Miracle-dz/UniFAR-FTUs huggingface dataset:
CLUE: COVID‐19 lung ultrasound in emergency department

Lung ultrasound (LUS) plays a critical role in the SARS‐CoV‐2 pandemic. Evidence is mounting on its utility to diagnose, assess the severity and as a triage tool in the ED. Sonographic features correlate well to computed tomography (CT) chest findings and a bedside LUS performed by a trained clinician along with clinical examination, could be an alternative to chest X‐ray and CT chest in these highly infectious patients. In this article, we have described a step‐by‐step approach to LUS in COVID patients and the CLUE (COVID‐19 LUS in the ED) protocol, which involves an anatomical parameter, the severity of lung changes, objectively scored using the validated LUS scoring system and a physiological parameter, oxygen requirement. We believe this CLUE protocol can help risk‐stratify patients presenting to ED with suspected COVID‐19 and aid clinicians in making appropriate disposition decisions.
Efficacy of Upfront Docetaxel With Androgen Deprivation Therapy for Castration-Sensitive Metastatic Prostate Cancer Among Minority Patients

Background: Upfront docetaxel (UD) with androgen deprivation therapy (ADT) has been demonstrated to improve survival outcomes in metastatic castration-sensitive prostate cancer (mCSPC). However, existing studies have included predominantly Caucasian patients. Study Question: To compare the efficacy of addition of UD to ADT in mCSPC to ADT alone among minority patients. Study Design: Retrospective study of mCSPC patients. Measures and Outcomes: Patients treated with UD and ADT between January 2014 and December 2017 (UD + ADT, n = 44) were compared with those treated with ADT alone between January 2008 and January 2017 (ADT, n = 38); patients of Caucasian ethnicity were excluded. The outcome of interest was progression-free survival (PFS), which was estimated using Kaplan–Meier analysis and Cox proportional hazard analysis. Results: Overall, 63 (76.8%) patients were African American and 16 (19.5%) were Hispanic. Fifty-five (67%) patients had high-volume mCSPC. The median follow-up was 14 months [95% confidence interval (CI): 10.4–16.5] for UD + ADT and 42 months (95% CI: 17–66.9) for ADT. Median PFS did not differ between groups: UD + ADT: 16 versus ADT: 18 months [hazard ratio (HR) for UD + ADT = 0.88, 95% CI: 0.48–1.62; P = 0.70]. In patients with high-volume disease, median PFS remained similar (UD + ADT: 16 vs. ADT: 14 months (HR for UD + ADT = 0.64, 95% CI: 0.33–1.25; P = 0.19). On multivariable analysis, prolonged time to nadir PSA, HR = 0.83 (95% CI: 0.76–0.90), was independently associated with PFS. The most common toxicities in UD + ADT were anemia and fatigue. Major limitations include small sample size and potential for selection bias due to the retrospective study design. Conclusions: In this retrospective review of a minority mCSPC cohort, UD + ADT was not associated with improved PFS compared with ADT alone. Although further study with larger sample size is needed, these results underscore the importance of ensuring accrual of minorities in clinical trials, reflective of the real-world setting.
Projecting the impact of equity-based pre-exposure prophylaxis implementation on racial disparities in HIV incidence among men who have sex with men.

BACKGROUND It is unknown what levels of pre-exposure prophylaxis (PrEP) use are needed to reduce racial disparities in HIV incidence among men who have sex with men (MSM). Using an agent-based model (ABM), we quantified the impact of achieving PrEP coverage targets grounded in equity on racial disparities in HIV incidence among MSM in an urban setting in the Southeastern United States. METHODS An ABM was adapted to simulate HIV transmission in a network of Black/African American and White MSM aged 18 to 39 years in the Atlanta-Sandy Springs-Roswell metropolitan area over ten years (2015-2024). Scenarios simulated coverage levels consistent with targets based on the ratio of the number of individuals using PrEP to the number of individuals newly diagnosed in a calendar year (i.e., the "PrEP-to-need ratio"), ranging from 1 to 10. Incidence rate ratios and differences were calculated as measures of disparities. RESULTS Without PrEP, the model predicted a rate ratio of 3.82 and a rate difference of 4.50 comparing HIV incidence in Black/African American and White MSM, respectively. Decreases in the rate ratio of at least 50% and in the rate difference of at least 75% were observed in all scenarios in which the PrEP-to-need ratio among Black/African American MSM was 10, regardless of the value among White MSM. CONCLUSION Significant increases in PrEP use are needed among Black/African American MSM to reduce racial disparities in HIV incidence. PrEP expansion must be coupled with structural interventions to address vulnerability to HIV infection among Black/African American MSM.
Role of folding kinetics of secondary structures in telomeric G-overhangs in the regulation of telomere maintenance in Saccharomyces cerevisiae

