Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence and risk factors associated with Eimeria species infection in cattle of different geographical regions of Indonesia

Abstract Background and Aim: Eimeria spp. are gastrointestinal protozoans that affect animal productivity, thereby causing symptoms that range from bloody diarrhea to death. These symptoms cause economic losses to farmers. The distribution of Eimeria spp. in cattle has, therefore, been reported to have spread widely, especially in the tropics and subtropics. Indonesia is a tropical country at high risk of Eimeria infections. This study aimed to identify the prevalence and risk factors related to the levels of eimeriosis in beef cattle originating from different geographic areas in Indonesia. Materials and Methods: Here, 817 fecal samples were collected from beef cattle in Indonesia, including 282 calves, 535 adults, 530 males, and 287 females. In addition, 156 semi-intensively and 661 intensively managed cattle were randomly collected. Then, fecal samples were analyzed by parasitology examinations. Results: Screening examination using the sugar flotation modification method showed that Eimeria spp. were prevalent in Indonesia, as 65.4% of the bacterial strain was detected. The prevalence of identified Eimeria spp. in Indonesia was highest in North Maluku (Maluku Island) (94.1%), whereas the lowest levels were observed in West Java (24.0%) (Java Island). The prevalence was also found to be higher in males (79.3%) than females (51.9%). Similarly, levels in semi-intensively managed cattle (66.7%) were higher than those subjected to intensive management (65.9%). However, its prevalence in calf and adult cattle was similar. Conclusion: Bovine eimeriosis spp. were detected at high prevalence in Indonesia, and high-level risks were observed in infected males, including those under the semi-intensive management. In addition, although the results from oocyst examinations were based on qualitative analysis, the endemicity levels of Eimeria spp. among farms in Indonesia should be considered because Eimeria spp. were distributed in most parts of Indonesia. Based on the results of this study, we provide the first information about the prevalence of bovine eimeriosis from different geographical locations in Indonesia, which have differing climates associated with the level of the existing risk factors. Hence, farmers are advised to pay more attention to strict biosecurity techniques on their farms, thereby favoring the early control of bovine eimeriosis.
Leprosy patients quality of life: a scoping review.

OBJECTIVE To explore the scientific evidence regarding the leprosy patients quality of life. METHOD Scoping review according to the Joanna Briggs Institute methodology, with articles indexed in PubMed, Cochrane, LILACS, Embase, CINAHL, Scopus, Web of Science, PsyINFO, INFOLEP, and Google Scholar databases, published in full in Portuguese, English, or Spanish. RESULTS Seventy-four studies were identified, with 71 of quantitative approach and 3 with a mixed method. There was a predominance of studies published in Brazil (58.1%), with an adult population, (97.3%) and recruited in reference centers for the treatment of leprosy (52.7%). There was greater use of the WHOQOL-bref (50%) and SF-36 (18.9%) instruments to assess quality of life. The study showed that the greatest impairment in quality of life was related to the delay in the diagnosis of the disease, to leprosy reactions, physical disabilities, neuropathic pain, and stigma. CONCLUSION Most studies were developed in endemic countries, with adults, and based on observational studies, and the worst scores obtained were associated with physical domain impairment.
Knowledge, Attitude, and Practice regarding Testicular Cancer and Testicular Self-Examination among Male Students Pursuing Bachelor's Degree in Bharatpur Metropolitan City, Chitwan, Nepal

