Miracle-dz/UniFAR-FTUs huggingface dataset:
Invasive plants facilitated by socioeconomic change harbor vectors of scrub typhus and spotted fever

Background Ecological determinants of most emerging vector-borne diseases are understudied, particularly for neglected tropical disease. Moreover, although socioeconomic impacts can have significant downstream effects on human risks to vector-borne diseases via a change in land cover, particularly facilitating the invasion of exotic plants, related studies remains very scarce. Scrub typhus and spotted fever are neglected diseases emerging around the globe and are transmitted by chigger mites and ticks infective of Orientia tsutsugamushi and Rickettsia spp. , respectively, with small mammals as the primary hosts of both vectors. Methodology/Principal findings We investigated how invasions of the plant Leucaena leucocephala caused by widespread abandonment of farmlands driven by industrialization affected abundance of chiggers and ticks in Penghu Island, Taiwan. We determined ectoparasite abundance by trapping small mammals in three types of habitats (invasion site, agricultural field, human residential) every two months for a year. Based on ectoparasite burdens, invasion sites harbored more chiggers and ticks than the other two habitats. Furthermore, hosts maintained higher burdens of both vectors in early winter and burdens of chiggers were more stable across seasons in invasion sites, suggesting that sites with invasive plants could be a temporary refuge for both vectors and might help mitigate the negative influence of unfavorable climate. Infective rates of O. tsutsugamushi in chiggers and Rickettsia in ticks were also consistently not lower in invasion sites. Top soil temperature and relative humidity were similar across the three habitats, but invasion sites contained more of the rat Rattus losea, on which chiggers and ticks were more engorged than those from the most commonly trapped species (Suncus murinus shrew), indicating that abundance of the host R. losea instead of microclimate might better determine the abundance of both vectors. Conclusions/Significance This study highlights an important but largely neglected issue that socioeconomic change can have unexpected consequences for human health induced particularly by invasive plants, which could become a hotspot for emerging infectious diseases but usually are very hard to be eradicated. In the future, a more comprehensive approach that integrates socio-economics, land use, exotic species, and human health should be considered to fully understand potential emergence of vector-borne diseases.
Anthocyanin Metabolites in Human Urine after the Intake of New Functional Beverages

Sugar intake abuse is directly related with the increase of metabolic diseases such as type 2 diabetes, obesity, and insulin resistance. Along this line, the development of new beverages using alternative sweeteners could help with combatting the pathophysiological disorders associated to the consumption of sugar. To provide evidence on this issue, in the present work, the bioavailability of anthocyanins was evaluated after the acute ingestion of a new maqui-citrus-based functional beverage rich in polyphenols, and supplemented with a range of sweeteners including sucrose (natural high caloric), stevia (natural non-caloric), and sucralose (artificial non-caloric), as an approach that would allow reducing the intake of sugars while providing bioactive phenolic compounds (anthocyanins). This approach allowed the evaluation of the maximum absorption and the diversity of metabolites excreted through urine. The beverages created were ingested by volunteers (n = 20) and the resulting anthocyanin metabolites in their urine were analyzed by UHPLC-ESI-MS/MS. A total of 29 degradation metabolites were detected: Caffeic acid, catechol, 3,4-dihidroxifenilacetic acid, hippuric acid, trans-ferulic acid, 2,4,6-trihydroxybenzaldehyde, trans-isoferulic acid, and vanillic acid derivatives, where peak concentrations were attained at 3.5 h after beverage intake. Sucralose was the sweetener that provided a higher bioavailability for most compounds, followed by stevia. Sucrose did not provide a remarkably higher bioavailability of any compounds in comparison with sucralose or stevia. The results propose two sweetener alternatives (sucralose and stevia) to sucrose, an overused high calorie sweetener that promotes some metabolic diseases.
Genetic Diversity of Bemisia tabaci (Gennadius) (Hemiptera: Aleyrodidae) Colonizing Sweet Potato and Cassava in South Sudan

