Miracle-dz/UniFAR-FTUs huggingface dataset:
Human Seroprevalence for Dengue, Ross River, and Barmah Forest viruses in Australia and the Pacific: A systematic review spanning seven decades

Background Dengue (DENV), Ross River (RRV) and Barmah Forest viruses (BFV) are the most common human arboviral infections in Australia and the Pacific Island Countries and Territories (PICTs) and are associated with debilitating symptoms. All are nationally notifiable in Australia, but routine surveillance is limited to a few locations in the PICTs. Understanding the level of human exposure to these viruses can inform disease management and mitigation strategies. To assess the historic and current seroprevalence of DENV, RRV and BFV in Australia and the PICTs we conducted a systematic literature review of all published quantitative serosurveys. Methodology and principal findings The Preferred Reporting of Items for Systematic Reviews and Meta-Analyses procedures were adopted to produce a protocol to systematically search for published studies reporting the seroprevalence of DENV, RRV and BFV in Australia and the PICTs. Data for author, research year, location, study population, serosurvey methods and positive tests were extracted. A total of 41 papers, reporting 78 serosurveys of DENV, RRV and BFV including 62,327 samples met the inclusion criteria for this review. Seroprevalence varied depending on the assay used, strategy of sample collection and location of the study population. Significant differences were observed in reported seropositivity depending on the sample collection strategy with clinically targeted sampling reporting the highest seroprevalence across all three viruses. Non-stratified seroprevalence showed wide ranges in reported positivity with DENV 0.0% – 95.6%, RRV 0.0% – 100.0%, and BFV 0.3% – 12.5%. We discuss some of the causes of variation including serological methods used, selection bias in sample collection including clinical or environmental associations, and location of study site. We consider the extent to which serosurveys reflect the epidemiology of the viruses and provide broad recommendations regarding the conduct and reporting of arbovirus serosurveys. Conclusions and significance Human serosurveys provide important information on the extent of human exposure to arboviruses across: (1) time, (2) place, and (3) person (e.g., age, gender, clinical presentation etc). Interpreting results obtained at these scales has the potential to inform us about transmission cycles, improve diagnostic surveillance, and mitigate future outbreaks. Future research should streamline methods and reduce bias to allow a better understanding of the burden of these diseases and the factors associated with seroprevalence. Greater consideration should be given to the interpretation of seroprevalence in studies, and increased rigour applied in linking seroprevalence to transmission dynamics.
Transcription of ncRNAs promotes repair of UV induced DNA lesions in Saccharomyces cerevisiae subtelomeres

Ultraviolet light causes DNA lesions that are removed by nucleotide excision repair (NER). The efficiency of NER is conditional to transcription and chromatin structure. UV induced photoproducts are repaired faster in the gene transcribed strands than in the non-transcribed strands or in transcriptionally inactive regions of the genome. This specificity of NER is known as transcription-coupled repair (TCR). The discovery of pervasive non-coding RNA transcription (ncRNA) advocates for ubiquitous contribution of TCR to the repair of UV photoproducts, beyond the repair of active gene-transcribed strands. Chromatin rules transcription, and telomeres form a complex structure of proteins that silences nearby engineered ectopic genes. The essential protective function of telomeres also includes preventing unwanted repair of double-strand breaks. Thus, telomeres were thought to be transcriptionally inert, but more recently, ncRNA transcription was found to initiate in subtelomeric regions. On the other hand, induced DNA lesions like the UV photoproducts must be recognized and repaired also at the ends of chromosomes. In this study, repair of UV induced DNA lesions was analyzed in the subtelomeric regions of budding yeast. The T4-endonuclease V nicking-activity at cyclobutene pyrimidine dimer (CPD) sites was exploited to monitor CPD formation and repair. The presence of two photoproducts, CPDs and pyrimidine (6,4)-pyrimidones (6-4PPs), was verified by the effective and precise blockage of Taq DNA polymerase at these sites. The results indicate that UV photoproducts in silenced heterochromatin are slowly repaired, but that ncRNA transcription enhances NER throughout one subtelomeric element, called Y’, and in distinct short segments of the second, more conserved element, called X. Therefore, ncRNA-transcription dependent TCR assists global genome repair to remove CPDs and 6-4PPs from subtelomeric DNA.
Nutritional status of children under five years old involved in a seasonal malaria chemoprevention study in the Nanyumbu and Masasi districts in Tanzania

