Miracle-dz/UniFAR-FTUs huggingface dataset:
The update and optimization of an eDNA assay to detect the invasive rusty crayfish (Faxonius rusticus)

Environmental DNA (eDNA) is nuclear or mitochondrial DNA shed into the environment, and amplifying this DNA can serve as a reliable, noninvasive way to monitor aquatic systems for the presence of an invasive species. Assays based on the collection of eDNA are becoming increasingly popular, and, when optimized, can aid in effectively and efficiently tracking invasion fronts. We set out to update an eDNA assay to detect the invasive rusty crayfish, Faxonius rusticus. We tested for species specificity compared to other stream crayfish and field tested the assay at sites with known presence (N = 3) and absence (N = 4) in the Juniata River watershed in central Pennsylvania, USA. To maximize sensitivity, we field tested different storage buffers (Longmire’s buffer and ethanol), DNA extraction methods (Qiagen’s DNEasy and PowerWater kits), and quantitative polymerase chain reaction (qPCR) chemistries (TaqMan and SYBR green). Our assay confirmed the presence data and performed optimally when filter samples were stored in Longmire’s buffer, DNA was extracted with DNeasy Blood and Tissue Kit, and TaqMan qPCR chemistry was utilized. With proper sample processing, our assay allows for accurate, noninvasive detection of F. rusticus in streams.
A New Hope in Type 2 Diabetes Mellitus Management: Sodium-Glucose Cotransporter 2 Inhibitors

Diabetes mellitus is a chronic disease that affects multiple organs and exhibits significant complications. The major outcomes of prolonged hyperglycemia are nephropathy, retinopathy, neuropathy, and cardiovascular events due to the glycation of lipids and proteins. To ensure a healthy lifestyle for diabetic patients, a treatment that delays the complications and simultaneously protects multiple organs is required. Sodium-glucose cotransporter inhibitors (SGLTi) inhibit the reabsorption of glucose from the kidney and shows promising benefits in renal and heart diseases. The major SGLT receptors are SGLT1 and SGLT2. Various trials are conducted to conclude their efficacy and show nephroprotective and cardioprotective roles independent of diabetic status. The FDA-approved SGLT2 inhibitors are empagliflozin (Jardiance®), canagliflozin (Invokana®), and dapagliflozin (Farxiga®), which are primarily used in type 2 diabetes mellitus (T2DM). They show a reduced rate of hospitalization for heart failure, cardiovascular disease mortality, all-cause mortality, and progression of diabetic kidney disease. It also shows improvement in the glycemic index; therefore, it is protective against the complications of diabetes irrespective of insulin release, thus avoids hypoglycemia. This review summarizes the data from the clinical trials that support the efficacy of SGLT2 inhibitors in reducing the risks of cardiovascular and renal outcomes in patients with T2DM.
Future of Wearable Health Devices: Smartwatches VS Smart Headphones

Received: 8 September 2021 Accepted: 12 September 2021 Today’s, the global life expectancy is increasing due to many factors, but the significant improvements in healthcare systems, and personal and environmental hygiene growing are the most important. In near future, we will be encountered with a significant need of social welfare and healthcare for this enormous growing aging population. Thus, it is a necessity to develop and implement new strategies and technologies to provide more efficient and better health care services with an affordable cost and less limited access among people especially with the aging population. Remote healthcare monitoring is introduced as a key solution to provide an efficient and cost-effective way instead of on-site clinical monitoring in hospitals and medical centers. The revolution technology in electronic and digital communication is an ability to design more reliable and adaptable wearable health devices for continuous monitoring a wide range of different physiological sign and activities in real-time and from distant. The new technology capabilities with the advantage of miniaturization improves human-machine connectivity with less disconformity during normal daily life activities (at work, at home, at sport, etc.). This technology could have a significant effect on health status awareness and quality care improvement via a better support in medical diagnosis and treatment [1]. The Wearable Medical Devices Market is growing rapidly, according to the latest medical market research, the market size is exceeded USD 25 billion in 2020 and is expected to grow at over 22.9% CAGR (Compound Annual Growth Rate) from 2021 to 2027. During COVID-19, this market has experienced increased demand by increasing focus on health management systems, daily health tracking and remote healthcare monitoring. Changing lifestyle will have an intensive effect on boosting personal health and fitness products demand. The main requirements in the concept design of a wearable health device are power, efficiency, privacy, security, reliability, connectivity, usability, portability, robustness, stability, multimodality, modifiability, maintainability, comfortable and ergonomics features. As a general feature, the present wearable health devices could monitor some physiological vital signs including heart rate, ECG, pulse oximeters, blood pressure, breath rate, and body temperature. These parameters indicate the overall health status of a person and have tremendous diagnostic value. For the foreseeable future, with the development of a miniaturized smart sensors, it is expected the wearable health devices to be complemented with chemical sensors that will provide continuous non-invasive chemical and metabolic measurements for better medical monitoring (e.g. in sweat for diabetes patients, pharmacokinetics process in the body, metabolic diseases, and others). For a reliable health monitoring system, the wearable health devices must be accurate and act reliable under multiple environmental conditions and activity Editorial
An Expanded Polyproline Domain Maintains Mutant Huntingtin Soluble in vivo and During Aging