Bemisia tabaci (Gennadius) is a polyphagous, highly destructive pest that is capable of vectoring viruses in most agricultural crops. Currently, information regarding the distribution and genetic diversity of B. tabaci in South Sudan is not available. The objectives of this study were to investigate the genetic variability of B. tabaci infesting sweet potato and cassava in South Sudan. Field surveys were conducted between August 2017 and July and August 2018 in 10 locations in Juba County, Central Equatoria State, South Sudan. The sequences of mitochondrial DNA cytochrome oxidase I (mtCOI) were used to determine the phylogenetic relationships between sampled B. tabaci. Six distinct genetic groups of B. tabaci were identified, including three non-cassava haplotypes (Mediterranean (MED), Indian Ocean (IO), and Uganda) and three cassava haplotypes (Sub-Saharan Africa 1 sub-group 1 (SSA1-SG1), SSA1-SG3, and SSA2). MED predominated on sweet potato and SSA2 on cassava in all of the sampled locations. The Uganda haplotype was also widespread, occurring in five of the sampled locations. This study provides important information on the diversity of B. tabaci species in South Sudan. A comprehensive assessment of the genetic diversity, geographical distribution, population dynamics, and host range of B. tabaci species in South Sudan is vital for its effective management.
Investigation of Neutral Losses and the Citrulline Effect for Modified H4 N-Terminal Pentapeptides

Tandem mass spectrometry is an indispensable tool in proteomics used for protein sequencing and quantitation. On the basis of the sequential fragments usually generated from peptide ions via collision-induced dissociation, electron-transfer dissociation, or a combination of the two, probabilistic database search engines could be used for the identification of the peptides. The correct localization of posttranslational modifications (PTMs) poses a more challenging problem than the general identification of proteins. Histones are involved in the regulation of DNA transcription via the wealth of PTMs on their N-terminal tail. In this study, we analyzed the histone H4 peptide SGRGK incorporating four different posttranslational modifications: citrullination, acetylation, phosphorylation, and arginine methylation at various positions. The pentapeptides model the enzymatic cleavage of the N-terminal tail of human histone H4 protein by LysC protease. Fragmentation of the peptides was investigated using higher-energy collisional dissociation (HCD), electron-transfer dissociation (ETD), and electron-transfer higher-energy collisional dissociation (EThcD) on an ultrahigh resolution and mass accuracy instrument. We found that while all three techniques have their unique characteristics, advantages, and pitfalls, EThcD generated the most fragment ion-rich spectra. Despite potential ambiguities regarding exact fragment identities, full sequence coverage and PTM mapping may also be achievable. We also found novel neutral losses from the charge-reduced precursors characteristic to citrullination in ETD and EThcD which may be used in proteomic applications. N-Terminal acetylation and arginine methylation could also be confirmed by their characteristic neutral losses from the charge-reduced precursors.
Evaluation of Hearing Thresholds by Using a Mobile Application in Children with Otitis Media with Effusion

Objective: Otitis media with effusion (OME) is the most common cause of hearing loss in children. Early diagnosis is important as hearing loss affects speech and language development in children. The aim of this study was to compare conventional audiometry with the Android mobile operating system application Hearing TestTM in the evaluation of hearing thresholds in children with OME and to determine the accuracy and reliability of the mobile application. Design and Study Sample: Fifty school-age children aged between 5 and 15 years with OME in at least 1 ear were included in the study. First, hearing thresholds were obtained by conventional audiometric methods and the degree of hearing loss was determined. Then, the hearing thresholds of the patients were measured using the smartphone-based Hearing TestTM application. The data were compared using Cohen’s kappa analysis. Results: OME was detected in 88 ears. There was no statistically significant correlation between the hearing threshold results obtained with the mobile phone and conventional audiometry at 500, 1,000, 2,000, and 4,000 Hz. Conclusion: The Android mobile phone application Hearing TestTM (version 1.1.3) is not an appropriate screening test to detect hearing loss in children with OME.
Cost-effectiveness of Imaging Protocols for Suspected Appendicitis