Background Malnutrition and malaria are common co-morbidities in low-income countries, especially among under-fives children. But the malnutrition situation in Masasi and Nanyumbu districts, its interaction with malaria infection and the influence of socioeconomic factors are not well understood. Methods Children aged between 3–59 months in Masasi and Nanyumbu were screened for nutritional status and malaria infection in the community. Nutritional status was determined using age and anthropometric parameters. Z-scores (weight for age (WAZ), height for age (HAZ) and weight for height (WHZ)) were calculated based on the World Health Organisation (WHO) growth reference curves. Malaria infection was determined using malaria rapid diagnostic test and microscopy. Hemoglobin concentration was assessed using HemoCue spectrophotometer, and anemia was classified as hemoglobin concentration < 11.0g/dL. Structured questionnaire was used to collect socio- demographic information electronically. Results A total of 2242 children, 1539 (68.6%) from Masasi and 1169 (52.1%) females were involved in the study. The mean z-scores (WAZ = -0.60 and HAZ = -1.56) were lower than the WHO reference population. The overall prevalence of malnutrition was 49%, and it was significantly higher in Nanyumbu (52.5%) than in Masasi (47.3%), (x2 = 5.045, p = 0.025). Prevalence of malnutrition was higher in boys (53.0%) than in girls (45.0%) (x2 = 13.9, p < 0.001). Stunting was the most prevalent component of undernutrition; it was slightly prevalent in Nanyumbu (46.5%) compared to Masasi (42.0%), (x2 = 3.624, p = 0.057) and in boys (48.2%) than in girls (39.1%), x2 = 17.44, p<0.001. Only 15.8% of the undernourished children had malaria infection. Sex, age group and anaemia were significantly associated with undernourishment (p<0.05), while district and malaria infection were marginally (p≤0.06) associated with undernourishment. None of the undernutrition indices was associated with malaria infection. Conclusion Undernutrition was highly prevalent in the study population and was influenced sex, age, anaemia and malaria infection. More emphasis is needed to address the malnutrition problem especially stunting in Masasi and Nanyumbu districts.
A Hybrid In Situ Approach for Cost Efficient Image Database Generation

The visualization of results while the simulation is running is increasingly common in extreme scale computing environments. We present a novel approach for in situ generation of image databases to achieve cost savings on supercomputers. Our approach, a hybrid between traditional inline and in transit techniques, dynamically distributes visualization tasks between simulation nodes and visualization nodes, using probing as a basis to estimate rendering cost. Our hybrid design differs from previous works in that it creates opportunities to minimize idle time from four fundamental types of inefficiency: variability, limited scalability, overhead, and rightsizing. We demonstrate our results by comparing our method against both inline and in transit methods for a variety of configurations, including two simulation codes and a scaling study that goes above 19K cores. Our findings show that our approach is superior in many configurations. As in situ visualization becomes increasingly ubiquitous, we believe our technique could lead to significant amounts of reclaimed cycles on supercomputers.
Drug use in patients with short bowel syndrome and intestinal failure.

INTRODUCTION In patients with short bowel syndrome (SBS), severe malabsorption may cause a need for parenteral support and, by definition, these patients suffer from SBS intestinal failure. Absorption of oral medications is likely diminished in patients with SBS intestinal failure and higher than normal doses may be required to achieve sufficient pharmacologic effect. We investigated the prescription patterns and oral dosages in a well-defined population of patients with non-malignant SBS intestinal failure. METHODS This was a cross-sectional analysis based on a cohort of adult patients with SBS intestinal failure treated with home parenteral support and registered in 2016 at the Department of Gastroenterology at the Copenhagen University Hospital - Rigshospitalet. The patients' clinical data and prescription patterns were extracted from electronic medical and medications records. RESULTS The patients in our cohort (n = 74) were primarily females (58%), the median age was 63 years (interquartile range (IQR): 52-72 years) and the median BMI was 22 kg/m2 (IQR: 19-26 kg/m2). Each patient was treated with a median of eight drugs (range: 1-20). Most (75%) of the medications were administered orally. Only codeine, levothyroxine and loperamide were prescribed in higher dosages than recommended in their product labelling. All medication-treated patients were prescribed between one and four different analgesics. CONCLUSION In our single-centre cohort of patients with SBS intestinal failure, orally administered medications were generally prescribed in recommended dosages. FUNDING none Trial registration. Approved by the Danish Data Protection Agency (BFH-2016-058, I-Suite no.: 04906) and the Danish Patient Safety Authority (3-3013-1884/1/).
The fecal microbiota transplantation response differs between patients with severe and moderate irritable bowel symptoms

