Miracle-dz/UniFAR-FTUs huggingface dataset:
High risk of microscopic colitis after Campylobacter concisus infection: population-based cohort study

Objective Microscopic colitis (MC) encompasses the two histopathological distinct entities of collagenous colitis (CC) and lymphocytic colitis (LC). In this Danish population-based cohort study, we examined the risk of MC following stool culture with Campylobacter concisus, C. jejuni, non-typhoidal Salmonella or a culture-negative stool test. Design We identified patients with a first-time positive stool culture with C. concisus, C. jejuni, non-typhoidal Salmonella or negative stool test, from 2009 through 2013 in North Denmark Region, Denmark, and matched each with 10 population comparisons. All subjects were followed up until 1 March 2018 using Systematised Nomenclature of Medicine codes from The Danish Pathology Register for incident diagnoses of CC and LC. We computed risk and adjusted HRs with 95% CIs for MC among patients and comparisons. Results We identified 962 patients with C. concisus, 1725 with C. jejuni, 446 with Salmonella and 11 825 patients with culture-negative stools. The MC risk and HR versus comparisons were high for patients with C. concisus (risk 6.2%, HR 32.4 (95% CI 18.9 to 55.6)), less for C. jejuni (risk 0.6%, HR 3.7 (95% CI 1.8 to 7.7)), low for Salmonella (risk 0.4%, HR 2.2 (95% CI 0.5 to 10.8)) and for patients with negative stool testing (risk 3.3%, HR 19.6 (95% CI 16.4 to 23.4)). After exclusion of the first year of follow-up, the HRs were 9.3 (95% CI 4.1 to 20.1), 2.2 (95% CI 0.9 to 5.4), 1.3 (95% CI 0.2 to 11.1) and 5.6 (95% CI 4.6 to 7.2), respectively. Conclusion A high risk of MC was observed following C. concisus in stools. Further studies are needed to elucidate any underlying biological mechanisms.
Influence of Plant Species on Microbial Activity and Denitrifier Population Development in Vegetated Denitrifying Wood-Chip Bioreactors

The microbial characteristics of four vegetated and one unplanted wood-chip bioreactors treating greenhouse effluent were investigated in a continuous experiment operated for over 2.5 years. The bioreactors were designed to reduce nitrate concentrations via naturally induced microbial denitrification. The vegetation type and reactor depth were both found to be significant factors in defining the mixed microbial activity. However, a consistent correlation between the abundance of the denitrifying communities and reactor depth could not be found across all reactors. The media samples from the unit planted with Typha angustifolia displayed higher microbial activities compared with the other reactors. This plant’s root-associated bacteria also demonstrated the greatest copies of the denitrifying genes nirK and nosZ. The most abundant denitrifier communities and those encoding the nosZ gene were found in the unplanted reactor, followed by the T. angustifolia unit. The T. angustifolia reactor demonstrated greater microbial activity and denitrification capacity at the depth of 20 cm, while the greatest denitrification capacity in the unplanted reactor was found at the depth of 60 cm. These findings indicated the importance of the T. angustifolia rhizosphere to support microbial community establishment and growth in the vicinity of the plant’s roots, although those populations may eventually develop in an unplanted environment.
The Arabidopsis Plastidial Glucose-6-Phosphate Transporter GPT1 is Dually Targeted to Peroxisomes via the Endoplasmic Reticulum[OPEN]

The metabolite transporter GPT1 is important for NADPH provision in both plastid and peroxisomes, mostly during pollen tube growth towards ovules, and is thus essential for fertilization in Arabidopsis. Studies on Glucose-6-phosphate (G6P)/phosphate translocator isoforms GPT1 and GPT2 reported the viability of Arabidopsis (Arabidopsis thaliana) gpt2 mutants, whereas heterozygous gpt1 mutants exhibited a variety of defects during fertilization/seed set, indicating that GPT1 is essential for this process. Among other functions, GPT1 was shown to be important for pollen and embryo-sac development. Because our previous work on the irreversible part of the oxidative pentose phosphate pathway (OPPP) revealed comparable effects, we investigated whether GPT1 may dually localize to plastids and peroxisomes. In reporter fusions, GPT2 localized to plastids, but GPT1 also localized to the endoplasmic reticulum (ER) and around peroxisomes. GPT1 contacted two oxidoreductases and also peroxins that mediate import of peroxisomal membrane proteins from the ER, hinting at dual localization. Reconstitution in yeast (Saccharomyces cerevisiae) proteoliposomes revealed that GPT1 preferentially exchanges G6P for ribulose-5-phosphate (Ru5P). Complementation analyses of heterozygous +/gpt1 plants demonstrated that GPT2 is unable to compensate for GPT1 in plastids, whereas GPT1 without the transit peptide (enforcing ER/peroxisomal localization) increased gpt1 transmission significantly. Because OPPP activity in peroxisomes is essential for fertilization, and immunoblot analyses hinted at the presence of unprocessed GPT1-specific bands, our findings suggest that GPT1 is indispensable in both plastids and peroxisomes. Together with its G6P-Ru5P exchange preference, GPT1 appears to play a role distinct from that of GPT2 due to dual targeting.
Biting Behavior and Molecular Identification of Aedes aegypti (Diptera: Culicidae) Subspecies in Some Selected Recent Yellow Fever Outbreak Communities in Northern Ghana

