Miracle-dz/UniFAR-FTUs huggingface dataset:
Dietary Protein Intake throughout Childhood Is Associated with the Timing of Puberty 1 – 3

Early puberty onset is associated with hormone-related cancers, but whether diet in childhood influences pubertal timing is controversial. We examined the association of protein intake in early and mid-childhood with the ages at take-off of the pubertal growth spurt (ATO), peak height velocity (APHV), and menarche in girls and voice break in boys using data from the longitudinal Dortmund Nutritional and Anthropometric Longitudinally Designed Study. Among participants who provided 3-d weighed dietary records at 12 mo, 18–24 mo, 3–4 y, and 5–6 y, 112 had sufficient anthropometric measurements between 6 and 13 y to allow estimation of ATO. Life-course plots were used to identify critical periods of total, animal, and vegetable protein intake (percentage of total energy intake) for pubertal timing. At these ages, the association between tertiles of protein intake (T1–T3) and the outcomes was investigated using multiple linear regression analysis. A higher total and animal protein intake at 5–6 y was related to an earlier ATO. In the highest tertile of animal protein intake at 5–6 y, ATO occurred 0.6 y earlier than in the lowest [(mean, 95% CI) T1: 9.6, 9.4–9.9 vs. T2: 9.4, 9.1–9.7 vs. T3: 9.0, 8.7–9.3 y; P-trend = 0.003, adjusted for sex, total energy, breast-feeding, birth year, and paternal university degree]. Similar findings were seen for APHV (P-trend = 0.001) and the timing of menarche/voice break (P-trend = 0.02). Conversely, a higher vegetable protein intake at 3–4 and 5–6 y was related to later ATO, APHV, and menarche/voice break (P-trend = 0.02–0.04). These results suggest that animal and vegetable protein intake in mid-childhood might be differentially related to pubertal timing. J. Nutr. 140: 565–571, 2010.
Metabolic Pathway Involved in 6-Chloro-2-Benzoxazolinone Degradation by Pigmentiphaga sp. Strain DL-8 and Identification of the Novel Metal-Dependent Hydrolase CbaA

ABSTRACT 6-Chloro-2-benzoxazolinone (CDHB) is a precursor of herbicide, insecticide, and fungicide synthesis and has a broad spectrum of biological activity. Pigmentiphaga sp. strain DL-8 can transform CDHB into 2-amino-5-chlorophenol (2A5CP), which it then utilizes as a carbon source for growth. The CDHB hydrolase (CbaA) was purified from strain DL-8, which can also hydrolyze 2-benzoxazolinone (BOA), 5-chloro-2-BOA, and benzamide. The specific activity of purified CbaA was 5,900 U · mg protein−1 for CDHB, with Km and k cat values of 0.29 mM and 8,500 s−1, respectively. The optimal pH for purified CbaA was 9.0, the highest activity was observed at 55°C, and the inactive metal-free enzyme could be reactivated by Mg2+, Ni2+, Ca2+, or Zn2+. Based on the results obtained for the CbaA peptide mass fingerprinting and draft genome sequence of strain DL-8, cbaA (encoding 339 amino acids) was cloned and expressed in Escherichia coli BL21(DE3). CbaA shared 18 to 21% identity with some metal-dependent hydrolases of the PF01499 family and contained the signature metal-binding motif Q127XXXQ131XD133XXXH137. The conserved amino acid residues His288 and Glu301 served as the proton donor and acceptor. E. coli BL21(DE3-pET-cbaA) resting cells could transform 0.2 mM CDHB into 2A5CP. The mutant strain DL-8ΔcbaA lost the ability to degrade CDHB but retained the ability to degrade 2A5CP, consistent with strain DL-8. These results indicated that cbaA was the key gene responsible for CDHB degradation by strain DL-8. IMPORTANCE 2-Benzoxazolinone (BOA) derivatives are widely used as synthetic intermediates and are also an important group of allelochemicals acting in response to tissue damage or pathogen attack in gramineous plants. However, the degradation mechanism of BOA derivatives by microorganisms is not clear. In the present study, we reported the identification of CbaA and metabolic pathway responsible for the degradation of CDHB in Pigmentiphaga sp. DL-8. This will provide microorganism and gene resources for the bioremediation of the environmental pollution caused by BOA derivatives.
Reevaluating “cluster failure” in fMRI using nonparametric control of the false discovery rate

