Miracle-dz/UniFAR-FTUs huggingface dataset:
A risk model to identify Legionella among patients admitted with community‐acquired pneumonia: A retrospective cohort study

Abstract Background Guidelines recommend testing hospitalized patients with community‐acquired pneumonia (CAP) for Legionella pneumophila only if the infection is severe or risk factors are present. There are no validated models for predicting Legionella. Objective To derive and externally validate a model to predict a positive Legionella test. Design, Setting and Participants Diagnostic study of adult inpatients with pneumonia using data from 177 US hospitals in the Premier Healthcare Database (training and hold‐out validation sets) and 12 Cleveland Clinic Health System (CCHS) hospitals (external validation set). We used multiple logistic regression to predict positive Legionella tests in the training set, and evaluated performance in both validation sets. Main Outcome and Measures The outcome was a positive Legionella test. Potential predictors included demographics and co‐morbidities, disease severity indicators, season, region, and presence of a local outbreak. Results Of 166,689 patients hospitalized for pneumonia, 43,070 were tested for Legionella and 642 (1.5%) tested positive. The strongest predictors of a positive test were a local outbreak (odds ratio [OR], 3.4), June–October occurrence (OR, 3.4), hyponatremia (OR, 3.3), smoking (OR, 2.4), and diarrhea (OR, 2.0); prior admission within 6 months (OR, 0.27) and chronic pulmonary disease (OR, 0.49) were associated with a negative test. Model c‐statistics were 0.79 in the Premier and 0.77 in the CCHS validation samples. High‐risk patients were only slightly more likely to have been tested than lower‐risk patients. Compared to actual practice, the model‐based testing strategy detected twice as many cases. Conclusions Although Legionella is an uncommon cause of pneumonia, patient characteristics can identify individuals at high risk, allowing for more efficient testing.
Use of the ISU FLUture multisequence identity tool for rapid interpretation of swine influenza A virus sequences in the United States

Rapid and reliable identification of the hemagglutinin (HA) and neuraminidase (NA) genetic clades of an influenza A virus (IAV) sequence from swine can inform control measures and multivalent vaccine composition. Current approaches to genetically characterize HA or NA sequences are based on nucleotide similarity or phylogenetic analyses. Public databases exist to acquire IAV genetic sequences for comparison, but personnel at the diagnostic or production level have difficulty in adequately updating and maintaining relevant sequence datasets for IAV in swine. Further, phylogenetic analyses are time intensive, and inference drawn from these methods is impacted by input sequence data and associated metadata. We describe here the use of the IAV multisequence identity tool as an integrated public webpage located on the Iowa State University Veterinary Diagnostic Laboratory (ISU-VDL) FLUture website: https://influenza.cvm. iastate.edu/. The multisequence identity tool uses sequence data derived from IAV-positive cases sequenced at the ISU-VDL, employs a BLAST algorithm that identifies sequences that are genetically similar to submitted query sequences, and presents a tabulation and visualization of the most genetically similar IAV sequence and associated metadata from the FLUture database. Our tool removes bioinformatic barriers and allows clients, veterinarians, and researchers to rapidly classify and identify IAV sequences similar to their own sequences to augment interpretation of results.
A review on low‐cost microscopes for Open Science

This article presents a review after an exhaustive search that yielded 23 works carried out in the last decade for the availability of optical microscopes with open hardware as a low‐cost alternative to commercial systems. These works were developed with the aim of covering needs within several areas such as: Bio Sciences research in institutions with limited resources, diagnosis of diseases and health screenings in large populations in developing countries, and training in educational contexts with a need for high availability of equipment and low replacement cost. The analysis of the selected works allows us to classify the analyzed solutions into two main categories, for which their essential characteristics are enumerated: portable field microscopes and multipurpose automated microscopes. Moreover, this work includes a discussion on the degree of maturity of the solutions in terms of the adoption of practices aligned with the development of Open Science.
Current perspectives on the diagnosis and management of fatigue in multiple sclerosis