Abstract Aedes aegypti (L.) (Diptera: Culicidae) is a diurnal feeder that lives in close association with human populations. It is the principal vector of yellow fever, dengue fever and the Zika Virus. Issues of arboviral diseases have been on the ascendency in most countries including Ghana where Aedes mosquito is the main vector of yellow fever. A comparative study of the biting behavior of Ae. aegypti and the identification of subspecies were undertaken using molecular technique. Standard human landing technique was used to collect both indoor and outdoor biting mosquitoes at three zones located in the Upper East (Bolgatanga), Upper West (Nadowli), and Northern (Damongo) Regions of Ghana during the dry and rainy seasons between 0600 and 1800 Greenwich Mean Time (GMT). All collected mosquitoes were identified morphologically using taxonomic keys. random amplified polymorphic DNA polymerase chain reaction was used to categorize Ae. aegypti into subspecies. Adult female Aedes mosquitoes identified formed 62% (n = 1,206) of all female mosquitoes collected. Aedes aegypti 98% and Aedes vittatus 2% were the only Aedes species identified. Bolgatanga recorded the largest number of Ae. aegypti 42%, whereas Nadowli 22% recorded the least. Aedes vittatus was observed in Nadowli. Aedes aegypti exhibited a bimodal biting behavior peaking at 0600–0800 GMT and 1500–1600 h GMT. Molecular findings revealed 69% Ae. aegypti aegypti and 31% Ae. aegypti formosus as the two subspecies (n = 110). This information is important for implementing effective vector control programs in the three regions of the northern Ghana.
Bacterial infections in the early period after liver transplantation in adults: A prospective single‐center cohort study

Liver transplantation (LT) is a potentially curative treatment for terminal stage hepatic diseases. Bacterial infections are the main causes of mortality and morbidity in the early period after LT. Identifying the risk factors could help in minimizing their development. We prospectively investigated the incidence, characteristics, and risk factors of bacterial infections among the recipients during hospitalization after LT and assigned a predictive score. All 389 consecutive adults who underwent LT at the main referral hospital of LT in Iran during 1 year were enrolled prospectively in a cohort study. Infection group consisted of 143 recipients (36.8%). Urinary tract and surgical site infections were the most frequent ones. Gram‐negative bacteria were more prevalent than Gram‐positive ones. Independent risk factors were female sex (relative risks = 2.13), age ≤ 43.5 years (3.70), hospital stay ≥ 9.5 days (5.22), abdominal reoperation (3.03), vancomycin‐resistant Enterococci colonization (5.52), hospitalization 3 months prior to LT (3.25), mechanical ventilation ≥48 hr (4.93), and renal replacement therapies (13.40). We developed a risk score for the prediction of bacterial infections with an area under the receiver operating characteristic curve of 0.85 (95% CI, 0.81–0.89) with sensitivity of 88% and specificity of 64%. In the infection group, mortality was higher than in controls (18.9% vs. 2.0%) with longer hospitalization (16 vs. 10 days; P < 0.001). We detected a high rate of bacterial infections leading to longer hospital stay and higher mortality rate. The formulated risk score can help predict bacterial infections; however, it requires clinical validation in further studies.
The Kaposi’s Sarcoma-Associated Herpesvirus (KSHV) gH/gL Complex Is the Predominant Neutralizing Antigenic Determinant in KSHV-Infected Individuals

