Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea

To improve and complete our knowledge of archaeal tRNA modification patterns, we have identified and compared the modification pattern (type and location) in tRNAs of three very different archaeal species, Methanococcus maripaludis (a mesophilic methanogen), Pyrococcus furiosus (a hyperthermophile thermococcale), and Sulfolobus acidocaldarius (an acidophilic thermophilic sulfolobale). Most abundant isoacceptor tRNAs (79 in total) for each of the 20 amino acids were isolated by two-dimensional gel electrophoresis followed by in-gel RNase digestions. The resulting oligonucleotide fragments were separated by nanoLC and their nucleotide content analyzed by mass spectrometry (MS/MS). Analysis of total modified nucleosides obtained from complete digestion of bulk tRNAs was also performed. Distinct base- and/or ribose-methylations, cytidine acetylations, and thiolated pyrimidines were identified, some at new positions in tRNAs. Novel, some tentatively identified, modifications were also found. The least diversified modification landscape is observed in the mesophilic Methanococcus maripaludis and the most complex one in Sulfolobus acidocaldarius. Notable observations are the frequent occurrence of ac4C nucleotides in thermophilic archaeal tRNAs, the presence of m7G at positions 1 and 10 in Pyrococcus furiosus tRNAs, and the use of wyosine derivatives at position 37 of tRNAs, especially those decoding U1- and C1-starting codons. These results complete those already obtained by others with sets of archaeal tRNAs from Methanocaldococcus jannaschii and Haloferax volcanii.
Association between Bone Density Values, Primary Stability and Histomorphometric Analysis of Dental Implant Osteotomy Sites on the Upper Jaw.

INTRODUCTION Sufficient bone volume, as well as the bone quality characteristics are necessary prerequisites to ensure optimal mechanical stability of the implants and subsequent osseointegration. AIM The aim of the present study was to assess the correlation between bone density values obtained by cone-beam computed tomography (CBCT), the primary stability of dental implants and the histomorphometric analysis of bone quality. MATERIALS AND METHODS Following tooth extraction, socket preservation with frieze-dried bone allograft or protein-rich fibrin (PRF) was performed on 30 patients with 30 maxillary teeth in the region from second premolar to second premolar. Four months after the procedure, CBCT was used to assess the bone density (Hounsfield units) in the area of extraction. Thirty bone samples were harvested from implant sites using a trephine drill. They were analyzed with Image J software. Immediately after placing the implant, the implant stability quotient was measured using the Osstell Idx device. RESULTS The results revealed significant correlations between bone density and primary stability along the vestibulo-oral (r=0.392, p=0.032) and mesiodistal axes (r=0.407, p=0.026). Bone density also correlated strongly with the percentage of newly formed bone (r=0.776, p<0.001). CONCLUSION Bone quality, in terms of bone density measured in CBCT and new bone formation are correlated to the primary stability of the dental implants and vice versa.
Gastrodin alleviates bone damage by modulating protein expression and tissue redox state

Fluorosis is a common disease characterized by disruptions in bone metabolism and enamel development. The production of reactive oxygen species is thought to play an important role in fluorosis. Gastrodin (4‐hydroxybenzylalcohol4‐O‐beta‐D‐glucopyranoside) has been reported to have antioxidative activity, and so here we examined whether gastrodin has protective effects against oxidative stress and bone tissue toxicity in rats with fluorosis. Wistar rats were given different doses of gastrodin 1 month after fluoride administration, and samples of blood, bone and teeth were collected after 2, 3 and 4 months; glutathione peroxidase glu, CAT and SOD levels in the fluorosis group were lower than those in the control group. Gastrodin treatment in rats ameliorated oxidative stress and fluoride accumulation that were induced by fluoride; treatment with 400 mg·kg−1 gastrodin protected trabecular bone structure and reduced femur and alveolar bone injury in rats with fluorosis. Enhanced expression of cysteinyl aspartate‐specific proteinase (caspase) 3, caspase‐9 and Bax and decreased expression of Bcl‐2 induced by fluoride were also reversed by gastrodin. In summary, the present data suggest that gastrodin, and in particular a dose of 400 mg·kg−1, can improve the antioxidative capacity of rats, reduce concentration of fluoride in tissues, alleviate bone damage and modulate expression of Bcl‐2, Bax, caspase‐3 and caspase‐9.
Brassy Flecking in the Salamander Plethodon c. cinereus, and the Validity of Plethodon huldae

