Miracle-dz/UniFAR-FTUs huggingface dataset:
SARS-CoV-2 Consensus-Sequence and Matching Overlapping Peptides Design for COVID19 Immune Studies and Vaccine Development

Synthetic antigens based on consensus sequences that represent circulating viral isolates are sensitive, time saving and cost-effective tools for in vitro immune monitoring and to guide immunogen design. When based on a representative sequence database, such consensus sequences can effectively be used to test immune responses in exposed and infected individuals at the population level. To accelerate immune studies in SARS-CoV-2 infection, we here describe a SARS-CoV-2 2020 consensus sequence (CoV-2-cons) which is based on more than 1700 viral genome entries in NCBI and encompasses all described SARS-CoV-2 open reading frames (ORF), including recently described frame-shifted and length variant ORF. Based on these sequences, we created curated overlapping peptide (OLP) lists containing between 1500 to 3000 peptides of 15 and 18 amino acids in length, overlapping by 10 or 11 residues, as ideal tools for the assessment of SARS-CoV-2-specific T cell immunity. In addition, CoV-2-cons sequence entropy values are presented along with variant sequences to provide increased coverage of the most variable sections of the viral genome. The identification of conserved protein fragments across the coronavirus family and the corresponding OLP facilitate the identification of T cells potentially cross-reactive with related viruses. This new CoV-2-cons sequence, together with the peptides sets, should provide the basis for SARS-CoV-2 antigen synthesis to facilitate comparability between ex-vivo immune analyses and help to accelerate research on SARS-CoV-2 immunity and vaccine development.
The Effect of Bacterial Endotoxin LPS on Serotonergic Modulation of Glutamatergic Synaptic Transmission

The release of the endotoxin lipopolysaccharides (LPS) from gram-negative bacteria is key in the induction of the downstream cytokine release from cells targeting cells throughout the body. However, LPS itself has direct effects on cellular activity and can alter synaptic transmission. Animals experiencing septicemia are generally in a critical state and are often treated with various pharmacological agents. Since antidepressants related to the serotonergic system have been shown to have a positive outcome for septicemic conditions impacting the central nervous system, the actions of serotonin (5-HT) on neurons also exposed to LPS were investigated. At the model glutamatergic synapse of the crayfish neuromuscular junction (NMJ), 5-HT primarily acts through a 5-HT2A receptor subtype to enhance transmission to the motor neurons. LPS from Serratia marcescens also enhances transmission at the crayfish NMJ but by a currently unknown mechanism. LPS at 100 µg/mL had no significant effect on transmission or on altering the response to 5-HT. LPS at 500 µg/mL increased the amplitude of the evoked synaptic excitatory junction potential, and 5-HT in combination with 500 µg/mL LPS continued to promote enhanced transmission. The preparations maintained responsiveness to serotonin in the presence of low or high concentrations of LPS.
A Wireless Implantable Passive Intra-Abdominal Pressure Sensing Scheme via Ultrasonic Imaging of a Microfluidic Device

In this article, we demonstrate a wireless and passive physiological pressure sensing scheme that utilizes ultrasound imaging of an implantable microfluidic based pressure sensitive transducer. The transducer consists of a sub-mm scale pressure sensitive membrane that covers a reservoir filled with water and is connected to a hydrophobic micro-channel. Applied pressure onto the transducer deflects the membrane and pushes the water from the reservoir into the channel; the water's travelling distance in the channel is a function of the applied pressure, which is quantitatively measured by using a 40 MHz ultrasound imaging system. The sensor presents a linear sensitivity of 42 kPa/mm and a spatial resolution of 1.2 kPa/30 μm in the physiological range of abdominal compartment syndrome. Reliability assessments of the transducer confirm its ability to remain functional after more than 600 cycles of pressure up to 55 kPa over the course of 2 days. Ex vivo experimental results verify the practical capability of the technology to effectively measure pressures under a 15 mm thick porcine skin. It is anticipated that this technology can be applied to a broad range of implantable pressure measurement, by simply tuning the thickness of the thin polydimethylsiloxane membrane and the geometry of the reservoir.
Next Generation Sequencing in MPNs. Lessons from the Past and Prospects for Use as Predictors of Prognosis and Treatment Responses