Huntington’s disease is a dominantly inherited neurodegenerative disorder caused by the expansion of a CAG repeat, encoding for the amino acid glutamine (Q), present in the first exon of the protein huntingtin. Over the threshold of Q39 HTT exon 1 (HTTEx1) tends to misfold and aggregate into large intracellular structures, but whether these end-stage aggregates or their on-pathway intermediates are responsible for cytotoxicity is still debated. HTTEx1 can be separated into three domains: an N-terminal 17 amino acid region, the polyglutamine (polyQ) expansion and a C-terminal proline rich domain (PRD). Alongside the expanded polyQ, these flanking domains influence the aggregation propensity of HTTEx1: with the N17 initiating and promoting aggregation, and the PRD modulating it. In this study we focus on the first 11 amino acids of the PRD, a stretch of pure prolines, which are an evolutionary recent addition to the expanding polyQ region. We hypothesize that this proline region is expanding alongside the polyQ to counteract its ability to misfold and cause toxicity, and that expanding this proline region would be overall beneficial. We generated HTTEx1 mutants lacking both flanking domains singularly, missing the first 11 prolines of the PRD, or with this stretch of prolines expanded. We then followed their aggregation landscape in vitro with a battery of biochemical assays, and in vivo in novel models of C. elegans expressing the HTTEx1 mutants pan-neuronally. Employing fluorescence lifetime imaging we could observe the aggregation propensity of all HTTEx1 mutants during aging and correlate this with toxicity via various phenotypic assays. We found that the presence of an expanded proline stretch is beneficial in maintaining HTTEx1 soluble over time, regardless of polyQ length. However, the expanded prolines were only advantageous in promoting the survival and fitness of an organism carrying a pathogenic stretch of Q48 but were extremely deleterious to the nematode expressing a physiological stretch of Q23. Our results reveal the unique importance of the prolines which have and still are evolving alongside expanding glutamines to promote the function of HTTEx1 and avoid pathology.
Cancer Provider and Survivor Experiences With Telehealth During the COVID-19 Pandemic

PURPOSE: The COVID-19 pandemic led to rapid shifts in cancer survivorship care, including the widespread use of telehealth. Given the swift transition and limited data on preferences and experiences around telehealth, we surveyed oncology providers and post-treatment survivors to better understand experiences with the transition to telehealth. METHODS: We distributed provider (MD, PA or NP, nurse, navigator, and social worker) and survivor surveys through the American College of Surgeons Commission on Cancer in mid-October 2020. Survivor surveys were also disseminated through patient advocacy organizations. We included questions on demographics, experiences with telehealth, and preferences for future telehealth utilization. RESULTS: Among N = 607 providers and N = 539 cancer survivors, there was overwhelmingly more support from providers than from survivors for delivery of various types of survivorship care via telehealth and greater comfort with telehealth technologies. The only types of appointments deemed appropriate for survivorship care by both > 50% of providers and survivors were discussion of laboratory results or imaging, assessment and/or management of cancer treatment symptoms, nutrition counseling, and patient navigation support. Only a quarter of survivors reported increased access to health care services (25.5%), and 32.0% reported that they would use telehealth again. CONCLUSION: Although there have been drastic changes in technological capabilities and billing reimbursement structures for telehealth, there are still concerns around delivery of a broad range of survivorship care services via telehealth, particularly from the patient perspective. Still, offering telehealth services, where endorsed by providers and if available and acceptable to cancer survivors, may provide more efficient and accessible care following the COVID-19 pandemic.
Chronic rejection as a persisting phantom menace in organ transplantation: a new hope in the microbiota?

Purpose of review The microbiota plays an important role in health and disease. During organ transplantation, perturbations in microbiota influence transplant outcome. We review recent advances in characterizing microbiota and studies on regulation of intestinal epithelial barrier function and mucosal and systemic immunity by microbiota and their metabolites. We discuss implications of these interactions on transplant outcomes. Recent findings Metagenomic approaches have helped the research community identify beneficial and harmful organisms. Microbiota regulates intestinal epithelial functions. Signals released by epithelial cells or microbiota trigger pro-inflammatory or anti-inflammatory effects on innate and adaptive immune cells, influencing the structure and function of the immune system. Assessment and manipulation of microbiota can be used for biomarkers for diagnosis, prognosis, and therapy. Summary The bidirectional dialogue between the microbiota and immune system is a major influence on immunity. It can be targeted for biomarkers or therapy. Recent studies highlight a close association of transplant outcomes with microbiota, suggesting exciting potential avenues for management of host physiology and organ transplantation.
Effect of Solution pH on the Dual Role of Dissolved Organic Matter in Sensitized Pollutant Photooxidation