Background Testicular cancer is a malignant tumor of the testicles, the male reproductive organs that produce sperm and testosterone. It is one of the most common cancers in young men. This form of cancer can be easily diagnosed by self-examination of testicles and is curable if detected early. Periodic self-examination must be performed for early detection. Due to lack of knowledge on testicular cancer and testicular self-examination techniques, patients can potentially miss early detection. This study is aimed at assessing the knowledge, attitude, and practice regarding testicular cancer and testicular self-examination among male college students pursuing a Bachelor's degree. Methods A web-based cross-sectional analytical study was adopted to assess the knowledge, attitude, and practice of testicular cancer and testicular self-examination among male college students pursuing a Bachelor's degree and living in Bharatpur Metropolitan City in the Chitwan District of Nepal. The snowball sampling technique was employed to identify the eligible participants. Collected data were entered in SPSS version 22 and analyzed by using the Chi-square test, Pearson's correlation, and binary logistic regression. Results Out of 402 respondents, majority (56.7%) had poor knowledge regarding testicular cancer and testicular self-examination and only 11.4% had performed testicular self-examination. The majority (67.2%) of the respondents had shown an unfavorable attitude towards testicular cancer (TC) and testicular self-examination (TSE). There was a significant association between the level of knowledge and marital status 4.516 (1.962-10.397) and ethnicity 2.606 (1.443-4.709). Likewise, age 0.396 (0.191-0.821) and marital status 0.347 (0.156-0.775) have been significantly associated with testicular self-examination practice. Regarding favorable attitude, age 0.362 (0.186-0.706) and sources of information from mass media 2.346 (1.328-4.143) have been associated significantly. Conclusion The study finding shows that the knowledge on testicular cancer and testicular self-examination was low. Due to lack of knowledge and trainings, the potential opportunities for early detection of testicular cancer are missed substantially. Periodic testicular self-examination is vital for early detection of testicular cancer. Hence, it is crucial to implement massive educational campaigns and trainings on testicular cancer and testicular self-examination techniques among young male groups.
Vitamin D supplementation and Covid‐19 outcomes: A systematic review, meta‐analysis and meta‐regression

Vitamin D has many protective properties and potential role against acute lung injury. Low serum vitamin D is associated with high risk of pneumonia and development of acute respiratory distress syndrome. This study sought to analyse the efficacy of vitamin D in improving the outcomes of coronavirus disease 2019 (Covid‐19) patients. Using specific keywords, we comprehensively searched the potential articles on PubMed, Europe PMC and ClinicalTrials.gov database until 8th May 2021. All published studies on Covid‐19 and vitamin D were retrieved. Statistical analysis was conducted using Review Manager 5.4 software. A total of 11 studies with 22,265 Covid‐19 patients were included in the meta‐analysis. Our data suggested that vitamin D supplementation was associated with reduction in intensive care unit admission rate (OR 0.27; 95% CI: 0.09–0.76, p = 0.010, I2 = 70%, random‐effect modelling); reduction of the need for mechanical ventilation (OR 0.34; 95% CI: 0.16–0.72, p = 0.005, I2 = 61%, random‐effect modelling) and reduction of mortality from Covid‐19 (OR 0.37; 95% CI: 0.21–0.66, p < 0.001, I2 = 50%, random‐effect modelling). Further analysis showed that the associations were influenced by age (p = 0.020). Our study suggests that vitamin D supplementation may offer beneficial effects on Covid‐19 outcomes. However, more randomized clinical trials are required to confirm this conclusion.
Direct-Contact Low-Frequency Ultrasound and Pulse Lavage Eradicates Biofilms on Implant Materials In Vitro

Pulse lavage (PL) debridement and ultrasound are both known to be the treatment of biofilm-related periprosthetic joint infection (PJI). However, the efficacy of these in combination is unknown in eradicating biofilm from the orthopaedic metal implant surface. This study was conducted to understand the efficacy of PL and ultrasound in combination in eradicating bacterial biofilms on titanium alloy in vitro. Biofilms of Staphylococcus aureus strains were grown on titanium alloy coupons for 24 h. Then, the coupons were taken to each treatment group: (i) debrided with PL, (ii) exposed to ultrasound, or (iii) exposed to both. An untreated biofilm was set as a control group. Viable plate count and confocal microscopy using live/dead staining was used to measure the amount of biofilm. Viable plate count showed an approximate two-log reduction in CFU/cm2 in PL alone, from an initial cell count on the mental surface of approximately 109 CFU/cm2. The ultrasound caused an approximate seven-log reduction, and the combination group eradicated viable biofilm bacteria completely. Confocal imaging corroborated the CFU data. Our results indicate that PL and ultrasound both are remarkably in eradicating biofilm, and the combination of PL and ultrasound is more effective than alone in reducing biofilm.
Initiation of migraine-related cortical spreading depolarization by hyperactivity of GABAergic neurons and NaV1.1 channels