In a substantial contribution to the fMRI field, Eklund et al. (1) use nonparametric methods to demonstrate that random field theory (RFT)-based familywise error (FWE) correction for cluster inference does not control errors appropriately, and this discrepancy is more pronounced for lenient cluster-defining thresholds (CDT). Moreover, they point to violations of RFT assumptions as the culprit for this discrepancy. Given these results, how should we interpret existing fMRI literature that used RFT-based, FWE-corrected P values ( p RFT - FWE )? To suggest caution is reasonable but incomplete; we require concrete, quantitative guidelines to enable appropriate calibration of skepticism. Here, we undertake an initial attempt at such guidance. We heed Eklund et al.’s (1) warning and prefer nonparametric null distributions to RFT. However, we focus on the false discovery rate (FDR) (2 … [↵][1]2To whom correspondence should be addressed. Email: kesslerd{at}umich.edu. [1]: #xref-corresp-1-1
Acquired TET2 mutation in one patient with familial platelet disorder with predisposition to AML led to the development of pre‐leukaemic clone resulting in T2‐ALL and AML‐M0

Familial platelet disorder with predisposition to acute myeloid leukaemia (FPD/AML) is characterized by germline RUNX1 mutations, thrombocytopaenia, platelet dysfunction and a risk of developing acute myeloid and in rare cases lymphoid T leukaemia. Here, we focus on a case of a man with a familial history of RUNX1R174Q mutation who developed at the age of 42 years a T2‐ALL and, 2 years after remission, an AML‐M0. Both AML‐M0 and T2‐ALL blast populations demonstrated a loss of 1p36.32‐23 and 17q11.2 regions as well as other small deletions, clonal rearrangements of both TCRγ and TCRδ and a presence of 18 variants at a frequency of more than 40%. Additional variants were identified only in T2‐ALL or in AML‐M0 evoking the existence of a common original clone, which gave rise to subclonal populations. Next generation sequencing (NGS) performed on peripheral blood‐derived CD34+ cells 5 years prior to T2‐ALL development revealed only the missense TET2P1962T mutation at a frequency of 1%, which increases to more than 40% in fully transformed leukaemic T2‐ALL and AML‐M0 clones. This result suggests that TET2P1962T mutation in association with germline RUNX1R174Q mutation leads to amplification of a haematopoietic clone susceptible to acquire other transforming alterations.
The kielin/chordin-like protein (KCP) attenuates high-fat diet-induced obesity and metabolic syndrome in mice

Obesity and its associated complications such as insulin resistance and non-alcoholic fatty liver disease are reaching epidemic proportions. In mice, the TGF-β superfamily is implicated in the regulation of white and brown adipose tissue differentiation. The kielin/chordin-like protein (KCP) is a secreted regulator of the TGF-β superfamily pathways that can inhibit both TGF-β and activin signals while enhancing bone morphogenetic protein (BMP) signaling. However, KCP's effects on metabolism and obesity have not been studied in animal models. Therefore, we examined the effects of KCP loss or gain of function in mice that were maintained on either a regular or a high-fat diet. KCP loss sensitized the mice to obesity and associated complications such as glucose intolerance and adipose tissue inflammation and fibrosis. In contrast, transgenic mice that expressed KCP in the kidney, liver, and adipose tissues were resistant to developing high-fat diet-induced obesity and had significantly reduced white adipose tissue. Moreover, KCP overexpression shifted the pattern of SMAD signaling in vivo, increasing the levels of phospho (P)-SMAD1 and decreasing P-SMAD3. Adipocytes in culture showed a cell-autonomous effect in response to added TGF-β1 or BMP7. Metabolic profiling indicated increased energy expenditure in KCP-overexpressing mice and reduced expenditure in the KCP mutants with no effect on food intake or activity. These findings demonstrate that shifting the TGF-β superfamily signaling with a secreted protein can alter the physiology and thermogenic properties of adipose tissue to reduce obesity even when mice are fed a high-fat diet.
Osteoinductive porous biphasic calcium phosphate ceramic as an alternative to autogenous bone grafting in the treatment of mandibular bone critical-size defects.

