Miracle-dz/UniFAR-FTUs huggingface dataset:
Purple Sulfur Bacteria Dominate Microbial Community in Brazilian Limestone Cave

The mineralogical composition of caves makes the environment ideal for inhabitation by microbes. However, the bacterial diversity in the cave ecosystem remains largely unexplored. In this paper, we described the bacterial community in an oxic chamber of the Sopradeira cave, an iron-rich limestone cave, in the semiarid region of Northeast Brazil. The microbial population in the cave samples was studied by 16S rDNA next-generation sequencing. A type of purple sulfur bacteria (PSB), Chromatiales, was found to be the most abundant in the sediment (57%), gravel-like (73%), and rock samples (96%). The predominant PSB detected were Ectothiorhodospiraceae, Chromatiaceae, and Woeseiaceae. We identified the PSB in a permanently aphotic zone, with no sulfur detected by energy-dispersive X-ray (EDX) spectroscopy. The absence of light prompted us to investigate for possible nitrogen fixing (nifH) and ammonia oxidizing (amoA) genes in the microbial samples. The nifH gene was found to be present in higher copy numbers than the bacterial-amoA and archaeal-amoA genes, and archaeal-amoA dominated the ammonia-oxidizing community. Although PSB dominated the bacterial community in the samples and may be related to both nitrogen-fixing and ammonia oxidizing bacteria, nitrogen-fixing associated gene was the most detected in those samples, especially in the rock. The present work demonstrates that this cave is an interesting hotspot for the study of ammonia-oxidizing archaea and aphotic PSB.
Fluoroquinolone-Resistant Streptococcus agalactiae Invasive Isolates Recovered in Argentina.

Background: Streptococcus agalactiae or group B Streptococcus (GBS) is an important pathogen in neonates and nonpregnant individuals. Epidemiological studies of GBS resistance to fluoroquinolones (FQs) in Latin America are scarce. This study aimed to determine the local prevalence of FQ resistance in the frame of a national, prospective multicenter study of invasive GBS infections and to investigate mechanisms of resistance, serotype distribution, and clonal relationships among resistant isolates. Methods: From July 2014 to July 2015, 162 invasive GBS isolates were collected from 86 health care centers in 32 Argentinean cities. All isolates were screened for FQ nonsusceptibility using a five-disc scheme: levofloxacin (LVX), ciprofloxacin, norfloxacin (NOR), ofloxacin, and pefloxacin (PF). LVX minimal inhibitory concentration (MIC) was determined by the agar dilution method. Sequencing of internal regions of gyrA and parC genes was performed. Capsular typing and genetic characterization of nonsusceptible isolates were assessed by latex agglutination, pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing. Results: Twenty-four of one hundred sixty-two GBS isolates exhibited no inhibition zones to all tested FQs with an MIC range of 16-32 mg/L for LVX, and one isolate with MIC = 1 mg/L showed no inhibition zones around NOR and PF discs. In all resistant isolates, point mutations were detected in both genes. Serotype Ib was prevalent (88%). One PFGE type accounted for 84% of the FQ-resistant isolates and belonged to serotype Ib, sequence type 10. Conclusions: The prevalence of FQ resistance was 14.8% likely to be associated with dissemination of an ST10/serotype Ib clone. The unexpected high rate of resistance emphasizes the relevance for continuous surveillance of GBS epidemiology and antibiotic susceptibility.
Celiac Immunogenic Potential of α-Gliadin Epitope Variants from Triticum and Aegilops Species

