Miracle-dz/UniFAR-FTUs huggingface dataset:
Metals and Breast Cancer Risk: A Prospective Study Using Toenail Biomarkers.

The role of metals in breast cancer is of interest because of their carcinogenic and endocrine disrupting capabilities. Evidence from epidemiologic studies remains elusive and prior studies have not investigated metal mixtures. In a case-cohort nested within the Sister Study cohort (enrolled 2003-2009; followed through September 2017), we measured 15 metals in toenails collected at enrollment in a race-stratified sample of 1495 cases and a sub-cohort of 1605 women. We estimated hazard ratios (HRs) and 95% confidence intervals (CIs) for each metal using Cox regression and robust variance. We used quantile g-computation to estimate the joint association between multiple metals and breast cancer risk. Average follow-up was 7.5 years. There was little evidence supporting an association for individual metals and breast cancer. An exception was molybdenum, which was associated with reduced incidence of overall breast cancer risk (3rd vs. 1st tertile HR=0.82 (95% CI: 0.67, 1.00)). An inverse association for antimony was observed among non-Hispanic Black women. Pre-defined groups of metals (all, non-essential, essential, and metalloestrogens) were not strongly associated with breast cancer. This study offers little support for metals individually or as mixtures as risk factors for breast cancer. Mechanisms for inverse associations with some metals warrant further study.
Pipeline for Analyzing Activity of Metabolic Pathways in Planktonic Communities Using Metatranscriptomic Data

In this article, we present our novel pipeline for analysis of metabolic activity using a microbial community's metatranscriptome sequence data set for validation. Our method is based on expectation-maximization (EM) algorithm and provides enzyme expression and pathway activity levels. Further expanding our analysis, we consider individual enzymatic activity and compute enzyme participation coefficients to approximate the metabolic pathway activity more accurately. We apply our EM pathways pipeline to a metatranscriptomic data set of a plankton community from surface waters of the Northern Gulf of Mexico. The data set consists of RNA-seq data and respective environmental parameters, which were sampled at two depths, six times a day over multiple 24-hour cycles. Furthermore, we discuss microbial dependence on day-night cycle within our findings based on a three-way correlation of the enzyme expression during antipodal times-midnight and noon. We show that the enzyme participation levels strongly affect the metabolic activity estimates: that is, marginal and multiple linear regression of enzymatic and metabolic pathway activity correlated significantly with the recorded environmental parameters. Our analysis statistically validates that EM-based methods produce meaningful results, as our method confirms statistically significant dependence of metabolic pathway activity on the environmental parameters, such as salinity, temperature, brightness, and a few others.
Endometriosis-associated cancer

Abstract Endometriosis will affect about 10% of the female population and not only can it significantly impact adversely on quality of life and result in infertility, but data are accumulating that malignant transformation is an important consideration. Endometriosis can be histologically typical or atypical, ovarian, superficial peritoneal or deep infiltrating. The precursor for malignant transformation appears to be the ovarian atypical endometriosis component. Ovarian cancer is the most important associated cancer, primarily endometrioid and clear cell cancer. These are the only subtypes wherein a direct clonal relationship between endometriosis, as a direct precursor, and cancer has been made. There is no substantive evidence to support an altered association of borderline cancers of the ovary, serous ovarian cancers and breast, endometrial or cervical cancers. This review provides an overview of the prevailing data pertaining to the molecular and genetic aberrations that accompany the transformation of atypical endometriosis to malignancy and the accumulated epidemiologic evidence which supports the association.
Belumosudil for chronic graft-versus-host disease after 2 or more prior lines of therapy: the ROCKstar Study

Chronic graft-versus-host disease (cGVHD) is a major cause of morbidity and late mortality after allogeneic hematopoietic stem cell transplantation. Cutler and colleagues report on a randomized phase 2 clinical trial of belumosudil, an oral ROCK2 inhibitor, in 132 patients with cGVHD requiring third- or later-line therapy. They found that treatment with 200 mg of belumosudil daily induces responses in 74% of patients, including those with cGVHD refractory to steroids, ruxolitinib, and ibrutinib. These data form the basis for this agent’s recent approval by the US Food and Drug Administration.
Appropriateness of Computed Tomography Scanning in the Diagnosis of Craniosynostosis

