Miracle-dz/UniFAR-FTUs huggingface dataset:
Combining Gene Expression Signature With Clinical Features for Survival Strati�cation of Gastric Cancer

Background: The AJCC staging system is considered as the golden standard in clinical practice. However, it remains some pitfalls in assessing the prognosis of gastric cancer (GC) patients with similar clinicopathological characteristics. We aim to develop a new clinic and genetic risk score (CGRS) to improve the prognosis prediction of GC patients. Methods: The gene expression pro�les of the training set from the Asian Cancer Research Group (ACRG) cohort were used for developing genetic risk score (GRS) by LASSO-Cox regression algorithms. CGRS was established by integrating GRS with clinical risk score (CRS) derived from Surveillance, Epidemiology, and End Results (SEER) database. GRS and CGRS were validated in ACRG validation set and other four independent GC cohorts with different data types, such as microarray, RNA sequencing, and qRT-PCR. Multivariable Cox regression was adopted to evaluate the independence of GRS and CGRS in prognosis evaluation. Results: We established GRS based on a nine-gene signature including APOD, CCDC92, CYS1, GSDME, ST8SIA5, STARD3NL, TIMEM245, TSPYL5, and VAT1. GRS and CGRS dichotomized GC patients into high and low risk groups with signi�cantly different prognosis in four independent cohorts, including our Zhejiang cohort (all HR > 1, all P < 0.001). Both GRS and CGRS were prognostic signatures independent of the AJCC staging system. Receiver operating characteristic (ROC) analysis showed that area under ROC curve of CGRS was larger than that of the AJCC staging system in most cohorts we studied. Nomogram and web tool (http://39.100.117.92/CGRS/) based on CGRS were developed for clinicians to conveniently assess GC prognosis in clinical practice. Conclusions: CGRS integrating genetic signature with clinical features shows strong robustness in predicting GC prognosis, and can be easily applied in clinical practice through the web application. web application been to conveniently predict the prognosis of GC patients in practice.
clusTCR: a Python interface for rapid clustering of large sets of CDR3 sequences

The T-cell receptor (TCR) determines the specificity of a T-cell towards an epitope. As of yet, the rules for antigen recognition remain largely undetermined. Current methods for grouping TCRs according to their epitope specificity remain limited in performance and scalability. Multiple methodologies have been developed, but all of them fail to efficiently cluster large data sets exceeding 1 million sequences. To account for this limitation, we developed clusTCR, a rapid TCR clustering alternative that efficiently scales up to millions of CDR3 amino acid sequences. Benchmarking comparisons revealed similar accuracy of clusTCR with other TCR clustering methods. clusTCR offers a drastic improvement in clustering speed, which allows clustering of millions of TCR sequences in just a few minutes through efficient similarity searching and sequence hashing. clusTCR was written in Python 3. It is available as an anaconda package (https://anaconda.org/svalkiers/clustcr) and on github (https://github.com/svalkiers/clusTCR).
Multi-Level Attention Network for Retinal Vessel Segmentation

Automatic vessel segmentation in the fundus images plays an important role in the screening, diagnosis, treatment, and evaluation of various cardiovascular and ophthalmologic diseases. However, due to the limited well-annotated data, varying size of vessels, and intricate vessel structures, retinal vessel segmentation has become a long-standing challenge. In this paper, a novel deep learning model called AACA-MLA-D-UNet is proposed to fully utilize the low-level detailed information and the complementary information encoded in different layers to accurately distinguish the vessels from the background with low model complexity. The architecture of the proposed model is based on U-Net, and the dropout dense block is proposed to preserve maximum vessel information between convolution layers and mitigate the over-fitting problem. The adaptive atrous channel attention module is embedded in the contracting path to sort the importance of each feature channel automatically. After that, the multi-level attention module is proposed to integrate the multi-level features extracted from the expanding path, and use them to refine the features at each individual layer via attention mechanism. The proposed method has been validated on the three publicly available databases, i.e. the DRIVE, STARE, and CHASE $\_$ DB1. The experimental results demonstrate that the proposed method can achieve better or comparable performance on retinal vessel segmentation with lower model complexity. Furthermore, the proposed method can also deal with some challenging cases and has strong generalization ability.
Involvement of Jordanian Head Nurses’ in Health Policy Development: A Cross-Sectional Study