The bone-induction capacity of a porous biphasic calcium phosphate (pBCP) using heterotopic implantation in mouse (mHI-model) and its efficacy as substitute for autograft in mandibular critical-size defect in rabbit (rabMCSD-model) was investigated. In mHI-model, pBCP was implanted into the thigh muscles and bone formation was histomorphometrically and immunohistochemically evaluated. In rabMCSD-model, 13 mm bone defects were treated with pBCP or autograft and bone repair comparatively evaluated by radiographic and histomorphometric methods. In mHI-model, formed bone and immunolabeling for bone morphogenetic protein-2 and osteopontin were observed in 90% of pBCP implanted samples after 12 weeks. In rabMCSD-model neither statistically significant difference was found in newly formed bone between pBCP and autograft groups at 4 weeks (18.8 ± 5.5% vs 27.1 ± 5.6%), 8 weeks (22.3 ± 2.7% vs 26.2 ± 5.1), and 12 weeks (19.6 ± 4.7% vs 19.6 ± 2.3%). At 12 weeks, the stability and contour of the mandible were restored in both treatments. Near tooth remaining, pBCP particles were covered by small amount of mineralized tissue exhibiting perpendicular attachments of collagen fiber bundles with histological characteristic of acellular cementum. Within the limitations of this study, it was concluded that pBCP is osteoinductive and able to stimulate the new formation of bone and cementum-like tissues in rabMCSD-model, suggesting that it may be an alternative to treatment of large bone defect and in periodontal regenerative therapy. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 106B: 1546-1557, 2018.
Surgical Treatment of Ulcerative Colitis

Ulcerative colitis (UC) is an ubiquitously distributed inflammatory bowel disease. Its incidence varies slightly between geographical areas, most likely because of either the different genetic patrimonies of the involved populations or several environmental factors. In socially evolved Countries UC incidence is of approximately 6 cases per 100.000 white adult individuals, with a prevalence of 40-100/100.000. This incidence notably decreases in Countries with lower socio-economic levels. Female gender is slightly more affected than male, with a gender ratio F/M of 1.5/1. The aetiology of UC still remains mainly unknown, even if a multifactorial genesis is now widely accepted. Unlike Crohn’s disease, UC is a continuous disease involving mainly the rectum, suddenly expanding proximally to the colon, with no alternation of healthy or diseased mucosal area. Figure 1 depicts the possible localization of UC at the time of clinical presentation (Binder et al., 1982; Stonnington et al., 1987)
Contribution Childhood and Adult Socioeconomic Position , Cumulative Lead Levels , and Pessimism in Later Life The VA Normative Aging Study

Pessimism, a general tendency toward negative expectancies, is a risk factor for depression and also heart disease, stroke, and reduced cancer survival. There is evidence that individuals with higher lead exposure have poorer health. However, low socioeconomic status (SES) is linked with higher lead levels and greater pessimism, and it is unclear whether lead influences psychological functioning independently of other social factors. The authors considered interrelations among childhood and adult SES, lead levels, and psychological functioning in data collected on 412 Boston area men between 1991 and 2002 in a subgroup of the VA Normative Aging Study. Pessimism was measured by using the Life Orientation Test. Cumulative (tibia) lead was measured by x-ray fluorescence. Structural equation modeling was used to quantify the relations as mediated by childhood and adult SES, controlling for age, health behaviors, and health status. An interquartile range increase in lead quartile was associated with a 0.37 increase in pessimism score (P < 0.05). Low childhood and adult SES were related to higher tibia lead levels, and both were also independently associated with higher pessimism. Lead maintained an independent association with pessimism even after childhood and adult SES were considered. Results demonstrate an interrelated role of lead burden and SES over the life course in relation to psychological functioning in older age.
Thermodynamics and Proton Transport in Nafion II. Proton Diffusion Mechanisms and Conductivity

A comprehensive pore transport model is proposed to describe proton diffusion within Nafion at various hydration levels by incorporating effects of water uptake and various proton transport mechanisms, namely, proton hopping along surface, Grotthuss diffusion, and ordinary mass diffusion of hydronium ions. The diffusion coefficients are predicted within a general random walk framework. The proton conductivity in contact with water vapor is accurately predicted as a function of relative humidity without any fitted parameters, considering the sorption isotherm proposed in the companion paper (Part I). A maximum conductivity in contact with liquid water is also predicted by the model for equivalent weight between 900 and 1000, in good agreement with the experimental measurements. The modeling framework could be extended to other proton conducting electrolytes for fuel cell applications. © 2005 The Electrochemical Society. All rights reserved.
Sensitivity analysis of Penalty-based Boundary Intersection on aggregation-based EMO algorithms