IT is well known that some individuals of Plethodon c. cinereus Green have a well defined reddish dorsal stripe and dark sides and that others are uniformly dark dorsally and laterally. Also, some are variously intermediate between the striped and dark phases, and some are erythristic. References to these color variations are found in many accounts of the species, a good general description occurring in Bishop (1941). The present paper discusses a feature of the coloration of P. c. cinereus that apparently has never been recorded in the literature, but which has, nevertheless, figured to some extent in the taxonomy of other species of Plethodon. While collecting P. c. cinereus in the Genesee River gorge at Rochester, New York, in the autumn of 1953, I was struck by the fact that the dark ones were conspicuously peppered with tiny light flecks. Microscopic examination in the laboratory revealed that this flecking was due to numerous individual iridophores distributed more or less evenly over the whole dorsum, upper sides, and upper surfaces of the legs. These small chromatophores, which show an iridescent golden or brassy color, are located just external to the melanophores which produce the ground color of the above mentioned areas. The iridophores usually are quite small (0.02-0.05 mm. in diameter) and relatively widely separated; occasionally those on the tail, and less often those on the head or lower back, are larger (0.1 mm.) and so close as to touch one another, giving the appearance of a reticulum. In an extreme instance of the latter
Farmers' information acceptance behavior in China.

This study attempts to provide insights into farmers’ information acceptance behavior in China. The paper proposes an integrated model based on the technology acceptance model (TAM). Correlation and regression analyses are used to investigate the determinants. The results show that income, attitude, risk preference, perceived usefulness, searching motivation and experience affect farmers’ agricultural information acceptance directly. Key words: Acceptance, technology acceptance model, perceived usefulness, perceived ease of use, perceived risk.
Plasma Glial Fibrillary Acidic Protein Levels Differ Along the Spectra of Amyloid Burden and Clinical Disease Stage.

BACKGROUND Measuring plasma glial fibrillary acidic protein (GFAP) alongside cortical amyloid-β (Aβ) may shed light on astrocytic changes in aging and Alzheimer's disease (AD). OBJECTIVE To examine associations between plasma GFAP and cortical Aβ deposition in older adults across the typical aging-to-AD dementia spectrum. METHODS We studied two independent samples from UCSF (Cohort 1, N = 50; Cohort 2, N = 37) covering the spectra of clinical severity (CDR Sum of Boxes; CDR-SB) and Aβ-PET burden. Aβ-PET was completed with either florbetapir or Pittsburgh Compound B and standardized uptake value ratios were converted to the Centiloid (CL) scale for analyses. All participants with CDR-SB > 0 were Aβ-PET positive, while clinically normal participants (CDR-SB = 0) were a mix of Aβ-PET positive and negative. Regression analyses evaluated main effect and interaction associations between plasma GFAP, Aβ-PET, and clinical severity. RESULTS In both cohorts, plasma GFAP increased linearly with Aβ-PET CLs in clinically normal older adults. In Cohort 2, which included participants with more severe clinical dysfunction and Aβ-PET burden, the association between Aβ and GFAP became curvilinear (inverted U-shape; quadratic model R2 change = 0.165, p = 0.009), and Aβ-PET interacted with CDR-SB (R2 change = 0.164, p = 0.007): older adults with intermediate functional impairment (CDR-SB = 0.5-4.0) showed a weak (negative) association between Aβ-PET CLs and plasma GFAP, while older adults with dementia (CDR-SB > 4.0) showed a strong, negative association of higher Aβ-PET CLs with lower plasma GFAP. CONCLUSION The relationship between astrocytic integrity and cortical Aβ may be highly dynamic, with linear, positive associations early in disease that diverge in more severe disease stages.
Long-term renal outcomes of IgA nephropathy presenting with different levels of proteinuria.