Spreading depolarizations (SDs) are involved in migraine, epilepsy, stroke, traumatic brain injury, and subarachnoid hemorrhage. However, the cellular origin and specific differential mechanisms are not clear. Increased glutamatergic activity is thought to be the key factor for generating cortical spreading depression (CSD), a pathological mechanism of migraine. Here, we show that acute pharmacological activation of NaV1.1 (the main Na+ channel of interneurons) or optogenetic-induced hyperactivity of GABAergic interneurons is sufficient to ignite CSD in the neocortex by spiking-generated extracellular K+ build-up. Neither GABAergic nor glutamatergic synaptic transmission were required for CSD initiation. CSD was not generated in other brain areas, suggesting that this is a neocortex-specific mechanism of CSD initiation. Gain-of-function mutations of NaV1.1 (SCN1A) cause familial hemiplegic migraine type-3 (FHM3), a subtype of migraine with aura, of which CSD is the neurophysiological correlate. Our results provide the mechanism linking NaV1.1 gain of function to CSD generation in FHM3. Thus, we reveal the key role of hyperactivity of GABAergic interneurons in a mechanism of CSD initiation, which is relevant as a pathological mechanism of Nav1.1 FHM3 mutations, and possibly also for other types of migraine and diseases in which SDs are involved.
Global gene expression analysis of pigeonpea with male sterility conditioned by A2 cytoplasm

Cytoplasmic male sterility(CMS), a maternally inherited trait, provides a promising means to harness yield gains associated with hybrid vigor. In pigeonpea [Cajanus cajan (L.) Huth], nine types of sterility‐inducing cytoplasm have been reported, of which A2 and A4 have been successfully deployed in hybrid breeding. Unfortunately, molecular mechanism of the CMS trait is poorly understood because of limited research invested. More recently, an association between a mitochondrial gene (nad7) and A4‐CMS has been demonstrated in pigeonpea; however, the mechanism underlying A2‐CMS still remains obscure. The current investigation aimed to analyze the differences in A2‐CMS line (ICPL 88039A) and its isogenic maintainer line (ICPL 88039B) at transcriptome level using next‐generation sequencing. Gene expression profiling uncovered a set of 505 genes that showed altered expression in response to CMS, of which, 412 genes were upregulated while 93 were downregulated in the fertile maintainer line vs. the CMS line. Further, gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and protein–protein interaction (PPI) network analyses revealed association of CMS in pigeonpea with four major pathways: glucose and lipid metabolism, ATP production, pollen development and pollen tube growth, and reactive oxygen species (ROS) scavenging. Patterns of digital gene expression were confirmed by quantitative real‐time polymerase chain reaction (qRT‐PCR) of six candidate genes. This study elucidates candidate genes and metabolic pathways having potential associations with pollen development and male sterility in pigeonpea A2‐CMS. New insights on molecular mechanism of CMS trait in pigeonpea will be helpful to accelerate heterosis utilization for enhancing productivity gains in pigeonpea.
High-throughput characterization of photocrosslinker-bearing ion channel variants to map residues critical for function and pharmacology

Incorporation of noncanonical amino acids (ncAAs) can endow proteins with novel functionalities, such as crosslinking or fluorescence. In ion channels, the function of these variants can be studied with great precision using standard electrophysiology, but this approach is typically labor intensive and low throughput. Here, we establish a high-throughput protocol to conduct functional and pharmacological investigations of ncAA-containing human acid-sensing ion channel 1a (hASIC1a) variants in transiently transfected mammalian cells. We introduce 3 different photocrosslinking ncAAs into 103 positions and assess the function of the resulting 309 variants with automated patch clamp (APC). We demonstrate that the approach is efficient and versatile, as it is amenable to assessing even complex pharmacological modulation by peptides. The data show that the acidic pocket is a major determinant for current decay, and live-cell crosslinking provides insight into the hASIC1a–psalmotoxin 1 (PcTx1) interaction. Further, we provide evidence that the protocol can be applied to other ion channels, such as P2X2 and GluA2 receptors. We therefore anticipate the approach to enable future APC-based studies of ncAA-containing ion channels in mammalian cells.
Expression and affinity purification of recombinant mammalian Mitochondrial Ribosomal Small Subunit (MRPS) proteins and protein-protein interaction analysis indicate putative role in tumorigenic cellular processes.