The ends of eukaryotic chromosomes typically contain a 3′ ssDNA G-rich protrusion (G-overhang). This overhang must be protected against detrimental activities of nucleases and of the DNA damage response machinery and participates in the regulation of telomerase, a ribonucleoprotein complex that maintains telomere integrity. These functions are mediated by DNA-binding proteins, such as Cdc13 in Saccharomyces cerevisiae, and the propensity of G-rich sequences to form various non-B DNA structures. Using CD and NMR spectroscopies, we show here that G-overhangs of S. cerevisiae form distinct Hoogsteen pairing–based secondary structures, depending on their length. Whereas short telomeric oligonucleotides form a G-hairpin, their longer counterparts form parallel and/or antiparallel G-quadruplexes (G4s). Regardless of their topologies, non-B DNA structures exhibited impaired binding to Cdc13 in vitro as demonstrated by electrophoretic mobility shift assays. Importantly, whereas G4 structures formed relatively quickly, G-hairpins folded extremely slowly, indicating that short G-overhangs, which are typical for most of the cell cycle, are present predominantly as single-stranded oligonucleotides and are suitable substrates for Cdc13. Using ChIP, we show that the occurrence of G4 structures peaks at the late S phase, thus correlating with the accumulation of long G-overhangs. We present a model of how time- and length-dependent formation of non-B DNA structures at chromosomal termini participates in telomere maintenance.
Population Genetic Structure of Codling Moth, Cydia pomonella (L.) (Lepidoptera: Tortricidae), in Different Localities and Host Plants in Chile

The codling moth, Cydia pomonella (L.) (Lepidoptera: Tortricidae), is a major pest introduced to almost all main pome fruit production regions worldwide. This species was detected in Chile during the last decade of the 19th century, and now has a widespread distribution in all major apple-growing regions. We performed an analysis of the genetic variability and structure of codling moth populations in Chile using five microsatellite markers. We sampled the codling moth along the main distribution area in Chile on all its main host-plant species. Low genetic differentiation among the population samples (FST = 0.03) was found, with only slight isolation by distance. According to a Bayesian assignment test (TESS), a group of localities in the coastal mountain range from the Bío-Bío Region formed a distinct genetic cluster. Our results also suggest that the codling moth that invaded the southernmost locality (Aysén Region) had two origins from central Chile and another unknown source. We did not find significant genetic differentiation between codling moth samples from different host-plant species. Our results indicate high genetic exchange among codling moth populations between the different Chilean regions and host plants.
Structural Characterization and α‐Glucosidase Inhibitory and Antioxidant Activities of Fucoidans Extracted from Saccharina japonica

Two sulfated fucoidan fractions (Lj3 and Lj5) were extracted from Saccharina japonica and then subjected to acid hydrolysis to obtain Lj3h and Lj5h. Lj3h and Lj5h were characterized using IR, methylation analysis, and mass spectrometry. It was found that Lj3h and Lj5h were homogeneous low molecular weight fucoidans. Specifically, Lj3h was composed of the main chain of 1,3‐linked α‐L‐fucopyranose residues with sulfate at C‐2 and/or C‐4 and three different monosaccharides (galactose, glucose, mannose) branched at C‐2 and/or C‐4 of fucose residue. Lj5h contained backbones of alternating galactopyranose residues and fucopyranose residues attached via a 1→3 linkage (galactofucan) and 1→6 linked galactan. The sulfation pattern was mainly located at C2/C4 fucose or galactose residues and more branches occupied at C‐4 of fucose residue and C‐2, C‐3 or/and C‐6 of galactose residue. In vitro assay indicated that, among the four fucoidans tested, only Lj5 showed potent α‐glucosidase inhibitory activity with IC50 of 153.27±22.89 μg/mL, and the two parent fucoidans, Lj3 and Lj5, showed better antioxidant activity than their derivatives. These findings highlight the structure and bioactivity diversity of Saccharina japonica‐derived fucoidans.
PD-L1 Expression and CD8+ Tumor-infiltrating Lymphocytes in Different Types of Tubo-ovarian Carcinoma and Their Prognostic Value in High-grade Serous Carcinoma