A decision-analytic model can simulate the optimal imaging strategy for appendicitis on the basis of a patient’s pretest probability of the disease. BrightcoveDefaultPlayer10.1542/6138659816001PEDS-VA_2019-1352 Video Abstract BACKGROUND: Inaccurate diagnosis of appendicitis leads to increased costs and morbidity. Ultrasound costs less than computed tomography (CT) or MRI but has lower sensitivity and may not visualize the appendix. METHODS: We conducted a cost-effectiveness analysis using a decision-analytic model of 10 imaging strategies for suspected appendicitis in a hypothetical cohort of patients: no imaging with discharge or surgery; CT only; MRI only; or staged approach with CT or MRI after 1) negative ultrasound result or ultrasound without appendix visualization, 2) ultrasound without appendix visualization, or 3) ultrasound without appendix visualization but with secondary signs of inflammation. Inputs were derived from published literature and secondary data (quality-of-life and cost data). Sensitivity analyses varied risk of appendicitis and proportion of visualized ultrasound. Outcomes were effectiveness (quality-adjusted life-years [QALYs]), total direct medical costs, and cost-effectiveness (cost per QALY gained). RESULTS: The most cost-effective strategy for patients at moderate risk for appendicitis is initial ultrasound, followed by CT if the appendix is not visualized but secondary signs are present (cost of $4815.03; effectiveness of 0.99694 QALYs). Other strategies were well above standard willingness-to-pay thresholds or were more costly and less effective. Cost-effectiveness was sensitive to patients’ risk of appendicitis but not the proportion of visualized appendices. CONCLUSIONS: Tailored approaches to imaging based on patients’ risk of appendicitis are the most cost-effective. Imaging is not cost-effective in patients with a probability <16% or >95%. For moderate-risk patients, ultrasound without secondary signs of inflammation is sufficient even without appendix visualization.
Alpha-Synuclein Physiology and Pathology: A Perspective on Cellular Structures and Organelles

Alpha-synuclein (α-syn) is localized in cellular organelles of most neurons, but many of its physiological functions are only partially understood. α-syn accumulation is associated with Parkinson’s disease, dementia with Lewy bodies, and multiple system atrophy as well as other synucleinopathies; however, the exact pathomechanisms that underlie these neurodegenerative diseases remain elusive. In this review, we describe what is known about α-syn function and pathophysiological changes in different cellular structures and organelles, including what is known about its behavior as a prion-like protein. We summarize current knowledge of α-syn and its pathological forms, covering its effect on each organelle, including aggregation and toxicity in different model systems, with special interest on the mitochondria due to its relevance during the apoptotic process of dopaminergic neurons. Moreover, we explore the effect that α-syn exerts by interacting with chromatin remodeling proteins that add or remove histone marks, up-regulate its own expression, and resume the impairment that α-syn induces in vesicular traffic by interacting with the endoplasmic reticulum. We then recapitulate the events that lead to Golgi apparatus fragmentation, caused by the presence of α-syn. Finally, we report the recent findings about the accumulation of α-syn, indirectly produced by the endolysosomal system. In conclusion, many important steps into the understanding of α-syn have been made using in vivo and in vitro models; however, the time is right to start integrating observational studies with mechanistic models of α-syn interactions, in order to look at a more complete picture of the pathophysiological processes underlying α-synucleinopathies.
Can Inositol Pyrophosphates Inform Strategies for Developing Low Phytate Crops?