The high global demand of wheat and its subsequent consumption arise from the physicochemical properties of bread dough and its contribution to the protein intake in the human diet. Gluten is the main structural complex of wheat proteins and subjects affected by celiac disease (CD) cannot tolerate gluten protein. Within gluten proteins, α-gliadins constitute the most immunogenic fraction since they contain the main T-cell stimulating epitopes (DQ2.5-glia-α1, DQ2.5-glia-α2, and DQ2.5-glia-α3). In this work, the celiac immunotoxic potential of α-gliadins was studied within Triticeae: diploid, tetraploid, and hexaploid species. The abundance and immunostimulatory capacity of CD canonical epitopes and variants (with one or two mismatches) in all α-gliadin sequences were determined. The results showed that the canonical epitopes DQ2.5-glia-α1 and DQ2.5-glia-α3 were more frequent than DQ2.5-glia-α2. A higher abundance of canonical DQ2.5-glia-α1 epitope was found to be associated with genomes of the BBAADD, AA, and DD types; however, the abundance of DQ2.5-glia-α3 epitope variants was very high in BBAADD and BBAA wheat despite their low abundance in the canonical epitope. The most abundant substitution was that of proline to serine, which was disposed mainly on the three canonical DQ2.5 domains on position 8. Interestingly, our results demonstrated that the natural introduction of Q to H at any position eliminates the toxicity of the three T-cell epitopes in the α-gliadins. The results provided a rational approach for the introduction of natural amino acid substitutions to eliminate the toxicity of three T-cell epitopes, while maintaining the technological properties of commercial wheats.
Can vaccination coverage be improved by reducing missed opportunities for vaccination? Findings from assessments in Chad and Malawi using the new WHO methodology

Background In 2015, the World Health Organization (WHO) updated the global methodology for assessing and reducing missed opportunities for vaccination (MOV), when eligible children have contact with the health system but are not vaccinated. This paper presents the results of two pilot assessments conducted in Chad and Malawi. Methods Using the ten-step global WHO MOV strategy, we purposively selected districts and health facilities, with non-probabilistic sampling of <24 month old children for exit interviews of caregivers and self-administered knowledge, attitudes, and practices (KAP) surveys of health workers. MOV were calculated based on a child’s documented vaccination history (i.e., from a home-based record (HBR) or a health facility vaccination register), including selected vaccines in the national schedule. Results Respondents included caregivers of 353 children in Chad and of 580 children in Malawi. Among those with documented vaccination history, 82% (195/238) were eligible for vaccination in Chad and 47% (225/483) in Malawi. Among eligible children, 51% (99/195) in Chad, and 66% (149/225) in Malawi had one or more MOV on the survey date. During non-vaccination visits, 77% (24/31) of children eligible for vaccination in Chad and 92% (119/129) in Malawi had a MOV compared to 46% (75/164) and 31% (30/96) during vaccination visits, respectively. Among health workers, 92% in Chad and 88% in Malawi were unable to correctly identify valid contraindications for vaccination. Conclusion The new MOV tool was able to characterize the type and potential causes of MOV. In both countries, the findings of the assessments point to two major barriers to full vaccination of eligible children—a lack of coordination between vaccination and curative health services and incomplete vaccination during vaccination visits. National immunization programs should explore tailored efforts to improve health worker practices and to increase vaccine delivery by making better use of existing health service contacts.
Kaempferol Attenuates LPS-Induced Striatum Injury in Mice Involving Anti-Neuroinflammation, Maintaining BBB Integrity, and Down-Regulating the HMGB1/TLR4 Pathway

Neuroinflammation has been demonstrated to be linked with Parkinson’s disease (PD), Alzheimer’s disease, and cerebral ischemia. Our previous investigation had identified that kaempferol (KAE) exerted protective effects on cortex neuron injured by LPS. In this study, the effects and possible mechanism of KAE on striatal dopaminergic neurons induced by LPS in mice were further investigated. The results showed that KAE improved striatal neuron injury, and increased the levels of tyrosine hydroxylase (TH) and postsynaptic density protein 95 (PSD95) in the striatum of mice. In addition, KAE inhibited the production of pro-inflammatory cytokines, including interleukin 1β (IL-1β), interleukin 6 (IL-6), tumor necrosis factor α (TNF-α), reduced the level of monocyte chemotactic protein-1 (MCP-1), intercellular cell adhesion molecule-1 (ICAM-1), and cyclooxygenase-2 (COX-2) in the striatum tissues. Furthermore, KAE protected blood-brain barrier (BBB) integrity and suppressed the activation of the HMGB1/TLR4 inflammatory pathway induced by LPS in striatum tissues of mice. In conclusion, these results suggest that KAE may have neuroprotective effects against striatum injury that is induced by LPS and the possible mechanisms are involved in anti-neuroinflammation, maintaining BBB integrity, and down-regulating the HMGB1/TLR4 pathway.
Site-Resolved Cu2 O Catalysis in the Oxidation of CO.