The myeloproliferative neoplasms (MPNs) are acquired hematological stem cell neoplasms characterized by driver mutations in JAK2, CALR, or MPL. Additive mutations may appear in predominantly epigenetic regulator, RNA splicing and signaling pathway genes. These molecular mutations are a hallmark of diagnostic, prognostic, and therapeutic assessment in patients with MPNs. Over the past decade, next generation sequencing (NGS) has identified multiple somatic mutations in MPNs and has contributed substantially to our understanding of the disease pathogenesis highlighting the role of clonal evolution in disease progression. In addition, disease prognostication has expanded from encompassing only clinical decision making to include genomics in prognostic scoring systems. Taking into account the decreasing costs and increasing speed and availability of high throughput technologies, the integration of NGS into a diagnostic, prognostic and therapeutic pipeline is within reach. In this review, these aspects will be discussed highlighting their role regarding disease outcome and treatment modalities in patients with MPNs.
An Examination on the Transmission of COVID-19 and the Effect of Response Strategies: A Comparative Analysis

The major purpose of this paper was to examine the transmission of COVID-19 and the associated factors that affect the transmission. A qualitative analysis was conducted by comparing the COVID-19 transmission of six countries: China, Korea, Japan, Italy, the USA, and Brazil. This paper attempted to examine the mitigation effectiveness for the transmission of COVID-19 and the pandemic severity. Time to reach the peak of daily new confirmed cases and the maximum drop rate were used to measure the mitigation effectiveness, while the proportion of confirmed cases to population and the mortality rate were employed to evaluate the pandemic severity. Based on the mitigation effectiveness, the pandemic severity, and the mortality rate, the six sample countries were categorized into four types: high mitigation effectiveness vs. low pandemic severity, middle mitigation effectiveness vs. low pandemic severity, high mitigation effectiveness vs. high pandemic severity, and low mitigation effectiveness vs. high pandemic severity. The results found that Korea and China had relatively higher mitigation effectiveness and lower pandemic severity, while the USA and Brazil had the opposite. This paper suggests that viral testing together with contacts tracing, strict implementation of lockdown, and public cooperation play important roles in achieving a reduction in COVID-19 transmission.
Executive Summary from American Radium Society's Appropriate Use Criteria on Neurocognition after stereotactic radiosurgery for multiple brain metastases.

BACKGROUND The ARS Appropriate Use Criteria brain malignancies panel systematically reviewed (PRISMA) published literature on neurocognitive outcomes after stereotactic radiosurgery (SRS) for patients with multiple brain metastases (BrM) to generate consensus guidelines. METHODS The panel developed 4 key questions (KQ) to guide systematic review. From 11,614 original articles, 12 were selected. The panel developed model cases addressing KQ and potentially controversial scenarios not addressed in the systematic review (that might inform future ARS projects). Based upon quality of evidence, the panel confidentially voted on treatment options using a 9-point scale of appropriateness. RESULTS The panel agreed that SRS-alone is usually appropriate for those with good performance status (PS) and 2-10 asymptomatic BrM, and usually not appropriate for >20 BrM. For 11-15 and 16-20 BrM there was (between 4 case variants) agreement that SRS-alone may be appropriate or disagreement on the appropriateness of SRS-alone. There was no scenario in which conventional whole brain radiotherapy (WBRT) was considered usually appropriate by most panelists. There were several areas of disagreement, including: hippocampal sparing WBRT for 2-4 asymptomatic BrM; WBRT for resected BrM amenable to SRS; fractionated- vs, single-fraction SRS for resected BrM, larger targets and/or brainstem metastases; optimal treatment (WBRT, hippocampal sparing WBRT, SRS-alone to all or select lesions) for patients with progressive extracranial disease, poor PS and no systemic options. CONCLUSIONS For patients with 2-10 BrM, SRS-alone is an appropriate treatment option for well-selected patients with good PS. Future study is needed for those scenarios in which there was disagreement among panelists.
Validation of the Raw National Aeronautics and Space Administration Task Load Index (NASA-TLX) Questionnaire to Assess Perceived Workload in Patient Monitoring Tasks: Pooled Analysis Study Using Mixed Models