ABSTRACT Introduction Fatigue is a common and debilitating symptom among multiple sclerosis (MS) patients with a prevalence up to 81% and with a considerable impact on quality of life. However, its subjective nature makes it difficult to define and quantify in clinical practice. Research aimed at a more precise definition and knowledge of this construct is thus continuously growing. Areas covered This review summarizes the most relevant updates available on PubMed up to 1 July 2022 regarding: the assessment methods that aim to measure the concept of fatigue (as opposed to fatigability), the possible treatment pathways currently available to clinicians, interconnection with the pathophysiological substrates and with the common comorbidities of MS, such as depression and mood disorders. Expert opinion The in-depth study of fatigue can help to better understand its actual impact on MS patients and can stimulate clinicians toward a more valid approach, through a targeted analysis of this symptom. Considering fatigue from a multidimensional perspective allows the use of patient-tailored methods for its identification and subsequent treatment by different professional figures. Better identification of methods and treatment pathways would reduce the extremely negative impact of fatigue on MS patients’ quality of life.
Thermoneutrality induces vascular dysfunction and impaired metabolic function in male Wistar rats: a new model of vascular disease

Objective: Cardiovascular disease is of paramount importance, yet there are few relevant rat models to investigate its pathology and explore potential therapeutics. Housing at thermoneutral temperature (30 °C) is being employed to humanize metabolic derangements in rodents. We hypothesized that housing rats in thermoneutral conditions would potentiate a high-fat diet, resulting in diabetes and dysmetabolism, and deleteriously impact vascular function, in comparison to traditional room temperature housing (22 °C). Methods: Male Wistar rats were housed at either room temperature or thermoneutral temperatures for 16 weeks on either a low or high-fat diet. Glucose and insulin tolerance tests were conducted at the beginning and end of the study. At the study's conclusion, vasoreactivity and mitochondrial respiration of aorta and carotid were conducted. Results: We observed diminished vasodilation in vessels from thermoneutral rats (P < 0.05), whereas high-fat diet had no effect. This effect was also observed in endothelium-denuded aorta in thermoneutral rats (P < 0.05). Vasoconstriction was significantly elevated in aorta of thermoneutral rats (P < 0.05). Diminished nitric oxide synthase activity and nitrotyrosine, and elevated glutathione activity were observed in aorta from rats housed under thermoneutral conditions, indicating a climate of lower nitric oxide and excess reactive oxygen species in aorta. Thermoneutral rat aorta also demonstrated less mitochondrial respiration with lipid substrates compared with the controls (P < 0.05). Conclusion: Our data support that thermoneutrality causes dysfunctional vasoreactivity, decreased lipid mitochondrial metabolism, and modified cellular signaling. These are critical observations as thermoneutrality is becoming prevalent for translational research models. This new model of vascular dysfunction may be useful for dissection of targetable aspects of cardiovascular disease and is a novel and necessary model of disease.
Emerging Japanese Encephalitis Virus Genotype V in Republic of Korea

Japanese encephalitis (JE) is a vaccine-preventable mosquito-borne disease caused by infection with the Japanese encephalitis virus (JEV). JEV has five genotypes, including genotype V (GV), which is considered ancestral to the other genotypes. The first GV strain, GV Muar, was isolated from a Malayan patient in 1952 and GV did not reappear for 57 years until GV XZ0934 was isolated from a mosquito sample in China. Since 2010, 21 GV strains have been identified in Republic of Korea (ROK). Both GV Muar and GV XZ0934 are more pathogenic than other GI/GIII strains and are serologically distinct. However, because the ROK’s GV strains have not been experimentally tested, their characteristics are not known. Characterization of the ROK’s isolates is needed to enable development of effective GV strain-based vaccines to protect against GV infections.
Discovery of a new class of triazole based inhibitors of acetyl transferase KAT2A

Abstract We have recently developed a new synthetic methodology that provided both N-aryl-5-hydroxytriazoles and N-pyridine-4-alkyl triazoles. A selection of these products was carried through virtual screening towards targets that are contemporary and validated for drug discovery and development. This study determined a number of potential structure target dyads of which N-pyridinium-4-carboxylic-5-alkyl triazole displayed the highest score specificity towards KAT2A. Binding affinity tests of abovementioned triazole and related analogs towards KAT2A confirmed the predictions of the in-silico assay. Finally, we have run in vitro inhibition assays of selected triazoles towards KAT2A; the ensemble of binding and inhibition assays delivered pyridyl-triazoles carboxylates as the prototype of a new class of inhibitors of KAT2A.
A review on AI-based medical image computing in head and neck surgery