MOEA/D is an evolutionary multi-objective optimization algorithm, which relies on decomposition methods such as, weighted-sum, Tchebycheff and Penalty-based Boundary Intersection (PBI) to convert a multi-objective problem into a set of single-objective problems. It is known that PBI can generate a more uniform set of solutions than the other decomposition methods. The drawback of PBI is that it has a penalty parameter (θ) that has to be specified by the user. This penalty parameter can affect the convergence rate of MOEA/D as well as the uniformity of solutions. Unfortunately, there are very limited studies on sensitivity analysis of MOEA/D on the penalty parameter of PBI. This paper is dedicated to a comprehensive analysis of PBI's penalty parameter, and its effect on a user-preference algorithm (R-MEAD2) and a non-user-preference algorithm (MOEA/D). Unlike the previous studies that only rely on Hypervolume as their performance measure, we study the effect of θ on convergence, uniformity, and the combination of convergence and uniformity independently. The experimental results suggest that user-preference algorithms consistently perform better with a relatively larger θ value as compared to their non-user-preference counterparts. The results also suggest that on some problems, such as multi-modal functions, convergence is the dominant factor on the overall performance, where a smaller θ is preferable. Conversely, on some other problems, a larger θ is suggested where uniformity is the dominant factor. Finally, we briefly investigate the relationship between θ and the number of objectives.
Fitting the right non-vitamin K antagonist oral anticoagulant to the right patient with non-valvular atrial fibrillation: an evidence-based choice

Abstract Atrial fibrillation (AF) is the most prevalent arrhythmia and is associated with an increased risk of ischemic stroke (IS) and systemic embolism (SE). Stroke prevention is a key element for the overall management of AF patients. The non-vitamin K antagonist oral anticoagulants (NOACs), such as dabigatran, rivaroxaban, apixaban and edoxaban, are at least as effective as warfarin in reducing IS/SE with a lower rate of major bleeding. Various analyses from the large Phase III randomized trials demonstrated different efficacy and safety of NOACs in specific subgroups of patients. The randomized trials are supplemented by effectiveness and safety data from real-world observational cohorts following the availability of these drugs for use in everyday clinical practice. Given the clinical heterogeneity of AF patients, the available data from trials and real-world studies allow us to fit the right NOAC to the particular patient’s characteristics, with the aim of optimizing outcomes for the individual patient. This review article aims to provide a summary of the evidence on the performance of NOACs in AF patients with specific clinical characteristics. Evidence-based suggestions are presented to provide a simple and viable strategy for clinicians for the choice of a particular NOAC. KEY MESSAGE Given the different performance of the new-oral anticoagulants in patients with the different clinical situation, evidence-based choice of fitting the right new-oral anticoagulants to the patients is provided in this review article.
Text Messaging Interventions on Cancer Screening Rates: A Systematic Review

Background Despite high-quality evidence demonstrating that screening reduces mortality from breast, cervical, colorectal, and lung cancers, a substantial portion of the population remains inadequately screened. There is a critical need to identify interventions that increase the uptake and adoption of evidence-based screening guidelines for preventable cancers at the community practice level. Text messaging (short message service, SMS) has been effective in promoting behavioral change in various clinical settings, but the overall impact and reach of text messaging interventions on cancer screening are unknown. Objective The objective of this systematic review was to assess the effect of text messaging interventions on screening for breast, cervical, colorectal, and lung cancers. Methods We searched multiple databases for studies published between the years 2000 and 2017, including PubMed, EMBASE, and the Cochrane Library, to identify controlled trials that measured the effect of text messaging on screening for breast, cervical, colorectal, or lung cancers. Study quality was evaluated using the Cochrane risk of bias tool. Results Our search yielded 2238 citations, of which 31 underwent full review and 9 met inclusion criteria. Five studies examined screening for breast cancer, one for cervical cancer, and three for colorectal cancer. No studies were found for lung cancer screening. Absolute screening rates for individuals who received text message interventions were 0.6% to 15.0% higher than for controls. Unadjusted relative screening rates for text message recipients were 4% to 63% higher compared with controls. Conclusions Text messaging interventions appear to moderately increase screening rates for breast and cervical cancer and may have a small effect on colorectal cancer screening. Benefit was observed in various countries, including resource-poor and non-English-speaking populations. Given the paucity of data, additional research is needed to better quantify the effectiveness of this promising intervention.
CAAT/enhancer binding protein–homologous protein deficiency attenuates liver ischemia/reperfusion injury in mice