Background Despite the importance of involving nurses in health policy, nurse’s involvement faces many challenges. Literature showed that there is a low level of nurses’ and nurse leaders’ involvement in health policy development. Aim The aims of this study were to examine (a) the level of Jordanian head nurses’ involvement in health policy development and their perceived benefits and barriers; (b) the relationships between level of knowledge, competence, and interest in health policy and the level of involvement in health policy development; and (c) the relationship between the level of self-efficacy (efficacy expectation and outcome expectation) and the level of involvement in health policy development. Methods A cross-sectional descriptive correlational study design was adopted in this study. A convenience sampling of 250 participants from hospitals affiliated to three health sectors in Jordan (private, governmental, and university) were recruited to complete a self-administered questionnaire. Descriptive statistics and Pearson correlation coefficient were used to answer the study questions. Results The results revealed a moderate level of involvement of head nurses in the policy development. The most frequent cited political activity was “providing written reports, consultations, research. ” “Lack of time” was the most perceived barrier, while “improving the health of the public” was the most perceived benefit. Workshops or sessions at conferences is the most indicated source of knowledge. Participants had an excellent level of skills with positive relationships between the competence and both of the levels of professional and personal involvement in health policy. Participants reported a low level of confidence in performing political activities as well as the impact of such activities on health outcomes. Positive relationship was indicated between self-efficacy and the levels of professional and personal involvement in political activities. Implications: Health policies affect nurses and their practice. Overcoming the barriers and enhancing the levels of head nurses’ knowledge and competence regarding health policies can help activating their roles in health policy development process. This will help in activating nurses’ role in health policy development, which in turn will have a positive impact on health outcomes.
APOBEC3F Constitutes a Barrier to Successful Cross-Species Transmission of Simian Immunodeficiency Virus SIVsmm to Humans

Viral zoonoses pose a significant threat to human health, and it is important to understand determining factors. SIVs infecting great apes gave rise to HIV-1. ABSTRACT Simian immunodeficiency virus infecting sooty mangabeys (SIVsmm) has been transmitted to humans on at least nine occasions, giving rise to human immunodeficiency virus type 2 (HIV-2) groups A to I. SIVsmm isolates replicate in human T cells and seem capable of overcoming major human restriction factors without adaptation. However, only groups A and B are responsible for the HIV-2 epidemic in sub-Saharan Africa, and it is largely unclear whether adaptive changes were associated with spread in humans. To address this, we examined the sensitivity of infectious molecular clones (IMCs) of five HIV-2 strains and representatives of five different SIVsmm lineages to various APOBEC3 proteins. We confirmed that SIVsmm strains replicate in human T cells, albeit with more variable replication fitness and frequently lower efficiency than HIV-2 IMCs. Efficient viral propagation was generally dependent on intact vif genes, highlighting the need for counteraction of APOBEC3 proteins. On average, SIVsmm was more susceptible to inhibition by human APOBEC3D, -F, -G, and -H than HIV-2. For example, human APOBEC3F reduced infectious virus yield of SIVsmm by ∼80% but achieved only ∼40% reduction in the case of HIV-2. Functional and mutational analyses of human- and monkey-derived alleles revealed that an R128T polymorphism in APOBEC3F contributes to species-specific counteraction by HIV-2 and SIVsmm Vifs. In addition, a T84S substitution in SIVsmm Vif increased its ability to counteract human APOBEC3F. Altogether, our results confirm that SIVsmm Vif proteins show intrinsic activity against human APOBEC3 proteins but also demonstrate that epidemic HIV-2 strains evolved an increased ability to counteract this class of restriction factors during human adaptation. IMPORTANCE Viral zoonoses pose a significant threat to human health, and it is important to understand determining factors. SIVs infecting great apes gave rise to HIV-1. In contrast, SIVs infecting African monkey species have not been detected in humans, with one notable exception. SIVsmm from sooty mangabeys has crossed the species barrier to humans on at least nine independent occasions and seems capable of overcoming many innate defense mechanisms without adaptation. Here, we confirmed that SIVsmm Vif proteins show significant activity against human APOBEC3 proteins. Our analyses also revealed, however, that different lineages of SIVsmm are significantly more susceptible to inhibition by various human APOBEC3 proteins than HIV-2 strains. Mutational analyses suggest that an R128T substitution in APOBEC3F and a T84S change in Vif contribute to species-specific counteraction by HIV-2 and SIVsmm. Altogether, our results support that epidemic HIV-2 strains acquired increased activity against human APOBEC3 proteins to clear this restrictive barrier.
Utility of Elastography for Differentiating Malignant and Benign Lymph Nodes During EBUS-TBNA