Inositol pyrophosphates (PP-InsPs) are an emerging class of “high-energy” intracellular signaling molecules, containing one or two diphosphate groups attached to an inositol ring, that are connected with phosphate sensing, jasmonate signaling, and inositol hexakisphosphate (InsP6) storage in plants. While information regarding this new class of signaling molecules in plants is scarce, the enzymes responsible for their synthesis have recently been elucidated. This review focuses on InsP6 synthesis and its conversion into PP-InsPs, containing seven and eight phosphate groups (InsP7 and InsP8). These steps involve two types of enzymes: the ITPKs that phosphorylate InsP6 to InsP7, and the PPIP5Ks that phosphorylate InsP7 to InsP8. This review also considers the potential roles of PP-InsPs in plant hormone and inorganic phosphate (Pi) signaling, along with an emerging role in bioenergetic homeostasis. PP-InsP synthesis and signaling are important for plant breeders to consider when developing strategies that reduce InsP6 in plants, as this will likely also reduce PP-InsPs. Thus, this review is primarily intended to bridge the gap between the basic science aspects of PP-InsP synthesis/signaling and breeding/engineering strategies to fortify foods by reducing InsP6.
Assessment of a Serologic Diagnostic Test and Kinetics of Antibody Development in Northern Pike Experimentally Infected with Viral Hemorrhagic Septicemia Virus.

Viral hemorrhagic septicemia virus (VHSV) is an ongoing cause of disease and mortality in freshwater fishes across the Great Lakes region of the Midwestern United States. Antibody detection assays such as enzyme-linked immunosorbent assay (ELISA) are nonlethal serological methods that can have significantly shorter turnaround times than the current validated viral detection diagnostic methodology for VHSV: cell culture with confirmation by polymerase chain reaction (PCR). This study evaluated an ELISA that detects nonneutralizing antinucleocapsid antibodies to VHSV in Northern Pike Esox lucius. Juvenile Northern Pike were experimentally infected with VHSV by intraperitoneal injection. The infected fish were monitored for 12 weeks for signs of disease, and weekly serum samples were obtained. An analysis of the survival data showed that mortality occurred significantly more quickly in inoculated fish than in control fish. Fish that were infected by injection showed a significant increase in antibody response by 2 weeks postinfection. However, variation in the rate and pattern of antibody response among the infected fish was high at any given point. The optimum window for detecting antibodies in Northern Pike is 2-12 weeks postinfection, which generally follows the median time to appearance of clinical signs (21 d postinfection). The receiver-operating characteristic curve analysis showed the ELISA to have a sensitivity of 80.5% and a specificity of 63.2% in Northern Pike, but these values can be adjusted by choosing different percent inhibition cutoffs, which may facilitate the use of the test for specific management goals. The results of this study offer insights into the disease progression and immune kinetics of VHSV, including interindividual variation, which will aid in the management of this economically important virus.
Contribution of diet to gut microbiota and related host cardiometabolic health: diet-gut interaction in human health

ABSTRACT Obesity and cardiometabolic diseases in both developed and developing counties in a state of nutrition transition are often related to diet, which also play a major role in shaping human gut microbiota. The human gut harbors diverse microbes that play an essential role in the well-being of their host. Complex interactions between diet and microorganisms may lead to beneficial or detrimental outcomes to host cardiometabolic health. Despite numerous studies using rodent models indicated that high-fat diet may disrupt protective functions of the intestinal barrier and contribute to inflammatory processes, evidence from population-based study is still limited. In our recent study of a 6-month randomized controlled-feeding trial, we showed that high-fat, low-carbohydrate diet was associated with unfavorable changes in gut microbiota, fecal microbial metabolites, and plasma proinflammatory factors in healthy young adults. Here, we provide an overview and extended discussion of our key findings, and outline important future directions.
Intravenous supplementation type and volume are associated with 1-year outcome and major complications in patients with chronic intestinal failure