Kaposi’s sarcoma-associated herpesvirus (KSHV) is the etiological agent of Kaposi’s sarcoma (KS), one of the most prevalent cancers of people living with HIV/AIDS in sub-Saharan Africa. The seroprevalence for KSHV is high in the region, and no prophylactic vaccine against the virus is available. In this study, we characterized the antigenic targets of KSHV-specific neutralizing antibodies (nAbs) in asymptomatic KSHV-infected individuals and KS patients with high nAbs titers. We quantified the extent to which various KSHV envelope glycoproteins (gB, ORF28, ORF68, gH, gL, gM, gN and gpK8.1) adsorbed/removed KSHV-specific nAbs from the plasma of infected individuals. Our study revealed that plasma from a majority of KSHV neutralizers recognizes multiple viral glycoproteins. Moreover, the breadth of nAbs responses against these viral glycoproteins varies among endemic KS, epidemic KS and asymptomatic KSHV-infected individuals. Importantly, among the KSHV glycoproteins, the gH/gL complex, but neither gH nor gL alone, showed the highest adsorption of KSHV-specific nAbs. This activity was detected in 80% of the KSHV-infected individuals regardless of their KS status. The findings suggest that the gH/gL complex is the predominant antigenic determinant of KSHV-specific nAbs. Therefore, gH/gL is a potential target for development of KSHV prophylactic vaccines.
64Cu-DOTATATE PET/CT and Prediction of Overall and Progression-Free Survival in Patients with Neuroendocrine Neoplasms

Overexpression of somatostatin receptors (SSTRs) in patients with neuroendocrine neoplasms (NENs) is used for both diagnosis and treatment. Receptor density may reflect tumor differentiation and thus be associated with prognosis. Noninvasive visualization and quantification of SSTR density is possible by SSTR imaging (SRI) using PET. Recently, we introduced 64Cu-DOTATATE for SRI, and we hypothesized that uptake of this tracer could be associated with overall survival (OS) and progression-free survival (PFS). Methods: We evaluated patients with NENs who underwent 64Cu-DOTATATE PET/CT SRI in 2 prospective studies. Tracer uptake was determined as the maximal SUV (SUVmax) for each patient. Kaplan–Meier analysis with log-rank was used to determine the predictive value of 64Cu-DOTATATE SUVmax for OS and PFS. Specificity, sensitivity, and accuracy were calculated for prediction of outcome at 24 mo after 64Cu-DOTATATE PET/CT. Results: In total, 128 patients with NENs were included and followed for a median of 73 mo (range, 1–112 mo). During follow-up, 112 experienced disease progression, and 69 died. The optimal cutoff for 64Cu-DOTATATE SUVmax was 43.3 for prediction of PFS, with a hazard ratio of 0.56 (95% confidence interval, 0.38–0.84) for patients with an SUVmax of more than 43.3. However, no significant cutoff was found for prediction of OS. In multiple Cox regression adjusted for age, sex, primary tumor site, and tumor grade, the SUVmax cutoff hazard ratio was 0.50 (range, 0.32–0.77) for PFS. The accuracy was moderate for predicting PFS (57%) at 24 mo after 64Cu-DOTATATE PET/CT. Conclusion: In this first study to report the association of 64Cu-DOTATATE PET/CT and outcome in patients with NENs, tumor SSTR density as visualized with 64Cu-DOTATATE PET/CT was prognostic for PFS but not OS. However, the accuracy of prediction of PFS at 24 mo after 64Cu-DOTATATE PET/CT SRI was moderate, limiting the value on an individual-patient basis.
Niche-processes induced differences in plant growth, carbon balance, stress resistance, and regeneration affect community assembly over succession

The relationship between plant traits and species relative abundance along environmental gradients can provide important insights on the determinants of community structure. Here we bring extensive data on six key traits (specific leaf area (SLA), seed mass, seed germination rate, height, leaf proline content and photosynthesis rate) to test trait-abundance relationships in a successional chronosequence of subalpine meadow plant communities. Our results show that in late-successional meadows, abundant species had higher values for seed mass, seed germination rate, and SLA, but had lower values for height, photosynthesis rate, and leaf proline content than rarer species. The opposite patterns of trait-abundance relationships were observed for early-successional meadows. Observations of strong trait convergence and divergence in these successional communities lend greater support for niche processes compared to neutral community assembly. We conclude that species’ niches that determine plant growth (plant height and photosynthesis rate), carbon balance (SLA, photosynthesis rate), regeneration (seed mass and seed germination rate), and abiotic stress resistance (leaf proline content) under different environmental conditions have strong influence on species relative abundance in these sub-alpine meadow communities during succession.
SHH Signaling Pathway Drives Pediatric Bone Sarcoma Progression