Background Patient monitoring is indispensable in any operating room to follow the patient’s current health state based on measured physiological parameters. Reducing workload helps to free cognitive resources and thus influences human performance, which ultimately improves the quality of care. Among the many methods available to assess perceived workload, the National Aeronautics and Space Administration Task Load Index (NASA-TLX) provides the most widely accepted tool. However, only few studies have investigated the validity of the NASA-TLX in the health care sector. Objective This study aimed to validate a modified version of the raw NASA-TLX in patient monitoring tasks by investigating its correspondence with expected lower and higher workload situations and its robustness against nonworkload-related covariates. This defines criterion validity. Methods In this pooled analysis, we evaluated raw NASA-TLX scores collected after performing patient monitoring tasks in four different investigator-initiated, computer-based, prospective, multicenter studies. All of them were conducted in three hospitals with a high standard of care in central Europe. In these already published studies, we compared conventional patient monitoring with two newly developed situation awareness–oriented monitoring technologies called Visual Patient and Visual Clot. The participants were resident and staff anesthesia and intensive care physicians, and nurse anesthetists with completed specialization qualification. We analyzed the raw NASA-TLX scores by fitting mixed linear regression models and univariate models with different covariates. Results We assessed a total of 1160 raw NASA-TLX questionnaires after performing specific patient monitoring tasks. Good test performance and higher self-rated diagnostic confidence correlated significantly with lower raw NASA-TLX scores and the subscores (all P<.001). Staff physicians rated significantly lower workload scores than residents (P=.001), whereas nurse anesthetists did not show any difference in the same comparison (P=.83). Standardized distraction resulted in higher rated total raw NASA-TLX scores (P<.001) and subscores. There was no gender difference regarding perceived workload (P=.26). The new visualization technologies Visual Patient and Visual Clot resulted in significantly lower total raw NASA-TLX scores and all subscores, including high self-rated performance, when compared with conventional monitoring (all P<.001). Conclusions This study validated a modified raw NASA-TLX questionnaire for patient monitoring tasks. The scores obtained correctly represented the assumed influences of the examined covariates on the perceived workload. We reported high criterion validity. The NASA-TLX questionnaire appears to be a reliable tool for measuring subjective workload. Further research should focus on its applicability in a clinical setting.
An Israeli RCT of PEERS®: Intervention Effectiveness and the Predictive Value of Parental Sensitivity

ABSTRACT Objectives: A Randomized Controlled Trial was conducted to evaluate the effectiveness of the Hebrew adaptation of the Program for the Education and Enrichment of Relational Skills (PEERS®), a parent-assisted intervention. Parental sensitivity (PS), measured in conflict and support contexts, was assessed as a predictor of adolescents’ intervention-related outcomes. Design: Eighty-two Hebrew-speaking adolescents (9 females), aged 12–17 years, and their parents (62 mothers), were randomly allocated into immediate intervention (II; n = 40) or delayed intervention control (DI; n = 42) groups. Participants were tested at three time-points (Pre-Post-Follow Up for II, Pre-Pre-Post for DI). Outcome measures included behavioral assessments of adolescents’ social communication (SC), a social-skills knowledge test, and self, parent, and teacher reported questionnaires. PS was assessed using support and conflict parent-adolescent interactions. Repeated measures ANOVAs were used to assess intervention effectiveness. SEM was used to examine PS pre- and post-intervention as predictors of adolescents’ immediate and follow-up outcomes. Results: The II group improved on adolescents’ measured SC and social knowledge, on parent-(but not teacher-) reported social skills, and on self-reported empathy. Gains maintained at follow-up. The DI group showed similar gains following their intervention. Adolescents’ intervention-related SC gains were negatively predicted by pre-intervention PS, and positively predicted by intervention-related PS changes in the support context. Pre-intervention PS in the conflict context positively predicted adolescent SC at follow-up. Conclusions: The Hebrew-adapted PEERS® is an effective intervention for adolescents with ASD. PS plays an important role in the promotion of SC in adolescents with ASD and should receive clinical attention.
Microalgae: A Promising Source of Valuable Bioproducts