MRPS group of proteins are structural constituents of the small subunit of mitoribosomes involved in translation. Recent studies indicate role in tumorigenic process, however, unlike cytosolic ribosomal proteins, knowledge on the role of MRPS proteins in alternate cellular processes is very limited. Mapping protein-protein interactions (PPIs) onto known cellular processes can be a valuable tool to identify novel protein functions. In this study, to identify PPIs of MRPS proteins, we have constructed thirty-one GST/MRPS fusion clones. GST/MRPS fusion proteins were confirmed by MALDI-TOF analysis. GST pull-downs were performed using eight GST/MRPS proteins (MRPS9, MRPS10, MRPS11, MRPS18B, MRPS31, MRPS33, MRPS38, MRPS39), GST alone as pull-down control, and HEK293 cell lysate as the source for anchor proteins followed by nLC/MS/MS analysis and probable PPIs of eight MRPS proteins were identified. Three PPIs from GST pull-downs and interaction between six MRPS proteins and p53 previously reported in PPI database were validated. The PPI network analysis revealed putative role in cellular processes with implications for tumorigenesis. Gene expression screening of a cancer cell line panel indicated overexpression of MRPS10 and MRPS31 in breast cancer. Co-expression module identification tool analysis of breast cancer gene expression and MRPS10 and MRPS31 PPIs revealed putative role for PPI with ACADSB in fatty acid oxidation process regulated by brain-derived neurotrophic factor (BDNF) signaling pathway.
Mask is All You Need: Rethinking Mask R-CNN for Dense and Arbitrary-Shaped Scene Text Detection

Due to the large success in object detection and instance segmentation, Mask R-CNN attracts great attention and is widely adopted as a strong baseline for arbitrary-shaped scene text detection and spotting. However, two issues remain to be settled. The first is dense text case, which is easy to be neglected but quite practical. There may exist multiple instances in one proposal, which makes it difficult for the mask head to distinguish different instances and degrades the performance. In this work, we argue that the performance degradation results from the learning confusion issue in the mask head. We propose to use an MLP decoder instead of the "deconv-conv" decoder in the mask head, which alleviates the issue and promotes robustness significantly. And we propose instance-aware mask learning in which the mask head learns to predict the shape of the whole instance rather than classify each pixel to text or non-text. With instance-aware mask learning, the mask branch can learn separated and compact masks. The second is that due to large variations in scale and aspect ratio, RPN needs complicated anchor settings, making it hard to maintain and transfer across different datasets. To settle this issue, we propose an adaptive label assignment in which all instances especially those with extreme aspect ratios are guaranteed to be associated with enough anchors. Equipped with these components, the proposed method named MAYOR achieves state-of-the-art performance on five benchmarks including DAST1500, MSRA-TD500, ICDAR2015, CTW1500, and Total-Text.
Physics of PT-Symmetric Quantum Systems at Finite Temperature

Parity-time (PT ) non-Hermitian (NH) system has significant effects on observable in a great variety of physical phenomena in NH physics. However, the PT -symmetric NH quantum system at finite temperature (the so-called thermal PT system) has never been addressed. In this letter, based on a controlled open quantum system coupling two separated environments, we proposed a design to realize a thermal PT system. After solving quantum master equation in the Gorini-KossakowskiSudarshan-Lindblad form, the unexpected, abnormal, universal properties of NH thermal states (the unique final states under time evolution) are explored, for example, the non-Boltzmann/Gibbs distribution, high-temperature non-thermalization effect, etc. To understand the anomalous behaviours in thermal PT system, we developed the quantum Liouvillian statistical theory – the generalization of usual quantum statistical theory to finite-temperature NH systems. With its help, we derived the analytical results of thermodynamic properties. In addition, we found that at EP a continuous thermodynamic phase transition occurs, of which there exists zero temperature anomaly. This discovery will open a door to novel physics for NH systems at finite temperature.
Quantum-classical hybrid neural networks in the neural tangent kernel regime