Background: Ultrasound elastography noninvasively estimates tissue hardness. Studies have evaluated elastography for differentiating malignant from benign lymph nodes during endobronchial ultrasound-guided transbronchial needle aspiration. Several methods of performing elastography are described with variable diagnostic accuracy. Methods: The aim of this study was to evaluate endobronchial ultrasound-guided elastography in differentiating malignant from benign mediastinal lymphadenopathy. We performed a systematic search of the PubMed and Embase databases to extract the relevant studies. A diagnostic accuracy meta-analysis was carried out to calculate the pooled sensitivity and specificity [with 95% confidence intervals (CIs)], and positive and negative likelihood ratios of elastography. Results: After a systematic search, 20 studies (1600 patients, 2712 nodes) were selected. The pooled sensitivity and specificity of elastography were 0.90 (95% CI, 0.84-0.94) and 0.79 (95% CI, 0.73-0.84), respectively. The summary receiver operating curve demonstrated an area under the curve for elastography of 0.90 (0.88-0.93). The positive and negative likelihood ratios and the diagnostic odds ratio were 4.3 (95% CI, 3.3-5.5), 0.12 (95% CI, 0.07-0.20), and 35 (95% CI, 19-63), respectively. Of the most commonly described methods, the color classification method (type 3 malignant vs. type 1 benign) demonstrated the highest area under the curve of 0.91 (0.88-0.93). There was significant heterogeneity and publication bias. Subgroup analyses indicated no significant difference between the sensitivity and specificity of quantitative and qualitative elastography methods. Conclusions: Ultrasound elastography is useful in differentiating malignant and benign lymph nodes during endobronchial ultrasound-guided transbronchial needle aspiration. However, elastography does not replace the requirement of lymph node aspiration.
Bio-Orthogonal Nanogels for Multiresponsive Release

Responsive nanogel systems are interesting for the drug delivery of bioactive molecules due to their high stability in aqueous media. The development of nanogels that are able to respond to biochemical cues and compatible with the encapsulation and the release of large and sensitive payloads remains challenging. Here, multistimuli-responsive nanogels were synthesized using a bio-orthogonal and reversible reaction and were designed for the selective release of encapsulated cargos in a spatiotemporally controlled manner. The nanogels were composed of a functionalized polysaccharide cross-linked with pH-responsive hydrazone linkages. The effect of the pH value of the environment on the nanogels was fully reversible, leading to a reversible control of the release of the payloads and a “stop-and-go” release profile. In addition to the pH-sensitive nature of the hydrazone network, the dextran backbone can be degraded through enzymatic cleavage. Furthermore, the cross-linkers were designed to be responsive to oxidoreductive cues. Disulfide groups, responsive to reducing environments, and thioketal groups, responsive to oxidative environments, were integrated into the nanogel network. The release of model payloads was investigated in response to changes in the pH value of the environment or to the presence of reducing or oxidizing agents.
Implications of State Scope-of-Practice Regulations for Pediatric Intensive Care Unit Nurse Practitioner Roles

