Miracle-dz/UniFAR-FTUs huggingface dataset:
The Evolution of Silicon Transport in Eukaryotes

Biosilicification (the formation of biological structures from silica) occurs in diverse eukaryotic lineages, plays a major role in global biogeochemical cycles, and has significant biotechnological applications. Silicon (Si) uptake is crucial for biosilicification, yet the evolutionary history of the transporters involved remains poorly known. Recent evidence suggests that the SIT family of Si transporters, initially identified in diatoms, may be widely distributed, with an extended family of related transporters (SIT-Ls) present in some nonsilicified organisms. Here, we identify SITs and SIT-Ls in a range of eukaryotes, including major silicified lineages (radiolarians and chrysophytes) and also bacterial SIT-Ls. Our evidence suggests that the symmetrical 10-transmembrane-domain SIT structure has independently evolved multiple times via duplication and fusion of 5-transmembrane-domain SIT-Ls. We also identify a second gene family, similar to the active Si transporter Lsi2, that is broadly distributed amongst siliceous and nonsiliceous eukaryotes. Our analyses resolve a distinct group of Lsi2-like genes, including plant and diatom Si-responsive genes, and sequences unique to siliceous sponges and choanoflagellates. The SIT/SIT-L and Lsi2 transporter families likely contribute to biosilicification in diverse lineages, indicating an ancient role for Si transport in eukaryotes. We propose that these Si transporters may have arisen initially to prevent Si toxicity in the high Si Precambrian oceans, with subsequent biologically induced reductions in Si concentrations of Phanerozoic seas leading to widespread losses of SIT, SIT-L, and Lsi2-like genes in diverse lineages. Thus, the origin and diversification of two independent Si transporter families both drove and were driven by ancient ocean Si levels.
A comparison of well-being indicators and affect regulation strategies between parents of children with disabilities and parents of typically developed children

Research to date has shown that the well-being of parents of children with disabilities is lower than that of parents of typically developed children. However, the vast majority of this research has been conducted with this exact purpose in mind, thus placing parents and their children’s disability in the spotlight, which may have resulted in a distortion in the participants’ answering process. In addition, participants were mostly chosen because they have or do not have a child with disabilities, while other relevant characteristics were poorly matched. The aim of the research described in this paper was to compare parents of children with disabilities to a corresponding group of parents of typically developed children in terms of various well-being indicators and specific sources of life satisfaction. This study was conducted within the framework of the Croatian Longitudinal Study of Well-Being (CRO-WELL) project. The sample used in this study consisted of 41 parents of children with disabilities. Each of these parents was matched to a very similar individual with typically developed children. Consequently, we obtained two samples in which the majority of participants were women, married, living in a large city, and employed, two-thirds of whom had completed secondary school education at least. Differences emerged regarding satisfaction with free time, indicating that parents of children with disabilities were less satisfied than parents of typically developed children. In addition, parents of children with disabilities felt pleasant less frequently. Both groups of parents used active affect regulation strategies more often than passive ones as tools to deal with negative emotions. Proactive strategies were related to higher well-being levels, while passive strategies were related to lower well-being levels, a trend that became particularly evident among parents of children with disabilities.
Systematic deficiency of aftershocks in areas of high coseismic slip for large subduction zone earthquakes

Aftershock deficiency in large-slip zones of major subduction zone earthquake ruptures indicates below-critical shear stress. Fault slip during plate boundary earthquakes releases a portion of the shear stress accumulated due to frictional resistance to relative plate motions. Investigation of 101 large [moment magnitude (Mw) ≥ 7] subduction zone plate boundary mainshocks with consistently determined coseismic slip distributions establishes that 15 to 55% of all master event–relocated aftershocks with Mw ≥ 5.2 are located within the slip regions of the mainshock ruptures and few are located in peak slip regions, allowing for uncertainty in the slip models. For the preferred models, cumulative deficiency of aftershocks within the central three-quarters of the scaled slip regions ranges from 15 to 45%, increasing with the total number of observed aftershocks. The spatial gradients of the mainshock coseismic slip concentrate residual shear stress near the slip zone margins and increase stress outside the slip zone, driving both interplate and intraplate aftershock occurrence near the periphery of the mainshock slip. The shear stress reduction in large-slip regions during the mainshock is generally sufficient to preclude further significant rupture during the aftershock sequence, consistent with large-slip areas relocking and not rupturing again for a substantial time.
The Prevalence of Thyroid Nodules and Their Association with Metabolic Syndrome Risk Factors in a Moderate Iodine Intake Area.