Microalgae are a group of autotrophic microorganisms that live in marine, freshwater and soil ecosystems and produce organic substances in the process of photosynthesis. Due to their high metabolic flexibility, adaptation to various cultivation conditions as well as the possibility of rapid growth, the number of studies on their use as a source of biologically valuable products is growing rapidly. Currently, integrated technologies for the cultivation of microalgae aiming to isolate various biologically active substances from biomass to increase the profitability of algae production are being sought. To implement this kind of development, the high productivity of industrial cultivation systems must be accompanied by the ability to control the biosynthesis of biologically valuable compounds in conditions of intensive culture growth. The review considers the main factors (temperature, pH, component composition, etc.) that affect the biomass growth process and the biologically active substance synthesis in microalgae. The advantages and disadvantages of existing cultivation methods are outlined. An analysis of various methods for the isolation and overproduction of the main biologically active substances of microalgae (proteins, lipids, polysaccharides, pigments and vitamins) is presented and new technologies and approaches aimed at using microalgae as promising ingredients in value-added products are considered.
Greater benefit of self-affirmation for prevention-focused individuals prior to threatening health messages

Abstract Objective Individuals are often defensive toward health messages that suggest they are putting their health at risk because such messages threaten their self-competence and integrity. Although self-affirmation can facilitate prevention behaviors in response to health messages, effects are variable. We examined whether disease prevention focus might strengthen self-affirmation’s effects in response to disease prevention messages, given that prevention-focused individuals are likeliest to be persuaded by those messages after self-affirmation attenuates defensiveness. Design In Study 1, participants were self-affirmed before a message about sexually transmitted infections. In Studies 2 and 3, individuals were self-affirmed prior to a message about alcohol and cancer risk. Main Outcome Measures Studies assessed intentions to use condoms, intentions to reduce alcohol, and willingness to drink alcohol in specific scenarios. Results In Study 1, self-affirmation facilitated condom use intentions among those higher in prevention focus. In Studies 2 and 3, self-affirmation facilitated lower willingness to consume alcohol among those high in prevention focus. A meta-analysis across the three studies indicated that self-affirmation improved intentions and willingness under high, but not low, prevention focus (d = 0.20, p = .003). Conclusion These findings demonstrate that health prevention-focus can strengthen self-affirmation’s effects, thereby improving responsiveness to health communications about behaviors that increase disease risk.
Spatial ecology of black rat snakes on Remington farms, Maryland

Black rat snakes (Elaphe o. obsoleta) are important predators of nesting birds and small mammals in fragmented landscapes. Thus, we used radiotelemetry to study movements of 32 black rat snakes at Remington Farms, Maryland, during 1988-89 to determine potential ways to minimize their depredations, Yearly home ranges were similar (P > 0.05) for males and females (x ± SE) (convex polygon, 9.49 ± 1.01 ha; 95% harmonic contour, 10.52 ± 1,24 ha), but males covered more (P < 0.05) of the home range earlier in the spring. Snakes were familiar with habitat features within their home range, returning to the same areas after prolonged absences. Snakes used forest edge, residential, hedgerow, and herbaceous/brush habitats more (P < 0.05-0.001) than expected by chance
Functionality of Native Starches in Food Systems: Cluster Analysis Grouping of Rheological Properties in Different Product Matrices

Industrial application of starch as a texture-forming agent is primarily limited to preparations obtained from waxy corn and potatoes. The main reason behind this is its functionality, which depends mostly on rheological properties. However, in food product matrices, these properties change. Despite the vast amount of information on the rheological properties of various starches, the rational choice of thickener appears to be an extremely difficult task. The aim of the work is to systemize the information on the rheological properties of most popular starches in matrices of various food products, applying principal component and cluster analyses. The investigated material is potato and corn starch of the normal and waxy varieties. Binary mixtures containing salts or sweetening agents, as well as four different food products (ketchup, mayonnaise, pudding, and jelly), are investigated. It was found that compared to normal varieties, waxy starches reveal many similar rheological properties in all investigated models and food systems. Furthermore, in most applications, one waxy starch variety may be substituted by another, with no significant impact on the rheological properties and texture of the food product. Moreover, waxy starch preparations are less altered by the presence of cosolutes, i.e., salts and sugar alcohols. Starch model systems were proven to be useful only for rapid thickener screening tests and cannot be recommended as a final reference for the quality design of food products.
Evaluation of autophagy‐related genes in Egyptian systemic lupus erythematosus patients