The prevalence and significance of programmed death-1 ligand (PD-L1) expression in different types of tubo-ovarian carcinoma have not been well defined. We evaluated PD-L1 expression and CD8+ tumor-infiltrating lymphocyte (TIL) density in whole tissue sections of 189 cases of tubo-ovarian carcinoma, including high-grade serous carcinoma (HGSC, n=100), clear cell carcinoma (CCC, n=24), endometrioid carcinoma (EmC, n=40), and mucinous carcinomas (MC, n=25). Using the tumor proportion score (TPS) with a 1% cutoff, PD-L1 expression was present in 21% of HGSC, 16.7% of CCC, 2.5% of EmC, and 4% of MC. Using the combined positive score (CPS) with a cutoff of 1, PD-L1 expression was present in 48% of HGSC, 25% of CCC, 20% of EmC, and 24% of MC. HGSC demonstrated significantly higher CD8+ TIL density than CCC (P=0.013238), EmC (P=0.01341), or MC (P=0.004556). In HGSC, CD8+ TIL density was directly correlated with PD-L1 positivity using either TPS (P=0.0008) or CPS (P=0.00011). Survival analysis of patients with high stage (stage III to IV) HGSC revealed PD-L1 positivity by TPS to be associated with improved progression-free survival (adjusted hazard ratio: 0.4912 vs. 2.036, P=0.0378). Although not statistically significant, a similar trend was observed in overall survival (adjusted hazard ratio: 0.3387 vs. 2.953, P=0.0548). In contrast, with CPS, no significant difference was identified between PD-L1-positive and negative groups in either progression-free survival (P=0.5086) or overall survival (P=0.7823). Neoadjuvant chemotherapy was associated with higher PD-L1 expression by TPS (P=0.00407) but not CPS. No significant difference in PD-L1 expression was detected in tumors from patients with germline BRCA1/2 mutations compared with germline mutation-negative tumors by either TPS or CPS. In conclusion, the prevalence of PD-L1 expression is variable in different types of tubo-ovarian carcinoma and is highest in HGSC. In high-stage HGSC, PD-L1 positivity in tumor cells is associated with an increased immune response and improved survival.
RNA-binding motifs of hnRNP K are critical for induction of antibody diversification by activation-induced cytidine deaminase

Significance Heterogeneous nuclear ribonucleoprotein K (hnRNP K), an RNA-binding protein, is the cofactor of activation-induced cytidine deaminase (AID) that induces DNA breaks in immunoglobulin (Ig) genes. Here, we elucidated that the GXXG and RGG RNA-binding motifs were critically necessary for class switch recombination and somatic hypermutation. Nuclear localization of hnRNP K and interaction with AID were also dependent on all of the RNA-binding motifs. This study clearly demonstrated that hnRNP K contributed to AID-dependent DNA breaks through its RNA-binding capacity, suggesting the possibility that hnRNP K holds and presents some editing target RNAs to AID, which eventually induces DNA breaks in Ig genes. Activation-induced cytidine deaminase (AID) is the key enzyme for class switch recombination (CSR) and somatic hypermutation (SHM) to generate antibody memory. Previously, heterogeneous nuclear ribonucleoprotein K (hnRNP K) was shown to be required for AID-dependent DNA breaks. Here, we defined the function of major RNA-binding motifs of hnRNP K, GXXGs and RGGs in the K-homology (KH) and the K-protein-interaction (KI) domains, respectively. Mutation of GXXG, RGG, or both impaired CSR, SHM, and cMyc/IgH translocation equally, showing that these motifs were necessary for AID-dependent DNA breaks. AID–hnRNP K interaction is dependent on RNA; hence, mutation of these RNA-binding motifs abolished the interaction with AID, as expected. Some of the polypyrimidine sequence-carrying prototypical hnRNP K-binding RNAs, which participate in DNA breaks or repair bound to hnRNP K in a GXXG and RGG motif-dependent manner. Mutation of the GXXG and RGG motifs decreased nuclear retention of hnRNP K. Together with the previous finding that nuclear localization of AID is necessary for its function, lower nuclear retention of these mutants may worsen their functional deficiency, which is also caused by their decreased RNA-binding capacity. In summary, hnRNP K contributed to AID-dependent DNA breaks with all of its major RNA-binding motifs.
A dual enzyme method for the establishment of long- and medium-term primary cultures of epithelial and fibroblastic cells from Atlantic salmon gills