Nurse practitioner (NP) advocacy efforts often focus on attaining full practice authority. While the effects of full practice authority in primary care are well described, implications for hospital-based NPs are less clear and may differ because of hospitals’ team-based care and administrative structure. This study examines associations between state scope-of-practice (SSOP) and clinical roles of hospital-based pediatric intensive care unit (PICU) NPs. We conducted a national survey to assess clinical roles of PICU NPs including daily patient care, procedural, and consultation responsibilities as well as hospital-level administrative oversight practices. We classified SSOP as full or limited (reduced or restricted SSOP) practice. We present descriptive statistics and evaluate differences in clinical roles and hospital-level administrative oversight based on SSOP. The final sample included 55 medical directors and 58 lead (senior or supervisory) NPs from 93 of the 140 (66.4%) PICUs with NPs. There were no significant differences in daily patient care, procedural, or consultation responsibilities based on SSOP (p > .05). However, NPs in full practice authority states were more likely to bill for care than those in limited practice states (66.7% vs. 31.8%, p = .003), while those in limited practice states were more likely to report to advanced practice managers (36.7% vs. 13%, p = .03). For PICU NPs, SSOP was not associated with variation in clinical responsibilities; conversely, there were differences in billing and reporting practices. Future work is needed to understand implications of variation in hospital-level administrative oversight.
Venoarterial extracorporeal membrane oxygenation as an early treatment for amniotic fluid embolism with cardiac arrest: A case report

Amniotic fluid embolism (AFE) is a rare but fatal obstetric complication, characterized by sudden cardiovascular collapse, respiratory failure, and disseminated intravascular coagulation. Maternal mortality associated with AFE is high, making early recognition and prompt treatment important. In AFE with cardiac arrest, survival following acute cardiopulmonary dysfunction is crucial. In recent years, venoarterial extracorporeal membrane oxygenation (VA‐ECMO) has attracted attention as an aggressive treatment for AFE with cardiac arrest. A 40‐year‐old woman experienced sudden cardiac arrest due to AFE during cesarean section. Cardiopulmonary resuscitation and VA‐ECMO (also called percutaneous cardiopulmonary support) were initiated early. Finally, she recovered without any complications. VA‐ECMO can provide temporary respiratory and hemodynamic support until cardiopulmonary function improves after a few days in intensive care. VA‐ECMO should be considered as an early treatment for AFE with cardiac arrest.
Efficacy and safety of convalescent plasma therapy in SARS‐CoV2 patients on hemodialysis

The passive immunization of patients with SARS‐CoV2 with convalescent plasma (CP) is theoretically beneficial in patients with end‐stage renal disease who are immunosuppressed and unable to mount an adequate immune response. Hence, this study was conducted to evaluate the safety and efficacy of CP in patients with chronic kidney disease on hemodialysis with moderate‐to‐severe SARS‐CoV2 infection.
The role of bacterial extracellular vesicles in chronic wound infections: Current knowledge and future challenges

Chronic wounds are a significant global problem with an increasing economic and patient welfare impact. How wounds move from an acute to chronic, non‐healing, state is not well understood although it is likely that it is driven by a poorly regulated local inflammatory state. Opportunistic pathogens such as Staphylococcus aureus and Pseudomonas aeruginosa are well known to stimulate a pro‐inflammatory response and so their presence may further drive chronicity. Studies have demonstrated that host cell extracellular vesicles (hEVs), in particular exosomes, have multiple roles in both increasing and decreasing chronicity within wounds; however, the role of bacterial extracellular vesicles (bEVs) is still poorly understood. The aim of this review is to evaluate bEV biogenesis and function within chronic wound relevant bacterial species to determine what, if any, role bEVs may have in driving wound chronicity. We determine that bEVs drive chronicity by both increasing persistence of key pathogens such as Staphylococcus aureus and Pseudomonas aeruginosa and stimulating a pro‐inflammatory response by the host. Data also suggest that both bEVs and hEVs show therapeutic promise, providing vaccine candidates, decoy targets for bacterial toxins or modulating the bacterial species within chronic wound biofilms. Caution should, however, be used when interpreting findings to date as the bEV field is still in its infancy and as such lacks consistency in bEV isolation and characterization. It is of primary importance that this is addressed, allowing meaningful conclusions to be drawn and increasing reproducibility within the field.
Early Prehospital Tranexamic Acid Following Injury Is Associated With a 30-day Survival Benefit