Disturbances in autophagy are known to be implicated in autoimmune disorders. Many studies have connected polymorphisms in autophagy‐related gene 5 (ATG‐5) to systemic lupus erythematosus (SLE). Our aim was the determination of the expression level of ATG‐5, Beclin‐1 and microtubule‐associated protein‐light chain 3 (LC‐3) in Egyptian SLE patients to investigate the impact of disturbances in autophagy genes on the incidence and progression of the disease. Also, we investigated the incidence of single nucleotide polymorphism (SNP) rs573775 in ATG‐5 gene among Egyptian SLE patients. Our results showed that the mean levels of Beclin‐1, LC‐3 and interleukin (IL)‐10 transcripts were significantly higher in SLE patients compared to healthy controls. The previous transcripts were positively correlated with SLE Disease Activity Index (SLEDAI). Beclin‐1 and LC‐3 transcripts were negatively correlated to complement component 3 (C3) levels. Only LC‐3 transcripts were negatively correlated to complement component 4 (C4). The rs573775 SNP of ATG‐5 with the variant allele was significantly associated with disease susceptibility, conferring a higher risk of SLE development. This variant allele was more prevalent in patients below 30 years, patients with anemia and in patients with anti‐double‐stranded DNA (dsDNA), confirming the essential role of ATG‐5 polymorphism in the susceptibility of Egyptian patients to SLE.
Case report of a vertical straight sinus with hydrocephalus and Chiari I malformation

The straight sinus is a division of the dural venous sinuses, found beneath the splenium of the corpus callosum. At the internal occipital protuberance, it comes together with the superior sagittal sinus and transverse sinus to form the torcular Herophili. It functions as a major site of venous drainage for the cerebellum, inferior sagittal sinus, and vein of Galen. Many morphological variations have been reported involving the angulation, positioning, and number of straight sinuses present. Patients with Chiari II and III malformations have been observed to have a high incidence of anatomical variation with their dural venous sinuses, including vertically oriented straight sinuses. Additionally, there is a high rate of hydrocephalus in this patient population. Herein, we report a vertically oriented straight sinus in a child.
Ellagic Acid and Its Microbial Metabolite Urolithin A Alleviate Diet-induced Insulin Resistance in Mice.

SCOPE We aimed at evaluating the effect of dietary ellagic acid (EA) and its microbial metabolite urolithin A (UA) on glucose metabolism and insulin resistance (IR) in mice with diet-induced IR. METHODS AND RESULTS DBA2J mice were fed a high fat/high sucrose diet (HF/HS) for 8 weeks to induce IR and then 0.1% EA, UA, or EA and UA combined (EA+UA) were added to the HF/HS-diet for another 8 weeks. UA significantly decreased fasting glucose and increased serum adiponectin compared with HF/HS-controls. During intraperitoneal insulin tolerance test, EA+UA significantly improved insulin-mediated glucose lowering effects at 15 and 120 min and reduced blood triglycerides compared with HF/HS-controls. Serum free fatty acids were significantly decreased by EA, UA and EA+UA. We observed differential expression of genes related to mitochondrial function by EA, UA and EA+UA in liver and skeletal muscle. Primary hepatocytes from IR-mice had higher proton leak, basal and ATP-linked oxygen consumption rates compared with healthy controls. EA and EA+UA but not UA reduced the proton leak in hepatocytes from IR-mice. CONCLUSION EA and UA induced different metabolic benefits in HF/HS diet induced IR mice. The effects of EA and UA on mitochondrial function suggest a potentially novel mechanism modulating metabolism. This article is protected by copyright. All rights reserved.