AIMS Proteinuria is a strong prognostic factor in IgA nephropathy (IgAN). However, the risk threshold of proteinuria for kidney disease progression remains in debate. This study aimed to evaluate the risk of different levels of proteinuria on renal outcomes in Chinese patients with IgAN. MATERIALS AND METHODS Patients with biopsy-proven primary IgAN were recruited and divided into four groups based on their proteinuria levels: ≤ 0.30 g/d, 0.31 - 0.50 g/d, 0.51 - 1.00 g/d, and > 1.00 g/d. The primary outcomes were composed by doubling of baseline serum creatinine (Scr) and end-stage renal disease (ESRD, defined as eGFR < 15 mL/min/1.73m2, initiation of dialysis or transplantation). RESULTS A total of 921 IgAN patients were enrolled in this study. During a median follow-up duration of 48 (34 - 62) months, higher risks of doubling of baseline Scr developed in patients with proteinuria 0.31 - 0.50 g/d (HR = 2.87, p = 0.04), 0.51 - 1.00 g/d (HR = 4.26, p = 0.002), and > 1.00 g/d (HR = 14.56, p < 0.001), while increased risks for ESRD were observed in patients with proteinuria 0.51 - 1.00 g/d (HR = 3.00, p = 0.02) and > 1.00 g/d (HR = 13.03, p < 0.001) in unadjusted Cox regression models. After adjusted for potential confounders, proteinuria 0.31 - 0.50 g/d (HR = 3.70, p = 0.04), 0.51 - 1.00 g/d (HR = 3.67, p = 0.02), and > 1.00 g/d (HR = 8.20, p < 0.001) remained to be significantly associated with higher risks of doubling of Scr, while only those with proteinuria > 1.00 g/d (HR = 6.04, p = 0.001) exhibited a markedly increased risk of ESRD. CONCLUSION Patients with proteinuria levels > 0.30 g/d already have a higher risk of doubling of baseline Scr, suggesting the necessity of early intervention in patients presenting with minimal proteinuria.
Strategies to Connect Low-Income Communities with the Proposed Sewerage Network of the Dhaka Sanitation Improvement Project, Bangladesh: A Qualitative Assessment of the Perspectives of Stakeholders

In Bangladesh, approximately 31% of urban residents are living without safely managed sanitation, the majority of whom are slum residents. To improve the situation, Dhaka Water Supply and Sewerage Authority (DWASA) is implementing the Dhaka Sanitation Improvement Project (DSIP), mostly funded by the World Bank. This study assessed the challenges and opportunities of bringing low-income communities (LICs) under a sewerage connection within the proposed sewerage network plan by 2025. We conducted nine key-informant interviews from DWASA and City Corporation, and 23 focus-group discussions with landlords, tenants, and Community Based Organisations (CBOs) from 16 LICs near the proposed catchment area. To achieve connections, LICs would require improved toilet infrastructures and have to be connected to main roads. Construction of large communal septic tanks is also required where individual toilet connections are difficult. To encourage connection in LICs, income-based or area-based subsidies were recommended. For financing maintenance, respondents suggested monthly fee collection for management of the infrastructure by dividing bills equally among sharing households, or by users per household. Participants also suggested the government’s cooperation with development-partners/NGOs to ensure sewerage connection construction, operation, and maintenance and prerequisite policy changes such as assuring land tenure.
Advances with lipid-lowering drugs for pediatric patients with familial hypercholesterolemia

ABSTRACT Introduction Familial hypercholesterolemia (FH) is a frequent genetic disorder characterized by elevated LDL-cholesterol (LDL-C) and early onset of atherosclerosis. Areas covered The authors provide an overview of the pediatric FH scenario, with emphasis on the role of statins as the preferred pharmacological therapy, discussing their potential benefits, as well as adverse effects, and the remaining uncertainties about their use in this population. They also comment on other lipid-lowering therapies. Expert opinion Statin therapy is recommended after the ages of 8–10 years old for heterozygous FH patients and can reduce LDL-C by 24–50% depending on drug type and dosage. For more severe cases, higher doses and adjuvant therapies like ezetimibe may be necessary and treatment should be started at diagnosis, as is the case of homozygous FH. Statins reduce progression of subclinical vascular disease and may reduce early cardiovascular events. The available evidence indicates safety of statins in children with no apparent harms related to growth, sexual maturation, steroid hormones, glucose levels, cognitive function, or muscle and liver problems, in comparison with placebo. Newer treatments like lomitapide, PCSK9 inhibitors, bempedoic acid and evinacumab need to be adequately evaluated in pediatric FH patients with more severe dyslipidemia.
Nuclear crowding and nonlinear diffusion during interkinetic nuclear migration in the zebrafish retina

