marcescens. Moreover, they had a potent effect also on the multiple-resistant clinical strains of uropathogenic Escherichia coli. Interestingly, the patches of fAM and cAM had no antimicrobial effect on any of the tested strains. We therefore prepared and stored AM patches according to the standard procedure for clinical use in ophthalmology, which includes the cryopreservation of antibiotic-treated AM, and performed antimicrobial efficiency assays. Our findings suggest that the ultrastructure of AM patches could enable the retention of added antibiotics. In addition, we also prepared gentamicin-resistant uropathogenic E. coli strains, which confirmed that the antimicrobial effect of antibiotic-treated AM patches can be attributed to the antibiotic alone. To summarize, here we describe novel protocols for preparation and storage of AM to ensure the preservation of its antimicrobial factors. Moreover, we describe the mechanism of AM retention of antibiotics, based on which the AM could potentially be used as a drug delivery vehicle in future clinically applicable approaches.
Stereotactically Injected Kv1.2 and CASPR2 Antisera Cause Differential Effects on CA1 Synaptic and Cellular Excitability, but Both Enhance the Vulnerability to Pro-epileptic Conditions

Purpose We present a case of voltage-gated potassium channel (VGKC) complex antibody-positive limbic encephalitis (LE) harboring autoantibodies against Kv1.2. Since the patient responded well to immunotherapy, the autoantibodies were regarded as pathogenic. We aimed to characterize the pathophysiological role of this antibody in comparison to an antibody against the VGKC-associated protein contactin-associated protein-2 (CASPR2). Methods Stereotactic injection of patient sera (anti-Kv1.2-associated LE or anti-CASPR2 encephalopathy) and a control subject was performed into the hippocampus of the anesthetized rat in vivo, and hippocampal slices were prepared for electrophysiological purposes. Using extra- and intracellular techniques, synaptic transmission, long-term potentiation (LTP) and vulnerability to pro-epileptic conditions were analyzed. Results We observed that the slope of the field excitatory postsynaptic potential (fEPSP) was significantly increased at Schaffer collateral-CA1 synapses in anti-Kv1.2-treated and anti-CASPR2-treated rats, but not at medial perforant path-dentate gyrus synapses. The increase of the fEPSP slope in CA1 was accompanied by a decrease of the paired-pulse ratio in anti-Kv1.2, but not in anti-CASPR2 tissue, indicating presynaptic site of anti-Kv1.2. In addition, anti-Kv1.2 tissue showed enhanced LTP in CA1, but dentate gyrus LTP remained unaltered. Importantly, LTP in slices from anti-CASPR2-treated animals did not differ from control values. Intracellular recordings from CA1 neurons revealed that the resting membrane potential and a single action potential were not different between anti-Kv1.2 and control tissue. However, when the depolarization was prolonged, the number of action potentials elicited was reduced in anti-Kv1.2-treated tissue compared to both control and anti-CASPR2 tissue. In contrast, polyspike discharges induced by removal of Mg2+ occurred earlier and more frequently in both patient sera compared to control. Conclusion Patient serum containing anti-Kv1.2 facilitates presynaptic transmitter release as well as postsynaptic depolarization at the Schaffer-collateral-CA1 synapse, but not in the dentate gyrus. As a consequence, both synaptic transmission and LTP in CA1 are facilitated and action potential firing is altered. In contrast, anti-CASPR2 leads to increased postsynaptic potentials, but without changing LTP or firing properties suggesting that anti-Kv1.2 and anti-CASPR2 differ in their cellular effects. Both patient sera alter susceptibility to epileptic conditions, but presumably by different mechanisms.
Effects of 11-Ketotestosterone on Development of the Previtellogenic Ovary in the Sterlet, Acipenser ruthenus

11-ketotestosterone (11-KT) is a non-aromatizable and the most potent androgen in a few teleost. It has been reported that 11-KT in serum had a high concentration and increased sharply before the period of yolk deposition in females of few fishes. The aim of this study was to analyze the role of 11-KT both in vivo and in vitro on ovarian development, related gene expression levels, Vitellogenin (Vtg) synthesis, and serum sex steroid concentrations in previtellogenic cultured sterlet (Acipenser ruthenus). Silastic strips embedded with 11-KT (5 or 25 mg/kg) were implanted in vivo for 30 days. Ovarian masculinization or sex reversal was not observed. Histological analysis showed that 11-KT promoted sterlet ovarian development in a dose-dependent manner. Vtg and testosterone (T) increased significantly, while 17β-estradiol (E2) decreased with no significant difference among groups. The expression of genes androgen receptor (ar), vtg and lipoprotein lipase (lpl) were significantly increased in liver. However, 11-KT had no effect on the expression of foxl2 and cyp19a1 in ovary. In vitro, after incubation with 11-KT (10 and 100 μM) for 5 days, both T and E2 concentrations increased in both hepatic explants and ovarian explants culture medium; the concentration of Vtg also increased in hepatic explants culture medium. The expression of ar, era, vtg, and lpl increased significantly in hepatic explants. However, only the expression of era significantly increased in cultured ovarian explants. Altogether, these results suggest that 11-KT induced ovarian development, as well as Vtg and lipid synthesis, and could be an important factor facilitating the initiation of Vtg synthesis in the liver of the previtellogenic sterlet.
Multi-Scale Landscape Influences on Genetic Diversity and Adaptive Traits in a Neotropical Savanna Tree

Changes in landscape structure can affect essential population ecological features, such as dispersal and recruitment, and thus genetic processes. Here, we analyze the effects of landscape metrics on adaptive quantitative traits variation, evolutionary potential, and on neutral genetic diversity in populations of the Neotropical savanna tree Tabebuia aurea. Using a multi-scale approach, we sampled five landscapes with two sites of savanna in each. To obtain neutral genetic variation, we genotyped 60 adult individuals from each site using 10 microsatellite loci. We measured seed size and mass. Seeds were grown in nursery in completely randomized experimental design and 17 traits were measured in seedlings to obtain the average, additive genetic variance (Va) and coefficient of variation (CVa%), which measures evolvability, for each trait. We found that habitat loss increased genetic diversity (He) and allelic richness (AR), and decreased genetic differentiation among populations (FST), most likely due to longer dispersal distance of pollen in landscapes with lower density of flowering individuals. Habitat amount positively influenced seed size. Seeds of T. aurea are wind-dispersed and larger seeds may be dispersed to short distance, increasing genetic differentiation and decreasing genetic diversity and allelic richness. Evolvability (CVa%) in root length decreased with habitat amount. Savanna trees have higher root than shoot growth rate in the initial stages, allowing seedlings to obtain water from water tables. Landscapes with lower habitat amount may be more stressful for plant species, due to the lower plant density, edge effects and the negative impacts of agroecosystems. In these landscapes, larger roots may provide higher ability to obtain water, increasing survival and avoiding dying back because of fire. Despite the very recent agriculture expansion in Central Brazil, landscape changes are affecting neutral and adaptive variation in T. aurea. Several populations have low additive genetic variation for some traits and thus, may have limited evolvability, which may jeopardize species long-term persistence. The effect of habitat loss on highly variable neutral loci may only be detected after a certain threshold of population size is attained, that could become dangerously small masking important losses of heterozygosity endangering species conservation.