Recently, quantum neural networks or quantum–classical neural networks (qcNN) have been actively studied, as a possible alternative to the conventional classical neural network (cNN), but their practical and theoretically-guaranteed performance is still to be investigated. In contrast, cNNs and especially deep cNNs, have acquired several solid theoretical basis; one of those basis is the neural tangent kernel (NTK) theory, which can successfully explain the mechanism of various desirable properties of cNNs, particularly the global convergence in the training process. In this paper, we study a class of qcNN composed of a quantum data-encoder followed by a cNN. The quantum part is randomly initialized according to unitary 2-designs, which is an effective feature extraction process for quantum states, and the classical part is also randomly initialized according to Gaussian distributions; then, in the NTK regime where the number of nodes of the cNN becomes infinitely large, the output of the entire qcNN becomes a nonlinear function of the so-called projected quantum kernel. That is, the NTK theory is used to construct an effective quantum kernel, which is in general nontrivial to design. Moreover, NTK defined for the qcNN is identical to the covariance matrix of a Gaussian process, which allows us to analytically study the learning process. These properties are investigated in thorough numerical experiments; particularly, we demonstrate that the qcNN shows a clear advantage over fully classical NNs and qNNs for the problem of learning the quantum data-generating process.
Basic nutritional investigation Influence of nutritional iron deficiency anemia on DNA stability and lipid peroxidation in rats

Objective: Oxidative stress results from an imbalance between the formation and neutralization of pro-oxidants. Disturbance of the pro-oxidant/antioxidant balance is also considered to be a causative factor underlying oxidative damage to cellular molecules, such as DNA, causing strand breaks. There is considerable controversy about the antioxidant status in iron-deficiency anemia (IDA), but scant information is available regarding DNA integrity. In the present study, we investigated the relation between DNA stability and hepatic antioxidant capacity in rats with induced IDA. Methods: Peripheral DNA damage was assessed using an alkaline comet assay. Further, the hepatic antioxidant enzyme glutathione peroxidase and the production of thiobarbituric acid-reactive substances were measured in control rats and in those with induced IDA. Results: Comparison of the control and anemic rats showed no differences in thiobarbituric acid-reactive substances production in the cytosolic fraction of hepatic cells. Nor were there any differences in liver glutathione peroxidase enzyme activity or DNA stability, as demonstrated by the percentage of DNA in the head (90.77 in control rats versus 88.23 in anemic rats), tail (9.23 in control rats versus 11.76 in anemic rats), and olive tail moment (0.155 in control rats versus 0.141 in anemic rats). Conclusion: IDA does not affect DNA stability or lipid peroxidation in rats, suggesting that there is enough compensatory capacity to keep antioxidant defenses high. © 2008 Elsevier Inc. All rights reserved.
Adaptive Few-Shot Learning PoC Ultrasound COVID-19 Diagnostic System

This paper presents a novel ultrasound imaging point-of-care (PoC) COVID-19 diagnostic system. The adaptive visual diagnostics utilize few-shot learning (FSL) to generate encoded disease state models that are stored and classified using a dictionary of knowns. The novel vocabulary based feature processing of the pipeline adapts the knowledge of a pretrained deep neural network to compress the ultrasound images into discrimative descriptions. The computational efficiency of the FSL approach enables high diagnostic deep learning performance in PoC settings, where training data is limited and the annotation process is not strictly controlled. The algorithm performance is evaluated on the open source COVID-19 POCUS Dataset to validate the system's ability to distinguish COVID-19, pneumonia, and healthy disease states. The results of the empirical analyses demonstrate the appropriate efficiency and accuracy for scalable PoC use. The code for this work will be made publicly available on GitHub upon acceptance.
Dyadic Clustering in International Relations

Quantitative empirical inquiry in international relations often relies on dyadic data. Standard analytic techniques do not account for the fact that dyads are not generally independent of one another. That is, when dyads share a constituent member (e.g., a common country), they may be statistically dependent, or “clustered. ” Recent work has developed dyadic clustering robust standard errors (DCRSEs) that account for this dependence. Using these DCRSEs, we reanalyzed all empirical articles published in International Organization between January 2014 and January 2020 that feature dyadic data. We find that published standard errors for key explanatory variables are, on average, approximately half as large as DCRSEs, suggesting that dyadic clustering is leading researchers to severely underestimate uncertainty. However, most (67% of) statistically significant findings remain statistically significant when using DCRSEs. We conclude that accounting for dyadic clustering is both important and feasible, and offer software in R and Stata to facilitate use of DCRSEs in future research.