Head and neck surgery is a fine surgical procedure with a complex anatomical space, difficult operation and high risk. Medical image computing (MIC) that enables accurate and reliable preoperative planning is often needed to reduce the operational difficulty of surgery and to improve patient survival. At present, artificial intelligence, especially deep learning, has become an intense focus of research in MIC. In this study, the application of deep learning-based MIC in head and neck surgery is reviewed. Relevant literature was retrieved on the Web of Science database from January 2015 to May 2022, and some papers were selected for review from mainstream journals and conferences, such as IEEE Transactions on Medical Imaging, Medical Image Analysis, Physics in Medicine and Biology, Medical Physics, MICCAI, etc. Among them, 65 references are on automatic segmentation, 15 references on automatic landmark detection, and eight references on automatic registration. In the elaboration of the review, first, an overview of deep learning in MIC is presented. Then, the application of deep learning methods is systematically summarized according to the clinical needs, and generalized into segmentation, landmark detection and registration of head and neck medical images. In segmentation, it is mainly focused on the automatic segmentation of high-risk organs, head and neck tumors, skull structure and teeth, including the analysis of their advantages, differences and shortcomings. In landmark detection, the focus is mainly on the introduction of landmark detection in cephalometric and craniomaxillofacial images, and the analysis of their advantages and disadvantages. In registration, deep learning networks for multimodal image registration of the head and neck are presented. Finally, their shortcomings and future development directions are systematically discussed. The study aims to serve as a reference and guidance for researchers, engineers or doctors engaged in medical image analysis of head and neck surgery.
Skeletal muscle biochemical origin of exercise intensity domains and their relation to whole-body V̇O2 kinetics

Abstract This article presents the biochemical intra-skeletal-muscle basis of exercise intensity domains: moderate (M), heavy (H), very heavy (VH) and severe (S). Threshold origins are mediated by a ‘Pi double-threshold’ mechanism of muscle fatigue, which assumes (1) additional ATP usage, underlying muscle V̇O2 and metabolite slow components, is initiated when inorganic phosphate (Pi) exceeds a critical value (Picrit); (2) exercise is terminated because of fatigue, when Pi reaches a peak value (Pipeak); and (3) the Pi increase and additional ATP usage increase mutually stimulate each other forming a positive feedback. M/H and H/VH borders are defined by Pi on-kinetics in relation to Picrit and Pipeak. The values of the ATP usage activity, proportional to power output (PO), for the M/H, H/VH and VH/S borders are lowest in untrained muscle and highest in well-trained muscle. The metabolic range between the M/H and H/VH border (or ‘H space’) decreases with muscle training, while the difference between the H/VH and VH/S border (or ‘VH space’) is only weakly dependent on training status. The absolute magnitude of the muscle V̇O2 slow-component, absent in M exercise, rises gradually with PO to a maximal value in H exercise, and then decreases with PO in VH and S exercise. Simulations of untrained, physically active and well-trained muscle demonstrate that the muscle M/H border need not be identical to the whole-body M/H border determined from pulmonary V̇O2 on-kinetics and blood lactate, while suggesting that the biochemical origins of the H/VH border reside within skeletal muscle and correspond to whole-body critical power.
Targeting gliovascular connexins prevents inflammatory blood-brain barrier leakage and astrogliosis