A dual enzyme disaggregation method using collagenase and then trypsin was developed that allowed the reproducible initiation of primary cultures from Atlantic salmon Salmo salar gills. Cultures had both epithelial and fibroblast morphology and persisted for an average of 20 passages. Growth was dependent upon a minimum concentration of 5% foetal calf serum (FCS) for fibroblasts and 10% FCS for epithelial cells. Growth was mostly independent of substrate, although epithelial cells showed increased growth on type I collagen gels. Matrigel™ cell culture substrate produced reduced growth of fibroblasts and did not benefit epithelial cell growth. Epithelial cells reacted with monoclonal antibodies (MAbs) against mammalian cytokeratins, and fibroblast cells reacted with MAbs against mammalian fibronectin and type I collagen. The method also produced two long-term cultures: one epithelial and one fibroblast that have been designated RGE-2 and RGF respectively.
Variation in search-phase calls of Lasiurus varius (Chiroptera: Vespertilionidae) in response to different foraging habitats

Abstract Intraspecific variability in echolocation calls could be an important factor hampering the accurate acoustic identification of species in the field. We studied variations in the echolocation behavior of Lasiurus varius in relation to habitat structure. Echolocation calls of L. varius reflected the degree of clutter present in its foraging areas. Bats foraging in an uncluttered habitat emitted longer and lower-bandwidth calls, with the lowest frequency values, whereas bats foraging in a cluttered habitat broadcast shorter and broadband signals, showing an increase in frequency content of their calls. Discriminant function analysis gave an overall classification of 76% of the calls emitted in the different flight situations. Our results highlight the need for independent recordings at each study area or habitat type to circumvent potential echolocation call variations, particularly in fragmented landscapes.
A Light-Weight Practical Framework for Feces Detection and Trait Recognition

Fecal trait examinations are critical in the clinical diagnosis of digestive diseases, and they can effectively reveal various aspects regarding the health of the digestive system. An automatic feces detection and trait recognition system based on a visual sensor could greatly alleviate the burden on medical inspectors and overcome many sanitation problems, such as infections. Unfortunately, the lack of digital medical images acquired with camera sensors due to patient privacy has obstructed the development of fecal examinations. In general, the computing power of an automatic fecal diagnosis machine or a mobile computer-aided diagnosis device is not always enough to run a deep network. Thus, a light-weight practical framework is proposed, which consists of three stages: illumination normalization, feces detection, and trait recognition. Illumination normalization effectively suppresses the illumination variances that degrade the recognition accuracy. Neither the shape nor the location is fixed, so shape-based and location-based object detection methods do not work well in this task. Meanwhile, this leads to a difficulty in labeling the images for training convolutional neural networks (CNN) in detection. Our segmentation scheme is free from training and labeling. The feces object is accurately detected with a well-designed threshold-based segmentation scheme on the selected color component to reduce the background disturbance. Finally, the preprocessed images are categorized into five classes with a light-weight shallow CNN, which is suitable for feces trait examinations in real hospital environments. The experiment results from our collected dataset demonstrate that our framework yields a satisfactory accuracy of 98.4%, while requiring low computational complexity and storage.
Rapid COVID-19 vaccine development