BACKGROUND To investigate the prevalence of thyroid nodules (TNs) and to evaluate the association between TNs and metabolic syndrome (MetS) in the moderate iodine intake area of Jiangsu, China. SUBJECTS AND METHODS A cross-sectional study was carried out in a Chinese community-based epidemiological investigation from January to December 2014. A questionnaire was completed by 6494 subjects (2427 men and 4067 women). Thyroid ultrasound was performed by using a 7.5-MHz linear probe. MetS was defined according to the 2006 International Diabetes Federation criteria. RESULTS The prevalence of TNs in the study population was 17.7% (12.9% for men and 20.6% for women) and significantly higher in subjects with MetS [MetS(+)] than in those without MetS [MetS(-)] (25.8% vs. 15.5%, χ2 = 78.471, P < 0.001). Binary logistic regression indicated that (in addition to female sex and increased age) increased fasting plasma glucose (FPG), waist circumference (WC), hypertension, and smoking were positively associated with the prevalence of TNs. CONCLUSIONS Our findings indicated a positive association between MetS and formation of TNs. Increased WC and FPG, as well as hypertension, might increase the prevalence of TNs.
Application of LSSVM and SMOTE on Seven Open Source Projects for Predicting Refactoring at Class Level

Source code refactoring consisting of modifying the structure of the source code without changing its functionality and external behavior. We present a method to predict refactoring candidates at class level which can help developers in improving their design and structure of source code while preserving the behavior. We propose a technique to predict refactoring candidates based on the application of a machine learning based framework. We use Least Squares Support Vector Machines (LS-SVM) as the learning algorithm, Principal Component Analysis (PCA) as a feature extraction technique and Synthetic Minority Over-sampling Technique (SMOTE) as a technique for handling imbalanced data. We start with 102 source code metrics as input features which are then reduced to 31 features after removing irrelevant and redundant features through statistical tests. We conduct a series of experiments on publicly available software engineering dataset consisting of seven open-source software systems in which the refactored classes are manually validated. We apply LS-SVM with three different functions: linear, polynomial and Radial Basis Function (RBF). Statistical significance test demonstrate that RBF kernel outperforms linear and polynomial kernel but there is no statistically significant difference between the performance of linear and polynomial kernel. Statistical significance test reveals that with-SMOTE technique outperforms without-SMOTE and all metrics outperforms PCA based metrics. The mean value of Area Under Curve (AUC) for LS-SVM RBF kernel is 0.96.
Manualization of Occupational Therapy Using Ayres Sensory Integration® for Autism

This article reports on the development of a Stage 3 manual (following pilot effectiveness study) for implementing occupational therapy using Ayres Sensory Integration® (OT/ASI) for children with autism spectrum disorders to enhance participation in daily occupations. Three stakeholder groups were surveyed to aid in translation of manual from research to practice (i.e., Stage 3 manual) and an expert consensus meeting was held to finalize recommendations. Data indicated that the manuals usability could be improved by including a section on frequently encountered problems and solutions, and by including video case examples. Also recommended were greater chapter uniformity, improved clarity of forms and charts, and inclusion of a glossary. Changes were made and subject to expert review and consensus using modified Delphi process. The Stage 3 manual has been rigorously vetted and is ready for practice and research replication.
The Dynamics of Hospital Use among Older People Evidence for Europe Using SHARE Data