The identification of the contribution of different surface sites to the catalytic activity of a catalyst nanoparticle is one of the most challenging issues in the fundamental studies of heterogeneous catalysis. We herein demonstrate an effective strategy of using a series of uniform cubic Cu2 O nanocrystals with different sizes to identify the intrinsic activity and contributions of face and edge sites in the catalysis of CO oxidation by a combination of reaction kinetics analysis and DFT calculations. Cu2 O nanocrystals undergo in situ surface oxidation forming CuO thin films during CO oxidation. As the average size of the cubic Cu2 O nanocrystals decreases from 1029 nm to 34 nm, the dominant active sites contributing to the catalytic activity switch from face sites to edge sites. These results reveal the interplay between the intrinsic catalytic activity and the density of individual types of surface sites on a catalyst nanoparticle in determining their contributions to the catalytic activity.
Identification of a novel mutation of FGFR3 gene in a large Chinese pedigree with hypochondroplasia by next-generation sequencing

Rationale: Hypochondroplasia (HCH) is the mildest form of chondrodysplasia characterized by disproportionate short stature, short extremities, and variable lumbar lordosis. It is caused by mutations in fibroblast growth factor receptor 3 (FGFR3) gene. Up to date, at least thirty mutations of FGFR3 gene have been found to be related to HCH. However, mutational screening of the FGFR3 gene is still far from completeness. Identification of more mutations is particularly important in diagnosis of HCH and will gain more insights into the molecular basis for the pathogenesis of HCH. Patient concerns: A large Chinese family consisting of 53 affected individuals with HCH phenotypes was examined. Diagnoses: A novel missense mutation, c.1052C>T, in FGFR3 gene was identified in a large Chinese family with HCH. On the basis of this finding and clinical manifestations, the final diagnosis of HCH was made. Interventions: Next-generation sequencing (NGS) of DNA samples was performed to detect the mutation in the chondrodysplasia-related genes on the proband and her parents, which was confirmed by Sanger sequencing in the proband and most of other living affected family members. Outcomes: A novel missense mutation, c.1052C>T, in the extracellular, ligand-binding domain of FGFR3 was identified in a large Chinese family with HCH. This heterozygous mutation results in substitution of serine for phenylalanine at amino acid 351 (p.S351F) and co-segregates with the phenotype in this family. Molecular docking analysis reveals that this unique FGFR3 mutation results in an enhancement of ligand-binding affinity between FGFR3 and its main ligand, fibroblast growth factor 9. Lessons: This novel mutation is the first mutation displaying an increase in ligand-binding affinity, therefore it may serve as a model to investigate ligand-dependent activity of FGF-FGFR complex. Our data also expanded the mutation spectrum of FGFR3 gene and facilitated clinic diagnosis and genetic counseling for this family with HCH.
Cavum Septum Pellucidum in the General Pediatric Population and Its Relation to Surrounding Brain Structure Volumes, Cognitive Function, and Emotional or Behavioral Problems

BACKGROUND AND PURPOSE: The cavum septum pellucidum, a cavity filled with CSF, is localized between the 2 lateral ventricles of the brain. The cavum is present in all neonates, but it typically closes within 5 months after birth. In some cases, this closure does not occur and a persistent or enlarged cavum septum pellucidum has been linked, in some studies, to psychiatric disorders. However, the clinical relevance in the general population is unknown. In this study, we examined the relationship between the cavum septum pellucidum and volumes of brain structures, cognitive function, and emotional and behavioral problems in children. MATERIALS AND METHODS: This study was embedded in the Generation R Study, a prospective cohort in Rotterdam, the Netherlands. MR imaging studies of 1070 children, 6–10 years of age, were systematically evaluated for the presence and length of a persistent cavum septum pellucidum. An enlarged cavum septum pellucidum was defined as a cavum length of ≥6 mm. Groups without, with persistent, and with enlarged cavum septi pellucidi were compared for brain structure volumes, nonverbal intelligence, and emotional and behavioral problems. RESULTS: The prevalence of cavum septi pellucidi in our sample was 4.6%. Children with an enlarged cavum septum pellucidum had a larger corpus callosum, greater thalamic and total white matter–to–total brain volume ratio, and smaller lateral ventricle volumes. We did not find a relationship between cavum septi pellucidi and cognitive function or emotional and behavioral problems. CONCLUSIONS: The cavum septum pellucidum is a normal structural brain variation without clinical implications in this population-based sample of school-aged children.
Harnessed viruses in the age of metagenomics and synthetic biology: an update on infectious clone assembly and biotechnologies of plant viruses