Abstract Objectives Fecal microbiota transplantation (FMT) is a promising intervention for patients with irritable bowel syndrome (IBS). The present study aimed to identify any differences in FMT response between patients with severe and moderate IBS symptoms. Materials and method The study included the 164 patients who participated in our previous study, of which 96 (58.5%) and 68 (41.5%) had severe (S-IBS-S) and moderate (Mo-IBS-S) IBS, respectively. The patients were randomly divided into a placebo group (own feces) and 30-g and 60-g (donor feces) FMT groups. Patients completed three questionnaires that assessed their symptoms and quality of life at baseline and at 2 weeks, 1 month, and 3 months after FMT, and provided fecal samples before and 1 month after FMT. The fecal bacteria were analyzed using the 16S rRNA gene in PCR DNA amplification covering the V3–V9 variable genes. Results Response rates of the placebo group did not differ between S-IBS-S and Mo-IBS-S patients at 2 weeks, 1 month and 3 months after FMT. The response rates in the active treatment group were higher in S-IBS-S patients than in Mo-IBS-S patients at each observation time. FMT reduced abdominal symptoms and fatigue and improved the quality of life in patients with both severe and moderate IBS. Patients with S-IBS-S had higher levels of Eubacterium siraeum, and lower levels of Eubacterium rectale than Mo-IBS-S, after FMT. Conclusion Patients with S-IBS-S have a higher response rate to FMT and a marked improvement in fatigue and in quality of life compared with those with Mo-IBS-S. The clinical trial registration number is NCT03822299 and is available at www.clinicaltrials. gov.
Antimicrobial susceptibility testing and molecular characterization of Neisseria gonorrhoeae in Tehran, Iran

Gonorrhea is a sexually transmitted infection occurring worldwide. Antimicrobial resistance (AMR) surveillance in Neisseria gonorrhoeae and associated molecular epidemiological studies are crucial to ascertain the spread of antibiotic-resistant and developing the local treatment guidelines. This study was performed to determine the antimicrobial susceptibility testing (AST) and molecular epidemiology of N. gonorrhoeae isolates in Tehran, Iran. During 1 July 2018–30 July 2020, a total of 500 urogenital (468 endocervical, 32 urethral) swabs were collected from patients with signs and symptoms of genitourinary infections presenting to two women's hospitals and one health center located center and south of Tehran. Specimens were cultured and examined for the presence of N. gonorrhoeae isolates by biochemical tests. MIC Test Strip determined the MICs of ceftriaxone, azithromycin, and ciprofloxacin. Neisseria gonorrhoeae multiantigen sequence typing (NG-MAST) was also performed. A total of 38 N. gonorrhoeae isolates were identified. The proportions of resistant N. gonorrhoeae isolates were as follows: ceftriaxone (MIC ≥0.125 μg/mL) 10.5% (4/38), azithromycin (MIC >1 μg/mL) 34% (13/38), and ciprofloxacin (MIC ≥1 μg/mL) 31.5% (12/38). In total, 25 different NG-MAST STs were identified. The STs comprised 1–4 isolates each, and the predominant ST was ST266 (n = 4). Our study demonstrates a diverse gonococcal population with high rates of resistance to azithromycin and evidence of resistance to ceftriaxone. The results have potential implications for antibiotic choice for the gonococcal treatment and highlight the need to broaden gonococcal AMR monitoring in Iran.
Molecular Pathways and Mechanisms of BRAF in Cancer Therapy.