Dissolved organic matter (DOM) has a dual role in indirect phototransformations of aquatic contaminants by acting both as a photosensitizer and an inhibitor. Herein, the pH dependence of the inhibitory effect of DOM and the underlying mechanisms were studied in more than 400 kinetic irradiation experiments over the pH range of 6–11. Experiments employed various combinations of one of three DOM isolates, one of two model photosensitizers, the model antioxidant phenol, and one of nine target compounds (TCs), comprising several aromatic amines, in particular anilines and sulfonamides, and 4-cyanophenol. Using model photosensitizers without antioxidants, the phototransformation of most TCs increased with increasing pH, even for TCs for which pH did not affect speciation. This trend was attributed to pH-dependent formation yields of TC-derived radicals and their re-formation to the parent TC. Analogous trends were observed with DOM as a photosensitizer. Comparison of model and DOM photosensitizer data sets showed increasing inhibitory effects of DOM on TC phototransformation kinetics with increasing pH. In systems with anilines as a TC and phenol as a model antioxidant, pH trends of the inhibitory effect could be rationalized based on the reduction potential difference (ΔEred) of phenoxyl/phenol and anilinyl/aniline couples. Our results indicate that the light-induced transformation of aromatic amines in the aquatic environment is governed by the pH-dependent inhibitory effects of antioxidant phenolic moieties of DOM and pH-dependent processes related to the formation of amine oxidation intermediates.
Variance-aware attention U-Net for multi-organ segmentation.

PURPOSE With the continuous development of deep learning based medical image segmentation technology, it is expected to attain more robust and accurate performance for more challenging tasks, such as multi-organs, small/irregular areas, and ambiguous boundary issues. METHODS We propose a variance-aware attention U-Net to solve the problem of multi-organ segmentation. Specifically, a simple yet effective variance-based uncertainty mechanism is devised to evaluate the discrimination of each voxel via its prediction probability. The proposed variance uncertainty is further embedded into an attention architecture, which not only aggregates multi-level deep features in a global-level but also enforces the network to pay extra attention to voxels with uncertain predictions during training. RESULTS Extensive experiments on challenging abdominal multi-organ CT dataset show that our proposed method consistently outperforms cutting-edge attention networks with respect to the evaluation metrics of Dice index (DSC), 95% Hausdorff distance (95HD) and average symmetric surface distance (ASSD). CONCLUSIONS The proposed network provides an accurate and robust solution for multi-organ segmentation and has the potential to be used for improving other segmentation applications.
Root dynamic growth strategies in response to salinity

Abstract Increasing soil salinization largely impacts crop yield worldwide. To deal with salinity stress, plants exhibit an array of responses, including root system architecture remodelling. Here, we review recent progress in physiological, developmental and cellular mechanisms of root growth responses to salinity. Most recent research in modulation of root branching, root tropisms, as well as in root cell wall modifications under salinity stress, is discussed in the context of the contribution of these responses to overall plant performance. We highlight the power of natural variation approaches revealing novel potential pathways responsible for differences in root salt stress responses. Together, these new findings promote our understanding of how salt shapes the root phenotype, which may provide potential avenues for engineering crops with better yield and survival in saline soils.
Predicting pituitary adenoma consistency with preoperative magnetic resonance elastography.

OBJECTIVE Pituitary adenoma is one of the most common primary intracranial neoplasms. Most of these tumors are soft, but up to 17% may have a firmer consistency. Therefore, knowing the tumor consistency in the preoperative setting could be helpful. Multiple imaging methods have been proposed to predict tumor consistency, but the results are controversial. This study aimed to evaluate the efficacy of MR elastography (MRE) in predicting tumor consistency and its potential use in a series of patients with pituitary adenomas. METHODS Thirty-eight patients with pituitary adenomas (≥ 2.5 cm) were prospectively evaluated with MRI and MRE before surgery. Absolute MRE stiffness values and relative MRE stiffness ratios, as well as the relative ratio of T1 signal, T2 signal, and diffusion-weighted imaging apparent diffusion coefficient (ADC) values were determined prospectively by calculating the ratio of those values in the tumor to adjacent left temporal white matter. Tumors were classified into three groups according to surgical consistency (soft, intermediate, and firm). Statistical analysis was used to identify the predictive value of the different radiological parameters in determining pituitary adenoma consistency. RESULTS The authors included 32 (84.21%) nonfunctional and 6 (15.79%) functional adenomas. The mean maximum tumor diameter was 3.7 cm, and the mean preoperative tumor volume was 16.4 cm3. Cavernous sinus invasion was present in 20 patients (52.63%). A gross-total resection was possible in 9 (23.68%) patients. The entire cohort's mean absolute tumor stiffness value was 1.8 kPa (range 1.1-3.7 kPa), whereas the mean tumor stiffness ratio was 0.66 (range 0.37-1.6). Intraoperative tumor consistency was significantly correlated with absolute and relative tumor stiffness (p = 0.0087 and 0.007, respectively). Tumor consistency alone was not a significant factor for predicting gross-total resection. Patients with intermediate and firm tumors had more complications compared to patients with soft tumors (50.00% vs 12.50%, p = 0.02) and also had longer operative times (p = 0.0002). CONCLUSIONS Whereas other MRI sequences have proven to be unreliable in determining tumor consistency, MRE has been shown to be a reliable tool for predicting adenoma consistency. Preoperative knowledge of tumor consistency could be potentially useful for surgical planning, counseling about potential surgical risks, and estimating the length of operative time.
Salmonella Typhi Vi capsule prime-boost vaccination induces convergent and functional antibody responses