Supplemental Digital Content is available in the text Introduction: Although physicians from a variety of specialties encounter infants with possible craniosynostosis, judicious use of computed tomography (CT) imaging is important to avoid unnecessary radiation exposure and healthcare expense. The present study seeks to determine whether differences in specialty of ordering physician affects frequency of resulting diagnostic confirmations requiring operative intervention. Methods: Radiology databases from 2 institutions were queried for CT reports or indications that included “craniosynostosis” or “plagiocephaly. ” Patient demographics, specialty of ordering physician, confirmed diagnosis, and operative interventions were recorded. Cost analysis was performed using the fixed unit cost for a head CT to calculate the expense before 1 study led to operative intervention. Results: Three hundred eighty-two patients were included. 184 (48.2%) CT scans were ordered by craniofacial surgeons, 71 (18.6%) were ordered by neurosurgeons, and 127 (33.3%) were ordered by pediatricians. One hundred four (27.2%) patients received a diagnosis of craniosynostosis requiring operative intervention. Craniofacial surgeons and neurosurgeons were more likely than pediatricians to order CT scans that resulted in a diagnosis of craniosynostosis requiring operative intervention (P < 0.001), with no difference between craniofacial surgeons and neurosurgeons (P = 1.0). The estimated cost of obtaining an impact CT scan when ordered by neurosurgeons or craniofacial surgeons as compared to pediatricians was $2369.69 versus $13,493.75. Conclusions: Clinicians who more frequently encounter craniosynostosis (craniofacial and neurosurgeons) had a higher likelihood of ordering CT images that resulted in a diagnosis of craniosynostosis requiring operative intervention. This study should prompt multi-disciplinary interventions aimed at improving evaluation of pretest probability before CT imaging.
Variable selection for a mark-specific additive hazards model using the adaptive LASSO

In HIV vaccine efficacy trials, mark-specific hazards models have important applications and can be used to evaluate the strain-specific vaccine efficacy. Additive hazards models have been widely used in practice, especially when continuous covariates are present. In this article, we conduct variable selection for a mark-specific additive hazards model. The proposed method is based on an estimating equation with the first derivative of the adaptive LASSO penalty function. The asymptotic properties of the resulting estimators are established. The finite sample behavior of the proposed estimators is evaluated through simulation studies, and an application to a dataset from the first HIV vaccine efficacy trial is provided.
Spatio-temporal Bayesian modeling of precipitation using rain gauge data from the Hubbard Brook Experimental Forest, New Hampshire, USA

Estimating precipitation volume over space and time is essential for many reasons such as evaluating air quality, determining the risk of flood and drought, making forest management decisions, and developing strategies for municipal water supplies. It is imperative to employ sound statistical methods for modeling data from a network of sparsely located rain gauges with known confidence. This paper proposes a spatiotemporal Bayesian model for estimating precipitation volumes using observations from a network of gauges. Based on Gaussian processes, the Bayesian model is able to interpolate at a high spatial resolution at each time point. Such interpolations are used to obtain various spatio-temporally aggregated statistics, such as annual precipitation volume in a local area. Markov chain Monte Carlo based model fitting, employed here, allows estimation of uncertainty that can be used in decision making. These methods are applied to a large data set of weekly precipitation volumes collected over the years 1997-2015 at the Hubbard Brook Experimental Forest (HBEF) in New Hampshire, USA. Using the proposed methodology we estimate trends in annual precipitation volumes spatially aggregated over nine gauged watersheds in the HBEF. The proposed modeling is also used to demonstrate a method for determining how to downsize a rain gauge network.
Botnet Attack Detection Using Local Global Best Bat Algorithm for Industrial Internet of Things