With the identification of activating mutations in BRAF across a wide variety of malignancies, substantial effort was placed in designing safe and effective therapeutic strategies to target BRAF. These efforts have led to the development and regulatory approval of three BRAF inhibitors as well as five combinations of a BRAF inhibitor plus an additional agent(s) to manage cancer such as melanoma, non-small cell lung cancer, anaplastic thyroid cancer, and colorectal cancer. To date, each regimen is effective only in patients with tumors harboring BRAFV600 mutations and the duration of benefit is often short-lived. Further limitations preventing optimal management of BRAF mutant malignancies are that treatments of non-V600 BRAF mutations have been less profound and combination therapy is likely necessary to overcome resistance mechanisms, but multi-drug regimens are often too toxic. With the emergence of a deeper understanding of how BRAF mutations signal through the RAS/mitogen activated protein kinase (MAPK) pathway, newer RAF inhibitors are being developed that may be more effective and potentially safer and more rational combination therapies are being tested in the clinic. In this review, we identify the mechanics of RAF signaling through the RAS/MAPK pathway, present existing data on single-agent and combination RAF targeting efforts, describe emerging combinations, summarize the toxicity of the various agents in clinical testing, and speculate as to where the field may be headed.
Care v. Caring: Obligation, Duty, and Love Among Latino Alzheimer’s Family Caregivers

The number of Latinos living with Alzheimer’s disease is projected to grow. Latinos currently make one-fifth of U.S. family caregivers. In this paper, we explore the cultural scripts and gendered practice of care in Latino families in relation to the underutilization of services to persons with Alzheimer’s disease and related dementias. We conducted interviews with 24 Latino caregivers in Miami-Dade, Florida representing six Latin American countries of origin. Interviews were analyzed using a grounded theory approach. We critically examined the concept of familism in order to better understand in-depth experiences of diverse Latino caregivers and concluded that an ethics of care model better elucidates the complexities of the care experience. Our analysis illustrates the ambivalence, contradictions, and changes in the beliefs and practice of care. These findings can help advance understanding among researchers and providers to develop a formal support system that is responsive to Latino caregiver needs.
Treatment of Intervertebral Disc Degeneration

Intervertebral disc degeneration (IDD) causes a variety of signs and symptoms, such as low back pain (LBP), intervertebral disc herniation, and spinal stenosis, which contribute to high social and economic costs. IDD results from many factors, including genetic factors, aging, mechanical injury, malnutrition, and so on. The pathological changes of IDD are mainly composed of the senescence and apoptosis of nucleus pulposus cells (NPCs), the progressive degeneration of extracellular matrix (ECM), the fibrosis of annulus fibrosus (AF), and the inflammatory response. At present, IDD can be treated by conservative treatment and surgical treatment based on patients' symptoms. However, all of these can only release the pain but cannot reverse IDD and reconstruct the mechanical function of the spine. The latest research is moving towards the field of biotherapy. Mesenchymal stem cells (MSCs) are regard as the potential therapy of IDD because of their ability to self‐renew and differentiate into a variety of tissues. Moreover, the non‐coding RNAs (ncRNAs) are found to regulate many vital processes in IDD. There have been many successes in the in vitro and animal studies of using biotherapy to treat IDD, but how to transform the experimental data to real therapy which can apply to humans is still a challenge. This article mainly reviews the treatment strategies and research progress of IDD and indicates that there are many problems that need to be solved if the new biotherapy is to be applied to clinical treatment of IDD. This will provide reference and guidance for clinical treatment and research direction of IDD.
Effect of different helmets against ground impact based on the in-depth reconstruction of electric two-wheeler accidents

Abstract Skull fracture and brain injury are frequent head injuries in electric two-wheeler (ETW) accidents, and the type of helmet and impact conditions affect the effectiveness of the helmet in protecting the rider’s head. The purpose of this study was to conduct in-depth reconstructions of rider’s head-to-ground impacts in ten ETW accidents by using a multi-body system combined with a finite element approach and to evaluate the effect of two typical full-face helmets (FFH) and one half-coverage helmet (HCH) through head accelerations and intracranial biomechanics injury metrics in ground impacts. The results showed that all three helmets reduced the risk of skull fracture in most cases, however, FFH performed better due to its wider protection area. In addition, three helmets showed varying degrees of overall reduction in measuring all indicators of brain injury. Although the effectiveness of the helmets on angular acceleration was largely influenced by the angle and location of impact, it was certain that wearing an FFH was more likely to reduce rotational head movements than an HCH, and that the FFH also offered the better advantage in reducing diffuse axonal injury (DAI) risk due to its better resistance to ejection in a crash.
A comprehensive study of the abdominal ganglia part 1: Celiac, phrenic and superior mesenteric ganglia