Primary bone tumors can be divided into two classes, benign and malignant. Among the latter group, osteosarcoma and Ewing sarcoma are the most prevalent malignant primary bone tumors in children and adolescents. Despite intensive efforts to improve treatments, almost 40% of patients succumb to the disease. Specifically, the clinical outcome for metastatic osteosarcoma or Ewing sarcoma remains poor; less than 30% of patients who present metastases will survive 5 years after initial diagnosis. One common and specific point of these bone tumors is their ability to deregulate bone homeostasis and remodeling and divert them to their benefit. Over the past years, considerable interest in the Sonic Hedgehog (SHH) pathway has taken place within the cancer research community. The activation of this SHH cascade can be done through different ways and, schematically, two pathways can be described, the canonical and the non-canonical. This review discusses the current knowledge about the involvement of the SHH signaling pathway in skeletal development, pediatric bone sarcoma progression and the related therapeutic options that may be possible for these tumors.
Planetary Milling and Self-Propagating High-Temperature Synthesis of Al-TiB2 Composites

The paper explores the influence of planetary milling on the temperature and velocity of Al-Ti-B powder mixture combustion and also on the structure and phase composition of the reaction products. It is found that the time increase of planetary milling modifies the structure of the powder particles, improves the density of compacted specimens, and increases the temperature and velocity of their combustion. These time dependences are extreme, with maximum values during 180 s planetary milling. Experiments show that the reaction products consist of an aluminum matrix with uniformly distributed particles of titanium diboride of not over 1 µm in size. The average particle size changes with the increase in the time of the planetary milling of the initial powder mixture.
Conformational Switching in Bcl-xL: Enabling Non-Canonic Inhibition of Apoptosis Involves Multiple Intermediates and Lipid Interactions

The inhibition of mitochondrial permeabilization by the anti-apoptotic protein Bcl-xL is crucial for cell survival and homeostasis. Its inhibitory role requires the partitioning of Bcl-xL to the mitochondrial outer membrane from an inactive state in the cytosol, leading to its extensive refolding. The molecular mechanisms behind these events and the resulting conformations in the bilayer are unclear, and different models have been proposed to explain them. In the most recently proposed non-canonical model, the active form of Bcl-xL employs its N-terminal BH4 helix to bind and block its pro-apoptotic target. Here, we used a combination of various spectroscopic techniques to study the release of the BH4 helix (α1) during the membrane insertion of Bcl-xL. This refolding was characterized by a gradual increase in helicity due to the lipid-dependent partitioning-coupled folding and formation of new helix αX (presumably in the originally disordered loop between helices α1 and α2). Notably, a comparison of various fluorescence and circular dichroism measurements suggested the presence of multiple Bcl-xL conformations in the bilayer. This conclusion was explicitly confirmed by single-molecule measurements of Förster Resonance Energy Transfer from Alexa-Fluor-488-labeled Bcl-xL D189C to a mCherry fluorescent protein attached at the N-terminus. These measurements clearly indicated that the refolding of Bcl-xL in the bilayer is not a two-state transition and involves multiple membranous intermediates of variable compactness.
Replication Protein A (RPA) Mediates Radio-Resistance of Glioblastoma Cancer Stem-Like Cells

Glioblastoma (GBM) is among the deadliest of solid tumors with median survival rates of approximately 12–15 months despite maximal therapeutic intervention. A rare population of self-renewing cells referred to as GBM cancer stem-like cells (GSCs) are believed to be the source of inevitable recurrence in GBM. GSCs exhibit preferential activation of the DNA damage response pathway (DDR) and evade ionizing radiation (IR) therapy by superior execution of DNA repair compared to their differentiated counterparts, differentiated GBM cells (DGCs). Replication Protein A (RPA) plays a central role in most of the DNA metabolic processes essential for genomic stability, including DNA repair. Here, we show that RPA is preferentially expressed by GSCs and high RPA expression informs poor glioma patient survival. RPA loss either by shRNA-mediated silencing or chemical inhibition impairs GSCs’ survival and self-renewal and most importantly, sensitizes these cells to IR. This newly uncovered role of RPA in GSCs supports its potential clinical significance as a druggable biomarker in GBM.
Oxidative Stress and Atopic Dermatitis