The blood-brain barrier is formed by capillary endothelial cells expressing connexin 37 (Cx37), Cx40, and Cx43 and is joined by closely apposed astrocytes expressing Cx43 and Cx30. We investigated whether connexin-targeting peptides could limit barrier leakage triggered by LPS-induced systemic inflammation in mice. Intraperitoneal LPS administration increased endothelial and astrocytic Cx43 expression; elevated TNF-α, IL-1β, IFN-γ, and IL-6 in plasma and IL-6 in the brain; and induced barrier leakage recorded over 24 hours. Barrier leakage was largely prevented by global Cx43 knockdown and Cx43/Cx30 double knockout in astrocytes, slightly diminished by endothelial Cx43 knockout, and not protected by global Cx30 knockout. Intravenous administration of Gap27 or Tat-Gap19 peptides just before LPS also prevented barrier leakage, and intravenously administered BAPTA-AM to chelate intracellular calcium was equally effective. Patch-clamp experiments demonstrated LPS-induced Cx43 hemichannel opening in endothelial cells, which was suppressed by Gap27, Gap19, and BAPTA. LPS additionally triggered astrogliosis that was prevented by intravenous Tat-Gap19 or BAPTA-AM. Cortically applied Tat-Gap19 or BAPTA-AM to primarily target astrocytes also strongly diminished barrier leakage. In vivo dye uptake and in vitro patch-clamp showed Cx43 hemichannel opening in astrocytes that was induced by IL-6 in a calcium-dependent manner. We conclude that targeting endothelial and astrocytic connexins is a powerful approach to limit barrier failure and astrogliosis.
Structural signatures: a web server for exploring a database of and generating protein structural features from human cell lines and tissues

Abstract Structural features of proteins provide powerful insights into biological function and similarity. Specifically, previous work has demonstrated that structural features of tissue and drug-treated cell line samples can be used to predict tissue type and characterize drug relationships, respectively. We have developed structural signatures, a web server for annotating and analyzing protein features from gene sets that are often found in transcriptomic and proteomic data. This platform provides access to a structural feature database derived from normal and disease human tissue samples. We show how analysis using this database can shed light on the relationship between states of single-cell RNA-sequencing lung cancer samples. These various structural feature signatures can be visualized on the server itself or downloaded for additional analysis. The structural signatures server tool is freely available at https://structural-server.kinametrix. com/.
Sanitizing Equipment and Personnel to Prevent the Spread of Hibiscus Mealybug [Nipaecoccus viridis (Hemiptera: Pseudococcidae)] in Florida Citrus

Abstract Hibiscus mealybug (Nipaecoccus viridis, Newstead) is an emerging and serious pest of citrus in Florida. Preventing the spread of hibiscus mealybug by sanitizing personnel and equipment such as individual protective covers can help limit new infestations. Two mealybug life stages, first instars (crawlers) and eggs inside ovisacs, were tested as they are the most likely to be accidentally transported on people and tools. Isopropanol sprays in 3 commercially available concentrations (50%, 70%, and 90%) were tested against crawlers and ovisacs, and steam treatments and hot water immersion were tested against ovisacs. All concentrations of isopropanol resulted in >90% incapacitation of mealybug crawlers, especially when two sprays of isopropanol were applied. However, no concentration of isopropanol reliably killed all mealybug eggs within ovisacs. Steam treatments and hot water immersion for 10 min or longer at 49°C and for 5 min or longer at 54.5°C resulted in 100% mortality of mealybug adults and eggs inside ovisacs. However, adults and ovisacs insulated inside of individual protective covers did not experience 100% mortality until 30 min or longer at 49°C, 10 min or longer at 54.5°C, and 5 min or longer at 60°C for steam treatments. Isopropanol sprays can effectively incapacitate the majority of hibiscus mealybug crawlers on personnel and tools, but are not effective against ovisacs. Steam treatments and hot water immersion can reliably lead to 100% mortality of ovisacs, but longer times and higher temperatures must be used for steam treatments if ovisacs are insulated by equipment. Graphical Abstract
Random Response Spectrum Analysis of Gravity Dam Classes: Simplified, Practical, and Fast Approach

The seismic risk of concrete dams may be assessed using various numerical techniques, ranging from simplified methods to linear and nonlinear ones. Such methods should be combined with probabilistic concepts to account for the randomness in both demand and capacity. This paper proposes a random version of a simplified response spectrum method (involving equivalent static lateral forces [ESLFs]) for gravity dams by means of propagating uncertainties through the input parameters. Input parameter sensitivity is quantified and the extended procedure is explained step by step. Results are then generalized for the different dam classes. The impacts of sampling size and technique (i.e., pseudo-random and quasi-random) are also discussed. A time-based performance is evaluated and fragility curves are derived. This method may be used during the initial stages of a design process or safety analysis for existing dams.
Novel single‐fed broadband circularly polarized antenna for GNSS applications