OBJECTIVE Hospital services use, which is a major driver of total health expenditures, is expected to rise over the next decades in Europe, especially because of population aging. The purpose of this article is to better understand the dynamics of older people's demand for hospital care over time in a cross-country setting. DATA SOURCE We used data from the Survey on Health, Ageing, and Retirement in Europe (SHARE), in 10 countries between 2004 and 2011. STUDY DESIGN We estimated a dynamic panel model of hospital admission for respondents aged 50 years or more. PRINCIPAL FINDINGS Following prior research, we found evidence of state dependence in hospital use over time. We also found that rise in frailty-among other health covariates-is a strong predictor of increased hospital use. Progression by one point on the frailty scale [0;5] is associated with an additional risk of about 2.1 percent on average. CONCLUSIONS Our results support promotion of early detection of frailty in primary care, and improvement of coordination between actors within the health system, as potential strategies to reduce avoidable or unnecessary hospital use among frail elderly.
Launaea taraxacifolia (Willd.) Amin ex C. Jeffrey inhibits oxidative damage and econucleotidase followed by increased cellular ATP in testicular cells of rats exposed to metropolitan polluted river water

Abstract Background: Humans are directly/indirectly exposed to hazardous chemicals from the aquatic environment. We investigated the protection of the Launea taraxacifolia methanolic extract (LTME) on the hydroxyl steroid dehydrogenases [(∆5-3β-hydroxyl steroid dehydrogenase (∆5-3β-HSD) and the ∆5-17β-hydroxyl steroid dehydrogenase (∆5-17β-HSD), testicular 5′-nucleotidase and lactate dehydrogenase (LDH)] activities as well as the key indicators of oxidative stress in germinal epithelial cells of rats induced with surulere polluted river water (SPRW). Methods: The animals were divided into six groups (n=8). Group I was given 1 mL of distilled water only, Group II received 1 mL of SPRW only, Group III received 200 mg/kg LTME before+1 mL of SPRW after, Group IV received 200 mg/kg LTME+1 mL of SPRW, Group V received 1 mL of SPRW before+200 mg/kg LTME after and Group VI received 200 mg/kg LTME only. The treatment was done via oral administration for 28 days. Results: The HPLC results showed the abundance of quercetin and quercitrin. The SPRW increased 5′-nucleotidase with the concomitant decrease of ∆5-3β-HSD, ∆5-17β-HSD and LDH activities in rats exposed in relation to the control. Similarly, the administration of the SPRW caused a systemic oxidative damage along with adverse histopathological changes in germinal epithelial cells. Conclusions: Interestingly, these alterations were differentially reversed by LTME via the elevation of steroidogenic enzymes and cellular ATP.
The Meshless Local Petrov-Galerkin (MLPG) Method for Solving Incompressible Navier-Stokes Equations

The truly Meshless Local Petrov-Galerkin (MLPG) method is extended to solve the incompressible Navier-Stokes equations. The local weak form is modi- fied in a very careful way so as to ovecome the so-called Babuska-Brezzi conditions. In addition, The upwinding scheme as developed in Lin and Atluri (2000a) and Lin and Atluri (2000b) is used to stabilize the convection operator in the streamline direction. Numerical results for benchmark problems show that the MLPG method is very promising to solve the convection dominated fluid mechanics problems. keyword: MLPG, MLS, Babuconditions, upwinding scheme, incompressible flow, Navier-Stokes equations.
The Utility of Bronchoscopy After Inhalation Injury Complicated by Pneumonia in Burn Patients: Results From the National Burn Repository