An important question in early neural development is the origin of stochastic nuclear movement between apical and basal surfaces of neuroepithelia during interkinetic nuclear migration. Tracking of nuclear subpopulations has shown evidence of diffusion - mean squared displacements growing linearly in time - and suggested crowding from cell division at the apical surface drives basalward motion. Yet, this hypothesis has not yet been tested, and the forces involved not quantified. We employ long-term, rapid light-sheet and two-photon imaging of early zebrafish retinogenesis to track entire populations of nuclei within the tissue. The time-varying concentration profiles show clear evidence of crowding as nuclei reach close-packing and are quantitatively described by a nonlinear diffusion model. Considerations of nuclear motion constrained inside the enveloping cell membrane show that concentration-dependent stochastic forces inside cells, compatible in magnitude to those found in cytoskeletal transport, can explain the observed magnitude of the diffusion constant.
Transcriptional and Metabolic Profiling of Potato Plants Expressing a Plastid-Targeted Electron Shuttle Reveal Modulation of Genes Associated to Drought Tolerance by Chloroplast Redox Poise

Water limitation represents the main environmental constraint affecting crop yield worldwide. Photosynthesis is a primary drought target, resulting in over-reduction of the photosynthetic electron transport chain and increased production of reactive oxygen species in plastids. Manipulation of chloroplast electron distribution by introducing alternative electron transport sinks has been shown to increase plant tolerance to multiple environmental challenges including hydric stress, suggesting that a similar strategy could be used to improve drought tolerance in crops. We show herein that the expression of the cyanobacterial electron shuttle flavodoxin in potato chloroplasts protected photosynthetic activities even at a pre-symptomatic stage of drought. Transcriptional and metabolic profiling revealed an attenuated response to the adverse condition in flavodoxin-expressing plants, correlating with their increased stress tolerance. Interestingly, 5–6% of leaf-expressed genes were affected by flavodoxin in the absence of drought, representing pathways modulated by chloroplast redox status during normal growth. About 300 of these genes potentially contribute to stress acclimation as their modulation by flavodoxin proceeds in the same direction as their drought response in wild-type plants. Tuber yield losses under chronic water limitation were mitigated in flavodoxin-expressing plants, indicating that the flavoprotein has the potential to improve major agronomic traits in potato.
Adoption of Mobile Health Apps in Dietetic Practice: Case Study of Diyetkolik

Background Dietetics mobile health apps provide lifestyle tracking and support on demand. Mobile health has become a new trend for health service providers through which they have been shifting their services from clinical consultations to online apps. These apps usually offer basic features at no cost and charge a premium for advanced features. Although diet apps are now more common and have a larger user base, in general, there is a gap in literature addressing why users intend to use diet apps. We used Diyetkolik, Turkey’s most widely used online dietetics platform for 7 years, as a case study to understand the behavioral intentions of users. Objective The aim of this study was to investigate the factors that influence the behavioral intentions of users to adopt and use mobile health apps. We used the Technology Acceptance Model and extended it by exploring other factors such as price-value, perceived risk, and trust factors in order to assess the technology acceptance of users. Methods We conducted quantitative research on the Diyetkolik app users by using random sampling. Valid data samples gathered from 658 app users were analyzed statistically by applying structural equation modeling. Results Statistical findings suggested that perceived usefulness (P<.001), perceived ease of use (P<.001), trust (P<.001), and price-value (P<.001) had significant relationships with behavioral intention to use. However, no relationship between perceived risk and behavioral intention was found (P=.99). Additionally, there was no statistical significance for age (P=.09), gender (P=.98), or previous app use experience (P=.14) on the intention to use the app. Conclusions This research is an invaluable addition to Technology Acceptance Model literature. The results indicated that 2 external factors (trust and price-value) in addition to Technology Acceptance Model factors showed statistical relevance with behavioral intention to use and improved our understanding of user acceptance of a mobile health app. The third external factor (perceived risk) did not show any statistical relevance regarding behavioral intention to use. Most users of the Diyetkolik dietetics app were hesitant in purchasing dietitian services online. Users should be frequently reassured about the security of the platform and the authenticity of the platform’s dietitians to ensure that users’ interactions with the dietitians are based on trust for the platform and the brand.
Fruit quality of grafted tomato plants grown under saline conditions