Finding the fastest pathway to vaccine availability includes the avoidance of safety pitfalls Rapid development of a vaccine to prevent coronavirus disease 2019 (COVID-19) is a global imperative, and defining the stakes and potential hurdles is critical because regulatory and medical decisions are based on benefit:risk calculations. The ability of viruses to achieve pandemic spread is diminished by establishing higher levels of community (herd) immunity, and a key question is whether protection against severe acute respiratory syndrome–coronavirus 2 (SARS-CoV-2) will happen by widespread deployment of an effective vaccine or by repeated waves of infection over the next few years until ∼60 to 70% of people develop immunity. Because the human population is naïve to SARS-CoV-2, the consequences of repeated epidemics will be unacceptably high mortality, severe economic disruption, and major adjustments to our way of life. Therefore, the benefit of developing an effective vaccine is very high, and even greater if it can be deployed in time to prevent repeated or continuous epidemics.
Improvement in yield of bread wheat cultivars released in Ethiopia from 1949 to 1987

Thirteen bread wheat ( Triticum aestivum L.) cultivars popular in the highlands of Ethiopia and representative of the period from 1949 to 1987 were studied for two cropping seasons in Ethiopia to estimate progress made in improving grain yield. The selected cultivars were grown with the effects of other genetic changes minimized by using fungicides to control foliar diseases, nets to prevent lodging, and periodic hand weeding to control weeds. Adequate levels of nutrients were also supplied. Significant differences were observed among cultivars for all crop parameters studied. The grain yield of bread wheat cultivars released since 1949 has increased at a mean rate of 77 kg ha-1yr-1 (2.21%) as measured in central Ethiopia and 50 Kg ha-1y-1(1.77%) under warmer and drier conditions in southeastern Ethiopia. Grain Yield was significantly and positively correlated with harvest index, grains m-2, spikelets spike-1 and grains spike-1. Genetic improvement has substantially increased the grain yield of rainfed bread wheat in the highlands of Ethiopia, resulting from an improved harvest index associated with an increased number of grains spike-1 and, as a result, grains m-2. Wheat breeders in Ethiopia should continue to emphasize spike fertility as a selection criterion for high grain yield.
Detection and Mitigation of DDoS Attacks Using Conditional Entropy in Software-defined Networking

Software-defined networking (SDN) is a relatively new technology that promotes network revolution. The most distinct characteristic of SDN is the transformation of control logic from the basic packet forwarding equipment to a centralized management unit called controller. However, the centralized control of the network resources is like a double-edged sword, for it not only brings beneficial features but also introduces single point of failure if the controller is under distributed denial of service (DDoS) attacks. In this paper, we introduce a light-weight approach based on conditional entropy to improve the SDN security with an aim of defending DDoS at the early stage. The experimental results show that the proposed method has a high average detection rate of 99.372%.
Sensorless Control of Dual Stator Winding Induction Machine Drive Using Sliding Mode Control Based Model Reference Adaptive System

This paper proposes an X-Model Reference Adaptive System (X-MRAS) based on Sliding Mode Control (SMC) for speed estimation of indirect vector controlled dual stator winding induction machine drive. The structure and performance of the proposed method are compared with classical MRAS and PI-X-MRAS. To confirm the robustness of the proposed method, the sensitivity analysis of estimated speed versus stator resistance variations for the classical, X-MRAS, and X-MRAS based on sliding mode control methods are assessed and compared. Unlike the classical MRAS and other methods, the proposed method does not involve the calculation of stator and rotor flux. Furthermore, the sensorless drive is stable in all four regions of operation. All speed estimation approaches have been simulated in MATLAB/SIMULINK environment on a dual stator winding induction machine. Simulation results illustrate the acceptable and robust performance of sensorless drive in the low-speed region as a result of employing a sliding mode control scheme.
A Transformer less Quadratic Buck-Boost Converter with Wide Range of Output Voltage and Low Switch Stresses

In this study, a transformer less quadratic buck-boost converter has been proposed. Quadratic form of voltage ratio has made it capable to obtain a wide range of output voltage. Other feature which has been concentrated is voltage stress of switches. It has been tried to decrease voltage stress of second switch. Moreover, two other quadratic buck-boost converter with similar properties to proposed one have been compared and have illustrated that the voltage stress of second switch in proposed converter is lower. Mathematical relations of efficiency have been expressed. Moreover, small signal analysis of proposed converter has been discussed and its bode diagram has been reported. All the mentioned analysis are done in Continuous Conduction Mode. Finally, simulation results of proposed converter which have been obtained by PLECS simulation engine, have been reported and discussed according to theoretical relations.