There are no guidelines to determine when bronchoscopy is appropriate in patients with inhalation injury complicated by pneumonia. We reviewed the National Burn Repository from 1998 to 2007 to determine if there is any difference in outcome in burn patients with inhalation injury and pneumonia who did and did not undergo bronchoscopy. Three hundred fifty-five patients with pneumonia did not undergo bronchoscopy, 173 patients underwent one bronchoscopy, and 96 patients underwent more than one bronchoscopy. Patients with a 30 to 59% surface area burn and pneumonia who underwent bronchoscopy had a decreased duration of mechanical ventilation compared with those who did not (21 days, 95% CI: 19–23 days vs 28 days, 95% CI: 25–31 days, P = .0001). When compared with patients who did not undergo bronchoscopy, patients having a single bronchoscopy had a significantly shorter length of intensive care unit stay and hospital stay (35 ± 3 vs 39 ± 2, P = .04, and 45 ± 3 vs 49 ± 2, P = .009). The hospital charges were on average much higher in those patients who did not undergo bronchoscopy, compared with those who did ($473,654 ± 44,944 vs $370,572 ± 36,602, P = .12). When compared with patients who did not undergo bronchoscopy, patients who did have one or more bronchoscopies showed a reduced risk of death by 18% (OR = 0.82, 95% CI: 0.53–1.27, P = .37). Patients with inhalation injury complicated by pneumonia seem to benefit from bronchoscopy. This benefit can be seen in a decreased duration of mechanical ventilation, decreased length of intensive care unit stay, and decreased overall hospital cost. In addition, there was a trend toward an improvement in mortality. The aggressive use of bronchoscopy after inhalation injury may be justified.
Association between Anxiety and Pain in Dental Treatment: A Systematic Review and Meta-analysis

Accumulating evidence has revealed that dental anxiety (DA), as a dispositional factor toward the dental situation, is associated with the state anxiety (SA) and pain related to dental procedures. However, conclusions from individual studies may be limited by the treatment procedures that patients received, the tools used to assess DA, or the treatment stages when anxiety or pain was assessed. It is unclear whether DA, at the study level, accounts for the variance in pretreatment SA. The impact of DA and SA on pain at different treatment stages has not been systematically investigated. To address these questions, we present novel meta-analytical evidence from 35 articles (encompassing 47 clinical groups) that investigated DA in a clinical group. Subgroup analyses revealed that the studies of surgical and nonsurgical procedures did not significantly differ in either DA or pretreatment SA. Furthermore, metaregressions revealed DA as a significant predictor that explained the variance in SA assessed before and during treatment but not after treatment. The findings suggest that patient DA has a significant impact on patient SA. Metaregressions revealed DA as a significant predictor that explained the variance in expected pain, pain during treatment and posttreatment pain. In contrast, pretreatment SA was a significant predictor that explained the variance in expected pain. The findings reveal that DA has a consistent impact on pain through the entire period of dental treatment. Altogether, the findings highlight the role of DA as an overall indicator for anxiety and pain, across different types of dental procedures or treatment stages. We conclude that anxiety should be assessed as a critical step not only in anxiety management for high-DA patients, but also in pain control for all dental patients.
Placental mitochondrial biogenesis and function was slightly changed by gestational hypercholesterolemia in full-term pregnant women

Abstract It was reported that high blood cholesterol levels increased the susceptibility to mitochondrial dysfunction. This study hypothesized that the gestational hypercholesterolemia (HC) could induce the mitochondrial dysfunction in term human placenta. The eligible pregnant women were recruited from Xuanwu Hospital in Beijing during their first prenatal visit (before their 10th week of pregnancy). In total, 19 pregnant women whose serum total cholesterol levels were higher than 7.25 mm at third trimester (measured at 36–38 weeks) were selected as gestational HC. Other 19 pregnant women with normal cholesterol level matched with age, pre-gestational body mass index, and the neonatal gender were included as the control group. Full-term placenta samples were collected. The mitochondrial DNA (mtDNA) copy number, messenger RNA (mRNA) expression of cytochrome c oxidase subunit I, adenosine triphosphate monophosphatase 6 (ATP6ase), citrate synthase, peroxisome proliferator-activated receptor-γ (PPARγ) co-activator 1α, PPARγ co-activator 1β and estrogen-related receptor-α, and the activity of mitochondrial respiratory chain enzyme complex were measured. Pregnancy outcomes were obtained by extraction from medical records and the labor ward register. The results showed that only placental mtDNA copy number and mRNA expression of ATP6ase were significantly decreased in HC group. No significant differences were detected of other measurements between the two groups. These findings indicated that gestational HC might not induce the damage of placental function seriously.
High rates of vessel noise disrupt foraging in wild harbour porpoises (Phocoena phocoena)