Background and aim No marker to categorise the severity of chronic intestinal failure (CIF) has been developed. A 1-year international survey was carried out to investigate whether the European Society for Clinical Nutrition and Metabolism clinical classification of CIF, based on the type and volume of the intravenous supplementation (IVS), could be an indicator of CIF severity. Methods At baseline, participating home parenteral nutrition (HPN) centres enrolled all adults with ongoing CIF due to non-malignant disease; demographic data, body mass index, CIF mechanism, underlying disease, HPN duration and IVS category were recorded for each patient. The type of IVS was classified as fluid and electrolyte alone (FE) or parenteral nutrition admixture (PN). The mean daily IVS volume, calculated on a weekly basis, was categorised as <1, 1–2, 2–3 and >3 L/day. The severity of CIF was determined by patient outcome (still on HPN, weaned from HPN, deceased) and the occurrence of major HPN/CIF-related complications: intestinal failure-associated liver disease (IFALD), catheter-related venous thrombosis and catheter-related bloodstream infection (CRBSI). Results Fifty-one HPN centres included 2194 patients. The analysis showed that both IVS type and volume were independently associated with the odds of weaning from HPN (significantly higher for PN <1 L/day than for FE and all PN >1 L/day), patients’ death (lower for FE, p=0.079), presence of IFALD cholestasis/liver failure and occurrence of CRBSI (significantly higher for PN 2–3 and PN >3 L/day). Conclusions The type and volume of IVS required by patients with CIF could be indicators to categorise the severity of CIF in both clinical practice and research protocols.
Polymorphisms within the ARNT2 and CX3CR1 Genes Are Associated with the Risk of Developing Invasive Aspergillosis

Invasive aspergillosis (IA) is a life-threatening infection that affects an increasing number of patients undergoing chemotherapy or allo-transplantation, and recent studies have shown that genetic factors contribute to disease susceptibility. In this two-stage, population-based, case-control study, we evaluated whether 7 potentially functional single nucleotide polymorphisms (SNPs) within the ARNT2 and CX3CR1 genes influence the risk of IA in high-risk hematological patients. ABSTRACT Invasive aspergillosis (IA) is a life-threatening infection that affects an increasing number of patients undergoing chemotherapy or allo-transplantation, and recent studies have shown that genetic factors contribute to disease susceptibility. In this two-stage, population-based, case-control study, we evaluated whether 7 potentially functional single nucleotide polymorphisms (SNPs) within the ARNT2 and CX3CR1 genes influence the risk of IA in high-risk hematological patients. We genotyped selected SNPs in a cohort of 500 hematological patients (103 of those had been diagnosed with proven or probable IA), and we evaluated their association with the risk of developing IA. The association of the most interesting markers of IA risk was then validated in a replication population, including 474 subjects (94 IA and 380 non-IA patients). Functional experiments were also performed to confirm the biological relevance of the most interesting markers. The meta-analysis of both populations showed that carriers of the ARNT2rs1374213G, CX3CR1rs7631529A, and CX3CR1rs9823718G alleles (where the RefSeq identifier appears as a subscript) had a significantly increased risk of developing IA according to a log-additive model (P value from the meta-analysis [PMeta] = 9.8 · 10−5, PMeta = 1.5 · 10−4, and PMeta =7.9 · 10−5, respectively). Haplotype analysis also confirmed the association of the CX3CR1 haplotype with AGCGG with an increased risk of IA (P = 4.0 · 10−4). Mechanistically, we observed that monocyte-derived macrophages (MDM) from subjects carrying the ARNTR2rs1374213G allele or the GG genotype showed a significantly impaired fungicidal activity but that MDM from carriers of the ARNT2rs1374213G and CX3CR1rs9823718G or CX3CR1rs7631529A alleles had deregulated immune responses to Aspergillus conidia. These results, together with those from expression quantitative trait locus (eQTL) data browsers showing a strong correlation of the CX3CR1rs9823718G allele with lower levels of CX3CR1 mRNA in whole peripheral blood (P = 2.46 · 10−7) and primary monocytes (P = 4.31 · 10−7), highlight the role of the ARNT2 and CX3CR1 loci in modulating and predicting IA risk and provide new insights into the host immune mechanisms involved in IA development.