Objective: We sought to characterize the timing of administration of prehospital tranexamic acid (TXA) and associated outcome benefits. Background: TXA has been shown to be safe in the prehospital setting post-injury. Methods: We performed a secondary analysis of a recent prehospital randomized TXA clinical trial in injured patients. Those who received prehospital TXA within 1 hour (EARLY) from time of injury were compared to those who received prehospital TXA beyond 1 hour (DELAYED). We included patients with a shock index of >0.9. Primary outcome was 30-day mortality. Kaplan-Meier and Cox Hazard regression were utilized to characterize mortality relationships. Results: EARLY and DELAYED patients had similar demographics, injury characteristics, and shock severity but DELAYED patients had greater prehospital resuscitation requirements and longer prehospital times. Stratified Kaplan-Meier analysis demonstrated significant separation for EARLY patients (N = 238, log-rank chi-square test, 4.99; P = 0.03) with no separation for DELAYED patients (N = 238, log-rank chi-square test, 0.04; P = 0.83). Stratified Cox Hazard regression verified, after controlling for confounders, that EARLY TXA was associated with a 65% lower independent hazard for 30-day mortality [hazard ratio (HR) 0.35, 95% confidence interval (CI) 0.19–0.65, P = 0.001] with no independent survival benefit found in DELAYED patients (HR 1.00, 95% CI 0.63–1.60, P = 0.999). EARLY TXA patients had lower incidence of multiple organ failure and 6-hour and 24-hour transfusion requirements compared to placebo. Conclusions: Administration of prehospital TXA within 1 hour from injury in patients at risk of hemorrhage is associated with 30-day survival benefit, lower incidence of multiple organ failure, and lower transfusion requirements.
EFFICIENT VEHICLE PARKING SYSTEM USING CLOUD BASED IOT

-The aim of this paper is to develop an intelligent parking system to reduce hiring people's costs and maximize the use of car park owners ' resources.The popular method of finding a parking space is currently manual where drivers typically find a place through luck and experience in the street.This method takes time and energy, which if the driver drives in a city with traffic density, can lead to the worst case of failure and to any parking space.Therefore, through cloud-based IOT and slot allocation through open source computer vision librarybased recognition tool, a smart car parking system is implemented with slot booking operation.The user can book any of the available slot in the webpage. This system takes away the unpredictability of finding a parking slot. This paper focuses on reducing time wasted on finding parking space nearby and ongoing through the filled parking slots. The end user is provided with a webpage to check the available parking slots. Inside a smart city a smart car parking system is a much needed to save time, fuel and even the environment from pollution.
Toward improvements for enhancement the productivity and color value of Monascus pigments: a critical review with recent updates

Abstract Monascus pigments are a kind of high-quality natural edible pigments fermented by Monascus filamentous fungi, which have been widely used in food, cosmetics, medicine, textiles, dyes and chemical industries as active functional ingredients. Moreover, Monascus pigments have a good application prospect because of a variety of biological functions such as antibacterial, antioxidation, anti-inflammatory, regulating cholesterol, and anti-cancer. However, the low productivity and color value of pigments restrict their development and application. In this review, we introduced the categories, structures, biosynthesis and functions of Monascus pigments, and summarized the current methods for improving the productivity and color value of pigments, including screening and mutagenesis of strains, optimization of fermentation conditions, immobilized fermentation, mixed fermentation, additives, gene knockout and overexpression technologies, which will help to develop the foundation for the industrial production of Monascus pigments.