Shipping is the dominant marine anthropogenic noise source in the world's oceans, yet we know little about vessel encounter rates, exposure levels and behavioural reactions for cetaceans in the wild, many of which rely on sound for foraging, communication and social interactions. Here, we used animal-borne acoustic tags to measure vessel noise exposure and foraging efforts in seven harbour porpoises in highly trafficked coastal waters. Tagged porpoises encountered vessel noise 17–89% of the time and occasional high-noise levels coincided with vigorous fluking, bottom diving, interrupted foraging and even cessation of echolocation, leading to significantly fewer prey capture attempts at received levels greater than 96 dB re 1 µPa (16 kHz third-octave). If such exposures occur frequently, porpoises, which have high metabolic requirements, may be unable to compensate energetically with negative long-term fitness consequences. That shipping noise disrupts foraging in the high-frequency-hearing porpoise raises concerns that other toothed whale species may also be affected.
Evaluation of SCORTEN on a Cohort of Patients With Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis Included in the RegiSCAR Study

The purpose of this study was to evaluate the severity-of-illness score called SCORTEN with respect to its predictive ability and by using data obtained in the RegiSCAR study, the most comprehensive European registry of patients with Stevens-Johnson syndrome (SJS) and toxic epidermal necrolysis (TEN). For advanced comparisons, an auxiliary score (AS) was defined using data obtained in a previous study. Three hundred sixty-nine patients with SJS/TEN were included in RegiSCAR between 2003 and 2005. The data needed for calculation of SCORTEN were available for 45% of patients. The score revealed a moderate predictive ability with a slight underestimation of the total number of in-hospital deaths by 11%, an area under the receiver operating characteristic curve of 0.75, and a Brier score of 0.14. Problems could be seen by analyzing subgroups such as patients with TEN. The AS was better calibrated but discriminated worse (area under the receiver operating characteristic curve: 0.72; Brier score: 0.14). With the help of a refined score derived from SCORTEN and AS, potential for a possible improvement could be demonstrated. The authors were able to show that the predictive ability of SCORTEN is acceptable. Although improvement might be possible, SCORTEN remains the tool of choice, whereas AS might be an alternative in retrospective settings with missing laboratory data.
Adapting to Artificial Intelligence Radiologists and Pathologists as Information Specialists

Artificial intelligence—the mimicking of human cognition by computers—was once a fable in science fiction but is becoming reality in medicine. The combination of big data and artificial intelligence, referred to by some as the fourth industrial revolution,1 will change radiology and pathology along with other medical specialties. Although reports of radiologists and pathologists being replaced by computers seem exaggerated,2 these specialties must plan strategically for a future in which artificial intelligence is part of the health care workforce. Radiologists have always revered machines and technology. In 1960, Lusted predicted “an electronic scannercomputer to examine chest photofluorograms, to separate the clearly normal chest films from the abnormal chest films. ”3 Lusted further suggested that “the abnormal chest films would be marked for later study by the radiologists. ”3 Lusted’s intuitions were prescient: interpreting radiographs is pattern recognition; computers can recognize patterns and may be helpful because some roentgenographic analyses can be automated. Nearly 60 years after Lusted’s prediction, Enlitic, a technology company in Silicon Valley, inputted images of normal radiographs and radiographs with fractures into a computerized database.4 Using deep learning, a refined version of artificial neural networks, the