Summary Tomato seedlings (cvs. ‘Fanny’ and ‘Goldmar’) were grafted onto the tomato rootstock hybrid AR-9704, using the cleft grafting method, and grown under greenhouse conditions. Tomato fruit yield and quality from plants exposed to 0, 30 or 60 mM NaCl, comparing grafted with ungrafted plants, was studied. Fruit yield was determined, and the chemical quality of fruit was analysed by measurements of sugars, lycopene, -carotene, ascorbic acid and mineral composition, and by determination of titratable acidity and soluble solids. Fruit yield was higher in grafted than in ungrafted plants for both varieties, for 0, 30 and 60 mM NaCl. Salinity increased soluble solids, glucose and fructose, mainly at 60 mM NaCl, while ascorbic acid increased significantly only for grafted plants at 0 mM NaCl. The concentrations of -carotene and lycopene were not affected by salinity, but a large increase due to grafting was observed for all treatments. Sodium, chloride and nitrate ion concentrations were higher in ungrafted than in grafted plants, for the 60 mM NaCl treatment. Thus, grafting could be a useful tool to increase tomato fruit quality.
Evaluation of the relationship between cardiac autonomic function and glucose variability and HOMA-IR in prediabetes

Aims: The present study aims to investigate the relationship between cardiac autonomic function (CAF) and glucose variability (GV) and HOMA-IR in subjects with prediabetes and normal glucose tolerance (NGT). Material and methods: Ninety-two subjects (59 with prediabetes and 33 with NGT), of mean age 50.3 ± 11.5 years, mean BMI 30.4 ± 6.0 kg/m2, were included in this cross-sectional study. Glucose tolerance was assessed by OGTT according to WHO 2006 criteria. Glucose, HbA1c, insulin, oxLDL, and 3-Nitrotyrosine were measured. CGM was performed with a blinded sensor (FreeStyle Libre Pro). CAF was assessed by ANX-3.0 technology. Results: GV indices were increased in prediabetes. CAF was suppressed in subjects with any stage of dysglycemia. The prevalence of cardiac autonomic dysfunction was higher in prediabetes −20.3% as compared to NGT −3.0%, p = 0.028. HOMA-IR [OR 1.5 (95% CI: 1.1–2.1), p = 0.010] and time in target range [OR 0.8 (95% CI: 0.67–0.97), p = 0.021] were found to be predictive variables for impaired CAF. Sympathetic and parasympathetic activity negatively correlated with mean glycemia and GV indices and were independently related to JINDEX in prediabetes (F[1, 47] = 5.76, p = 0.021 and F[1, 47] = 5.94, p = 0.019, respectively); and to time above target range in NGT (F[1, 18] = 4.48, p = 0.049 and F[1, 18] = 4.65, p = 0.046, respectively). Conclusion: CAF is declined in prediabetes and seems to be related to GV and HOMA-IR at early stages of dysglycemia.
Air Pollutants and Daily Hospital Admissions for Psychiatric Care: A Review.

OBJECTIVE Air pollution is a major environmental risk to health. Ambient (outdoor) air pollution in both cities and rural areas was estimated to cause 4.2 million premature deaths worldwide in 2016. In this review, the authors sought to briefly summarize original research investigating the short-term effects of air pollution exposure on mental health. METHODS A systematic search of the electronic databases PubMed, Scopus, and Web of Science was conducted (from any time until March 4, 2019) to identify research studies reporting associations between daily levels of air pollutants and daily admissions to hospitals or emergency departments (EDs) for psychiatric disorders and symptoms. A final set of 19 articles was reviewed. RESULTS The results of all selected studies showed statistically significant associations between daily hospital admissions and ED visits for mental disorders and daily levels of some or all air pollutants considered, including particulate matter (PM) of variable sizes (in micrometers given in subscripts; PM2.5 and PM10), sulfur dioxide, carbon monoxide, nitrogen oxide, and ozone. The strongest and more consistent evidence across studies was found for PM2.5 and PM10. CONCLUSIONS The results summarized in this review extend the evidence that air pollution may contribute either to worsening of psychiatric symptoms or to the decision to seek treatment for a large group of mental diseases and conditions, including severe psychiatric disorders such as schizophrenia and depression.