Ischemia/reperfusion injury (IRI) is one of the main causes of liver dysfunction after liver surgery. Involvement of endoplasmic reticulum (ER) stress in various diseases has been demonstrated, and CAAT/enhancer binding protein–homologous protein (CHOP) is a transcriptional regulator that is induced by ER stress. It is also a key regulator of ER stress‐mediated apoptosis. The aim of this study was to investigate the role of CHOP in liver IRI. Wild type (WT) and CAAT/enhancer binding protein–homologous protein knockout (CHOP–/–) mice were subjected to 70% liver warm ischemia/reperfusion for 60 minutes. At different times after reperfusion, liver tissues and blood samples were collected for evaluation. Induction of ER stress including CHOP expression was ascertained. Liver damage was evaluated based on serum liver enzymes, liver histology, and neutrophil infiltration. Hepatocyte death including apoptosis was assessed. Liver warm IRI induced ER stress in both WT and CHOP–/– mice. In addition, CHOP expression was up‐regulated in WT mice. At 6 hours after reperfusion, liver damage was attenuated in CHOP–/– mice. On the basis of terminal deoxynucleotidyl transferase–mediated deoxyuridine triphosphate nick‐end labeling staining, apoptotic and necrotic cells were significantly reduced in CHOP–/– mice. CHOP deficiency also reduced the cleavage of caspase 3 and expression of the proapoptotic protein B cell lymphoma 2–associated X protein. Liver IRI induces CHOP expression, and CHOP deficiency attenuates liver IRI by inhibiting apoptosis. Elucidation of the function of CHOP in liver IRI may contribute to further investigation for a therapy against liver IRI associated with the ER stress pathway. Liver Transplantation 24 645–654 2018 AASLD.
Prediction and Localization of Student Engagement in the Wild

Digital revolution has transformed the traditional teaching procedures, students are going online to access study materials. It is realised that analysis of student engagement in an e-learning environment would facilitate effective task accomplishment and learning. Well known social cues of engagement/disengagement can be inferred from facial expressions, body movements and gaze patterns. In this paper, student's response to various stimuli (educational videos) are recorded and cues are extracted to estimate variations in engagement level. We study the association of a subject's behavioral cues with his/her engagement level, as annotated by labelers. We have localized engaging/non-engaging parts in the stimuli videos using a deep multiple instance learning based framework, which can give useful insight into designing Massive Open Online Courses (MOOCs) video material. Recognizing the lack of any publicly available dataset in the domain of user engagement, a new ‘in the wild’ dataset is curated. The dataset: Engagement in the Wild contains 264 videos captured from 91 subjects, which is approximately 16.5 hours of recording. Detailed baseline results using different classifiers ranging from traditional machine learning to deep learning based approaches are evaluated on the database. Subject independent analysis is performed and the task of engagement prediction is modeled as a weakly supervised learning problem. The dataset is manually annotated by different labelers and the correlation studies between annotated and predicted labels of videos by different classifiers are reported. This dataset creation is an effort to facilitate research in various e-learning environments such as intelligent tutoring systems, MOOCs, and others.
Spam Detection in Social Media Employing Machine Learning Tool for Text Mining

In recent time, online social networks have been affected by various unwanted threats. Although they provided us with an open platform to share our thoughts with others, however, due to misuse of this powerful resource, general users are in endangered condition. For example, YouTube has been used as a promotional ground by various artist to upload their music videos, movie trailers, etc. and viewers can post their opinion on them. Unfortunately, often malicious users use to post phishing website links, advertisements, and fraudulent information in the comments section, which may transmit viruses or malwares. So, these harmful comments need to be identified in order to continue flawless service of social media. In this study, we have been implemented several classification algorithm to sort out the spam comments on YouTube videos from the legitimate one, their performance measures have been analysed as well as performance of ensemble classifier over single classifier algorithm in the context of text classification has also been highlighted.