Patients with pancreatic cancer, chronic pancreatitis and other abdominal pain syndromes may develop debilitating pain throughout the course of their illness with little to no relief by most conventional methods. While some form of relief is experienced by patients, not all benefit from these procedures and side effects, while transitory in most cases are severe and often not expected. Our aim was therefore to investigate the anatomy surrounding the abdominal sympathetic ganglia, the target for the invasive procedures in an attempt to understand the variations in results.
Investigational drugs for ischemic stroke: what’s in the clinical development pipeline for acute phase and prevention?

ABSTRACT Introduction Stroke is a leading cause of disability and mortality and its burden expected to increase. The only approved drug for acute ischemic stroke (IS) is the intravenous thrombolytic alteplase. The risk of bleeding complications is one of the reasons for the undertreatment of eligible patients. Numerous drugs are currently being developed to improve safety-efficacy. Areas covered We reviewed literature from 1 January 2000, to 15 January 2022 for the development and testing of novel drugs with the aim of targeting treatment at prevention of ischemic stroke: PubMed, MEDLINE, Google Scholar, and ClinicalTrial.gov. Expert opinion The pathophysiology of IS involves multiple pathways causing cerebral artery obstruction and brain tissue ischemia. Data suggest that tenecteplase is a promising fibrinolytic agent with a superior efficacy-safety profile, compared to alteplase. Current guidelines consider a short-term cycle of mannitol or hypertonic saline to be advisable in patients with space-occupying hemispheric infarction. Regarding primary and secondary prevention, research is primarily focused on identifying mechanisms to improve the safety-efficacy profile using a ‘hemostasis-sparing’ approach. Further evaluation on those agents that have shown promise for their risk/benefit profiles, would benefit greatly a neurologist’s capacity to successfully prevent and treat IS patients.
Downregulation of EHT1 and EEB1 in Saccharomyces cerevisiae Alters the Ester Profile of Wine during Fermentation

EHT1 and EEB1 are the key Saccharomyces cerevisiae genes involved in the synthesis of ethyl esters during wine fermentation. We constructed single (Δeht1, Δeeb1) and double (Δeht1Δeeb1) heterogenous mutant strains of the industrial diploid wine yeast EC1118 by disrupting one allele of EHT1 and/or EEB1. In addition, the aromatic profile of wine produced during fermentation of simulated grape juice by these mutant strains was also analyzed. The expression levels of EHT1 and/or EEB1 in the relevant mutants were less than 50% of the wild-type strain when grown in YPD medium and simulated grape juice medium. Compared to the wild-type strain, all mutants produced lower amounts of ethyl esters in the fermented grape juice and also resulted in distinct ethyl ester profiles. ATF2, a gene involved in acetate ester synthesis, was expressed at higher levels in the EEB1 downregulation mutants compared to the wild-type and Δeht1 strains during fermentation, which was consistent with the content of acetate esters. In addition, the production of higher alcohols was also markedly affected by the decrease in EEB1 levels. Compared to EHT1, EEB1 downregulation had a greater impact on the production of acetate esters and higher alcohols, suggesting that controlling EEB1 expression could be an effective means to regulate the content of these aromatic metabolites in wine. Taken together, the synthesis of ethyl esters can be decreased by deleting one allele of EHT1 and EEB1 in the diploid EC1118 strain, which may modify the ester profile of wine more subtly compared to the complete deletion of target genes.
Deployment Strategy of Wireless Sensor Networks: A Survey

For wireless sensor network (WSN), the first step is to deploy sensor nodes effectively into the target area. In fact, node deployment will greatly influence the lifetime and performance of WSN system. In this paper, we summarized the evolution of sensing models frequently used. Some main models' property is analyzed in details. The strategies are classified into three classes (static deployment, mobile deployment and hybrid deployment) based on the mobility of sensor nodes. Then, the typical algorithms and ideas are introduced and commented. Different performance evaluation factors for sensor network are also depicted. Finally, the developing direction of future research is discussed and anticipated.