Summary Recent metagenomic studies have provided an unprecedented wealth of data, which are revolutionizing our understanding of virus diversity. A redrawn landscape highlights viruses as active players in the phytobiome, and surveys have uncovered their positive roles in environmental stress tolerance of plants. Viral infectious clones are key tools for functional characterization of known and newly identified viruses. Knowledge of viruses and their components has been instrumental for the development of modern plant molecular biology and biotechnology. In this review, we provide extensive guidelines built on current synthetic biology advances that streamline infectious clone assembly, thus lessening a major technical constraint of plant virology. The focus is on generation of infectious clones in binary T‐DNA vectors, which are delivered efficiently to plants by Agrobacterium. We then summarize recent applications of plant viruses and explore emerging trends in microbiology, bacterial and human virology that, once translated to plant virology, could lead to the development of virus‐based gene therapies for ad hoc engineering of plant traits. The systematic characterization of plant virus roles in the phytobiome and next‐generation virus‐based tools will be indispensable landmarks in the synthetic biology roadmap to better crops.
The effects of age and cognitive load on peripheral-detection performance

Age-related declines in both peripheral vision and cognitive resources could contribute to the increased crash risk of older drivers. However, it is unclear whether increases in age and cognitive load result in equal detriments to detection rates across all peripheral target eccentricities (general interference effect) or whether these detriments become greater with increasing eccentricity (tunnel effect). In the current study we investigated the effects of age and cognitive load on the detection of peripheral motorcycle targets (at 5°–30° eccentricity) in static images of intersections. We used a dual-task paradigm in which cognitive load was manipulated without changing the complexity of the central (foveal) visual stimulus. Each image was displayed briefly (250 ms) to prevent eye movements. When no cognitive load was present, age resulted in a tunnel effect; however, when cognitive load was high, age resulted in a general interference effect. These findings suggest that tunnel and general interference effects can co-occur and that the predominant effect varies with the level of demand placed on participants' resources. High cognitive load had a general interference effect in both age groups, but the effect attenuated at large target eccentricities (opposite of a tunnel effect). Low cognitive load had a general interference effect in the older but not the younger group, impairing detection of motorcycle targets even at 5° eccentricity, which could present an imminent collision risk in real driving.
FON4 prevents the multi‐floret spikelet in rice

The spikelet is the specific unit of the grass inflorescence, and produces a variable number of florets (1-40) depending on whether the species displays determinate or indeterminate growth. Spikelet morphogenesis therefore plays an important role in crop yield; for example, in wheat (Triticum aestivum) inflorescences with the indeterminate spikelet, the spikelet meristem is continuously active and produces a plethora of lateral floral meristems, leading to the formation of variable numbers of florets. In inflorescences of rice (Oryza sativa) and maize (Zea mays) with the determinate spikelet, the spikelet meristem produces the fixed numbers of lateral floral meristems, after which its fate is terminated as a terminal floral meristem, resulting in the formation of one or two florets. This article is protected by copyright. All rights reserved.
Growth Hormone (GH) Therapy During the Transition Period: Should We Think about Early Retesting in Patients with Idiopathic and Isolated GH Deficiency?