Atopic dermatitis is a common chronic/chronically relapsing inflammatory skin disease, with increasing worldwide prevalence. Etiopathogenesis is complex and multifactorial, with a mix of genetic, immunological and environmental aspects. Like in other chronic inflammatory diseases, oxidative stress plays an important pathogenetic role. We reviewed in vivo research studies on humans about oxidative stress and atopic dermatitis. Although sometimes contrasting, overall, they suggest that oxidative stress may have a significant role in atopic dermatitis, but our understanding is still incomplete, at least concerning in vivo data, because of limitations of available literature. Research consists of 33 papers published in 28 years, was not always performed on large study populations, represents a limited number of countries and ethnicities—not always in proportion to their size—and is scattered over multiple papers that, in the majority of cases, cannot be pooled and/or compared because many biomarkers were studied, in different tissues and with different methods. Further, larger studies appear warranted and necessary to shed more light on this aspect of atopic dermatitis, which is important not only to improve our understanding of this disease, but also for potential clinical and therapeutic implications.
The Effect of Different Doses of Zearalenone in Feed on the Bioavailability of Zearalenone and Alpha-Zearalenol, and the Concentrations of Estradiol and Testosterone in the Peripheral Blood of Pre-Pubertal Gilts

The objective of this study was to determine the effect of long-term (48 days), per os administration of specific zearalenone (ZEN) doses (20 and 40 μg ZEN/kg BW in experimental groups EI and EII, which were equivalent to 200% and 400% of the upper range limit of the no-observed-adverse-effect-level (NOAEL), respectively) on the bioavailability of ZEN and the rate of changes in estradiol and testosterone concentrations in the peripheral blood of pre-pubertal gilts. ZEN and α-ZEL levels were similar until day 28. After day 28, α-ZEL concentrations increased significantly in group EI, whereas a significant rise in ZEN levels was noted in group EII. The presence of estradiol in peripheral blood plasma was not observed until day 20 of the experiment. Spontaneous secretion of estradiol was minimal, and it was determined at very low levels of up to 10 pg/mL in EI and EII groups. Testosterone concentrations ranged from 4 to 9 ng/mL in all groups. A decrease in the concentrations of both analyzed hormones was reported in the last stage of the experiment. The results of the experiment indicate that: (i) The bioavailability of ZEN in peripheral blood has low diagnostic value, (ii) exposure to low doses of ZEN induces minor changes in the concentrations of the analyzed hormones, which could lead to situational supraphysiological hormone levels and changes in endogenous hormonal balance.
Psychometric properties of an Arabic translation of the modified fatigue impact scale in patients with multiple sclerosis

Abstract Purpose To translate and validate the modified fatigue impact scale into Arabic (MFIS-A) in patients with multiple sclerosis (MS). Methods A total of 116 patients with relapsing remitting MS and 59 healthy participants were recruited. Fifty patients filled the MFIS-A twice with one week difference. Reliability was assessed by measuring Cronbach’s α and intraclass correlation coefficient (ICC). The MFIS-A was correlated with the fatigue severity scale (FSS), the vitality domain of the Short Form 36 (SF-36V), the fatigue visual analogue scale (VAS-F), and the Beck Depression Inventory II (BDI-II) to assess validity. Dimensionality of the MFIS-A was investigated. A receiver operating characteristic (ROC) curve analysis was done and specificity and sensitivity were calculated. Results Factor analysis (based on 116 patients) revealed that the MFIS-A consists of two subscales: the physical/social and the cognitive subscales. The MFIS-A showed excellent test–retest reliability (ICC = 0.920) and internal consistency (Cronbach’s α = 0.968). The minimal detectable change with 95% confidence interval was 14.68 (32.0%). The MFIS-A showed strong positive correlation with FSS and BDI-II, moderate positive correlation with VAS-F, negative moderate correlation with SF-36V, and weak correlation with EDSS. The MFIS-A differentiated healthy participants from patients with 79.3% sensitivity and 89.8% specificity. Conclusions The MFIS-A showed good validity and reliability indicating its usefulness as an assessment measure for patients with MS. IMPLICATIONS FOR REHABILITATION MFIS-A is a valid and reliable tool for fatigue evaluation for patients with relapsing remitting MS. The optimal cutoff scores of the total MFIS-A, the physical/social, and cognitive subscales which indicate fatigue are 35.5, 18.5, and 15.5, respectively. Changes of 14.68 or more points may indicate a clinically important change (a true change) in fatigue in patients with MS.