This letter presents the design of a broadband microstrip CP antenna using single‐fed technique. The feeding network is integrated within the coupling feed patch to simplify the structure. The proposed antenna is designed for Global Navigation satellite System (GNSS) operating at 1575.42 ± 10.23 MHz (GPS: L1 band), 1559∼1592 MHz (Galileo: E2‐L1‐E1 band), 1602 ± 5.625 MHz (GLONASS: L1 band) and 1559.052∼1591.788 MHz & 1610∼1626.5 MHz (BeiDou Navigation Satellite System B1 and L band). Another advantage of this antenna is the much wider bandwidth in both VSWR and 3 dB axial‐ratio compared with traditional single‐fed CP antennas. Details of design, simulated and experimental results of this CP antenna are presented and discussed. The measured results confirm the validity of this design which meet the requirement of GNSS applications.
Isokinetic muscle evaluation of the knee joint in athletes of the Under-19 and Under-21 Male Brazilian National Volleyball Team

The vertical jump is a basic volleyball practice that demands a high ability to generate strength and work in the muscles involved, mainly in the quadriceps muscle. Due to such demand, muscle imbalances between extensor and flexor muscles may be present, causing an overloading on the muscle-tendinous structures of the knee joint. Thus, the establishment of normal parameters for the muscle function related to that joint in volleyball athletes is necessary. Therefore, the purpose of this study was to assess through isokinetic dynamometry the peak torque, work peak, agonist/antagonist ratio, and fatigue index of the flexor and extensor of the knee among both volleyball athlete population. The isokinetic flexion and extension tests of the knees were performed in the concentric-concentric seat mode at 60 and 300o/sec. velocity in thirty-six athletes (20 under 19-under 21, and 16 under 21). The data allowed to set the parameters for the muscle function of the knee joint among athletes of the 2003 Under 19-Under 21 and Under 21 Brazilian National Team Selection of Male Volleyball. Athletes presented peak torque and work peak values normalized by the body mass to the upper quadriceps to the mean normal values for the athletes and non-athletes populations. Compared to other categories, the under 21 athletes presented significantly higher values for the agonist/antagonist ratio, and peak work ratio of the knee flexors at 60o/sec. velocity. Furthermore, the agonist/antagonist ratio was lower than the reference value expected for both categories, thus characterizing predominance in the extensor musculature over the flexor musculature. The fatigue index was close to what would be expected for the majority of athletes. The present study may be useful as comparison basis for future studies aiming evaluate the isokinetic muscle function in volleyball players.
Flexible devices: from materials, architectures to applications

Flexible devices, such as flexible electronic devices and flexible energy storage devices, have attracted a significant amount of attention in recent years for their potential applications in modern human lives. The development of flexible devices is moving forward rapidly, as the innovation of methods and manufacturing processes has greatly encouraged the research of flexible devices. This review focuses on advanced materials, architecture designs and abundant applications of flexible devices, and discusses the problems and challenges in current situations of flexible devices. We summarize the discovery of novel materials and the design of new architectures for improving the performance of flexible devices. Finally, we introduce the applications of flexible devices as key components in real life.
The Fall of the Firefly: An Assessment of a Failed Project Strategy

Choices made early in a project determine future success. Missteps in early phases will cause trouble later in the project's life cycle. The U.S. Air Force's acquisition of the T-3A “Firefly” trainer was just such a troubled project. Rather than develop a new aircraft, the Air Force decided to save time and money by buying a commercial off-the-shelf (COTS) trainer. But significant aircraft modifications undermined the integrity of the COTS strategy. This paper suggests four project lessons: Any project must be managed as a system of interrelated parts; a project strategy must be flexible to accommodate changing circumstances; testing must be done in realistic environments; and concurrency carries with it benefits and dangers.