The need for timely identification of Distributed Denial-of-Service (DDoS) attacks in the Internet of Things (IoT) has become critical in minimizing security risks as the number of IoT devices deployed rapidly grows globally and the volume of such attacks rises to unprecedented levels. Instant detection facilitates network security by speeding up warning and disconnection from the network of infected IoT devices, thereby preventing the botnet from propagating and thereby stopping additional attacks. Several methods have been developed for detecting botnet attacks, such as Swarm Intelligence (SI) and Evolutionary Computing (EC)-based algorithms. In this study, we propose a Local-Global best Bat Algorithm for Neural Networks (LGBA-NN) to select both feature subsets and hyperparameters for efficient detection of botnet attacks, inferred from 9 commercial IoT devices infected by two botnets: Gafgyt and Mirai. The proposed Bat Algorithm (BA) adopted the local-global best-based inertia weight to update the bat’s velocity in the swarm. To tackle with swarm diversity of BA, we proposed Gaussian distribution used in the population initialization. Furthermore, the local search mechanism was followed by the Gaussian density function and local-global best function to achieve better exploration during each generation. Enhanced BA was further employed for neural network hyperparameter tuning and weight optimization to classify ten different botnet attacks with an additional one benign target class. The proposed LGBA-NN algorithm was tested on an N-BaIoT data set with extensive real traffic data with benign and malicious target classes. The performance of LGBA-NN was compared with several recent advanced approaches such as weight optimization using Particle Swarm Optimization (PSO-NN) and BA-NN. The experimental results revealed the superiority of LGBA-NN with 90% accuracy over other variants, i.e., BA-NN (85.5% accuracy) and PSO-NN (85.2% accuracy) in multi-class botnet attack detection.
Connecting the evolution of thermally pulsing asymptotic giant branch stars to the chemistry in their circumstellar envelopes – I. Hydrogen cyanide

We investigate the formation of hydrogen cyanide (HCN) in the inner circumstellar envelopes of thermally pulsing asymptotic giant branch (TP-AGB) stars. A dynamic model for periodically shocked atmospheres, which includes an extended chemo-kinetic network, is for the first time coupled to detailed evolutionary tracks for the TP-AGB phase computed with the COLIBRI code. We carried out a calibration of the main shock parameters (the shock formation radius and the effective adiabatic index) using the circumstellar HCN abundances recently measured for a populous sample of pulsating TP-AGB stars. Our models recover the range of the observed HCN concentrations as a function of the mass-loss rates, and successfully reproduce the systematic increase of HCN moving along the M-S-C chemical sequence of TP-AGB stars, that traces the increase of the surface C/O ratio. The chemical calibration brings along two important implications: i) the first shock should emerge very close to the photosphere, and ii) shocks are expected to have a dominant isothermal character in the denser region close to the star (within ~ 3-4 R), implying that radiative processes should be quite efficient. Our analysis also suggests that the HCN concentrations in the inner circumstellar envelopes are critically affected by the H-H2 chemistry during the post-shock relaxation stages.
Family‐Based Tests of Association in the Presence and Absence of Known Linkage

Correlation among sibling marker genotypes may invalidate the results of family‐based tests of association in the presence of linkage. We apply an empirical variance estimation method, which is implemented in the program package FBAT, on Caucasian families with asthma in the presence and absence of linkage and compare the results with those obtained using the TDT (TDTEX‐PAIRS) on the same data sets. Our results indicate that both tests generally perform comparably in either setting. © 2001 Wiley‐Liss, Inc.
Anxiolytic Effect of Two Tobacco Essential Oils (Nicotiana tabacum Linn.) on Mice

Tobacco (Nicotiana tabacum Linn.) is a famous traditional herb used in folk medicine. The essential oils of tobacco have been demonstrated in modern studies to possess antioxidant, anti-inflammatory, and neuroprotective properties, while its anxiolytic effect has not been reported. The purpose of this study was to evaluate the anxiolytic effect of Yunnan tobacco essential oil (YTO) and Zimbabwe tobacco essential oil (ZTO) on mice. The constituents of YTO and ZTO were analyzed by GC/MS. The anxiolytic effect of YTO and ZTO (0.1%, 1%, and 10%, v/v) on male ICR mice was evaluated in the light–dark box test (LDB) and the elevated plus maze test (EPM) test via inhalation and transdermal administration. After the behavioral tests, salivary corticosterone levels in mice were measured. The behavioral analysis showed that the administration of both YTO and ZTO elevated the time that the mice spent in the light chamber in the LDB test compared to the untreated control. In the EPM test, YTO and ZTO increased the time spent in open arms and the number of entries into the open arms. In addition, both YTO and ZTO significantly decreased salivary corticosterone levels in mice (p ≤ 0.001). In summary, our results demonstrated that inhalation and transdermal administration of both YTO and ZTO showed anxiolytic effect on male ICR mice.
Cyanide, Nitrates and Nitrite Contents of Livestock Feeds in Umuahia, Nigeria