Description Prime-boost vaccination with S. Typhi Vi capsule induces convergent antibodies whose function depends on specificity and avidity. Antibody responses to typhoid vaccine Typhoid fever is caused by the bacterial pathogen Salmonella Typhi (S. Typhi), which infects about 10 million to 13 million people annually. The recently developed Vi-TCV vaccine, consisting of the S. Typhi Vi capsular polysaccharide conjugated to tetanus toxoid, is highly effective against typhoid fever. However, the repertoire and functionality of antibodies induced by Vi-TCV vaccination are not well defined. Dahora et al. measured antibody repertoire, avidity maturation, epitope specificity, and functional responses after prime-boost vaccination in human participants. Prime-boost vaccination induced convergent, functional antibodies that target both immunodominant and subdominant Vi epitopes, which had the ability to mediate Fc-dependent effector functions. These findings will inform vaccine design strategies to broaden S. Typhi epitope targeting and provide increased protection against typhoid fever. Vaccine development to prevent Salmonella Typhi infections has accelerated over the past decade, resulting in licensure of new vaccines, which use the Vi polysaccharide (Vi PS) of the bacterium conjugated to an unrelated carrier protein as the active component. Antibodies elicited by these vaccines are important for mediating protection against typhoid fever. However, the characteristics of protective and functional Vi antibodies are unknown. In this study, we investigated the human antibody repertoire, avidity maturation, epitope specificity, and function after immunization with a single dose of Vi-tetanus toxoid conjugate vaccine (Vi-TT) and after a booster with plain Vi PS (Vi-PS). The Vi-TT prime induced an IgG1-dominant response, whereas the Vi-TT prime followed by the Vi-PS boost induced IgG1 and IgG2 antibody production. B cells from recipients who received both prime and boost showed evidence of convergence, with shared V gene usage and CDR3 characteristics. The detected Vi antibodies showed heterogeneous avidity ranging from 10 μM to 500 pM, with no evidence of affinity maturation after the boost. Vi-specific antibodies mediated Fc effector functions, which correlated with antibody dissociation kinetics but not with association kinetics. We identified antibodies induced by prime and boost vaccines that recognized subdominant epitopes, indicated by binding to the de–O-acetylated Vi backbone. These antibodies also mediated Fc-dependent functions, such as complement deposition and monocyte phagocytosis. Defining strategies on how to broaden epitope targeting for S. Typhi Vi and enriching for antibody Fc functions that protect against typhoid fever will advance the design of high-efficacy Vi vaccines for protection across diverse populations.
The Impact of the Closure of the Live Poultry Market due to COVID-19 on the Avian Influenza Virus in Nanchang, Jiangxi Province, China

ABSTRACT. This article aims to understand the changes in the detection rates of H5, H7, and H9 subtypes of avian influenza viruses (AIVs) in the live poultry markets (LPMs) in Nanchang City, Jiangxi Province, before and after the outbreak of the COVID-19. From 2019 to 2020, we monitored the LPM and collected specimens, using real-time reverse transcription polymerase chain reaction technology to detect the nucleic acid of type A AIV in the samples. The H5, H7, and H9 subtypes of influenza viruses were further classified for positive results. We analyzed 1,959 samples before and after the outbreak and found that the positive rates of avian influenza A virus (39.69%) and H9 subtype (30.66%) after the outbreak were significantly higher than before the outbreak (26.84% and 20.90%, respectively; P < 0.001). In various LPMs, the positive rate of H9 subtypes has increased significantly (P ≤ 0.001). Positive rates of the H9 subtype in duck, fecal, daub, and sewage samples, but not chicken samples, have increased to varying degrees. This study shows that additional measures are needed to strengthen the control of AIVs now that LPMs have reopened after the relaxing of COVID-19–related restrictions.