To investigate growth hormone (GH) secretion at the transition age, retesting of all subjects who have undergone GH replacement therapy is recommended when linear growth and pubertal development are complete to distinguish between transitional and persistent GH deficiency (GHD). Early retesting of children with idiopathic and isolated GHD (i.e., before the achievement of final height and/or the adult pubertal stage) can avoid possible over-treatment. Here, we report data from our population with idiopathic and isolated GHD to encourage changes in the management and timing of retesting. We recruited 31 patients (19 males) with idiopathic GHD who received recombinant GH (rGH) for at least 2 years. All of the patients were retested at the transition age at least 3 months after rGH discontinuation. Permanent GHD was defined as a GH peak of <19 ng/mL after administration of growth hormone–releasing hormone (GHRH) + arginine as a provocative test. Permanent GHD was confirmed in only five of 31 patients (16.13%). None of these patients presented low serum insulin-like growth factor (IGF)-1 levels (<−2 standard deviation score (SDS)). Only one male patient with an IGF-1 serum level lower than −2 SDS showed a normal GH stimulation response, with a GH peak of 44.99 ng/mL. Few patients with idiopathic and isolated GHD demonstrated persistence of the deficit when retested at the transition age, suggesting that the timing of retesting should be anticipated to avoid overtreatment.
Real-time measurement of pedestrian flow using processing of ITV images

On developpe la mesure automatique en temps reel de l'ecoulement des pietons basee sur l'information de brillance des images en vue de controler l'ecoulement des pietons sur des routes ou dans des constructions urbaines, en extrayant relativement peu de points d'echantillonnage a partir d'une image ITV mobile
Evaluation of Nutrition Risk Screening Score 2002 (NRS) assessment in hospitalized chronic kidney disease patient

Background Although chronic kidney disease (CKD) patients are particularly prone to malnutrition, systematic nutritional screening is rarely routinely performed during hospitalization. The primary aim of this study was to determine the prevalence of malnutrition (as captured by the nutritional screening score NRS) in hospitalized CKD patients and explore the impact of malnutrition on hospital mortality. Methods All patients admitted to the tertiary nephrology department of the University hospital of Bern Inselspital over a period of 12 months were included in this observational study. The risk for malnutrition was assessed within 24h of admission by the NRS. Demographic, clinical, and outcome data were extracted from the patient database. The primary outcome was in-hospital mortality. The secondary outcomes were length of hospitalization and hospitalization costs. Multilevel mixed-effect logistic regression model analysis was performed to determine the association of in-hospital mortality and risk of malnutrition (NRS score≥3). Results We included 696 eligible hospitalizations of 489 CKD patients. Hospitalized patients had a median age of 64 years (interquartile range (IQR), 52–72), 35.6% were at risk of malnutrition (NRS≥3). After adjustment for the identified confounders (Case weight, Barthel index, and CKD stage) multivariate analysis confirmed an independent and significant association between higher in-hospital mortality with NRS≥3 [OR 2.92 (95% CI: 1.33–6.39), P<0.001]. Furthermore, in multivariate analysis the risk of malnutrition was associated with longer length of hospitalization [Geometric mean ratio: 1.8 (95% CI: 1.5–2.0), p<0.001] and with increased hospitalization costs [Geometric mean ratio: 1.7 (95% CI: 1.5–1.9), p<0.001]). Conclusions Malnutrition in CKD patients, as captured by NRS>3, is highly prevalent among hospitalized CKD patient and associated with prolonged hospital stay and increased in-hospital mortality.
Soil Zinc Is Associated with Serum Zinc But Not with Linear Growth of Children in Ethiopia

To our knowledge, the relationships among soil zinc, serum zinc and children’s linear growth have not been studied geographically or at a national level in any country. We use data from the cross-sectional, nationally representative Ethiopian National Micronutrient Survey (ENMS) (n = 1776), which provided anthropometric and serum zinc (n = 1171) data on children aged 6–59 months. Soil zinc levels were extracted for each child from the digital soil map of Ethiopia, developed by the Africa Soil Information Service. Children’s linear growth was computed using length/height and age converted into Z-scores for height-for-age. Multi-level mixed linear regression models were used for the analysis. Nationally, 28% of children aged 6–59 months were zinc deficient (24% when adjusted for inflammation) and 38% were stunted. Twenty percent of households in the ENMS were located on zinc-deficient soils. Soil zinc (in mg/kg) was positively associated with serum zinc (in µg/dL) (b = 0.9, p = 0.020) and weight-for-height-Z-score (b = 0.05, p = 0.045) but linear growth was not associated with soil zinc (p = 0.604) or serum zinc (p = 0.506) among Ethiopian preschool children. Intervention studies are needed to determine whether there are causal links between soil and human zinc status.