The cyanide nitrate and nitrite contents in pig feeds from six different farms in Umuahia, Nigeria were assayed using spectrophotometric and enzymatic methods. Enzymatic analysis of the feed samples indicated mean total cyanide level of 59.30 +3.72 - 361.90 + 11.2mg -1 DM. The mean cyanide content of cyanogenic plant materials used in the feed formulation ranged from 85.60 + 13.2 - 888.10 + 23.17mgkg -1 . Observation was made that the cyanide measured in these feed samples were higher than the recommended dietary cyanogens levels for both non-ruminants and ruminants; 100mg HCN equivalent kg -1 for cassava ration. The mean levels of nitrate and nitrite ranged 25.5 + 2.76mg - 285.5 + 12.70 and 2.20 + 0.3 - 218.80 + 13.42mg kg -1 DM respectively. The toxicological and nutritional significance of the results obtained are discussed.
Model for Rolling Angle

A new method was proposed to estimate the rolling angle of a droplet on a superhydrophobic surface. Based on the relationship between the adhesion work and the force moment of the spherical droplet, a rolling angle model was established. For smooth surfaces, the equation we obtained is sin α ≥ [(4γl)/(g·δ)]·[(3π2)/(ρm2)]1/3[(1 + cos θ)2/(3 + cos θ)][(2 + cos θ)/(1 – cos θ)]2/3, and for rough surfaces, the equation is sin α ≥ [(4fγl)/(g·δ)]·[(3π2)/(ρm2)]1/3{[(1 + q cos θY)(1 + cos θ)]/(3 + cos θ)}[(2 + cos θ)/(1 – cos θ)]2/3. The relationship between the rolling angle, the contact angle, and the surface structure was investigated. The equations we obtained revealed the factors that have important influences on the rolling angle, including the surface roughness, the trapped air, the mass of droplet, and the chemical composition of the surface. The simulation results showed that the rolling angle decreases with the increases of the contact angle, the surface roughness, the proportion of trapped air, the weig.
Distributed Secure Services Based on IoT and Blockchain for e-Health Remote Care

Nowadays, the Internet of Thing (IoT) is a potentially powerful solution for eHealth applications. It is a smart technology that provides remote care in real time and requires low latency health data processing and transmission. The large number of connected objects to Cloud can be a problem for low-latency workloads, which is the case of several health mobile applications. To this end, Fog Computing, has emerged, where Cloud computing is extended to the edge of the network to reduce latency and network congestion. It provides a highly virtualized platform that provides health data storage on remote public Cloud servers to which users cannot be fully trusted, especially when we are dealing with sensitive data like health data. In fact, it becomes necessary to rethink a new more robust secure technique. To provide such technique, we proposed a new secure solution called IoToDChain for e-Health mobile application, based on cryptographic techniques especially Elliptic Curve Diffie Hellman-RSA and the Blockchain paradigm. They exchange of a secret key in confidential and robust manner and protect patients’ privacy in a mobile-Fog-Cloud environment. The experiments achieved promising results for good data protection against the most known attacks in healthcare systems.
A novel petal up-regulated PhXTH7 promoter analysis in Petunia hybrida by using bioluminescence reporter gene.

Flower opening is an important phenomenon in plant that indicates the readiness of the flower for pollination leading to petal expansion and pigmentation. This phenomenon has great impact on crop yield, which makes researches of its mechanism attractive for both plant physiology study and agriculture. Gene promoters directing the expression in petal during the petal cell wall modification and expansion when flower opens could be a convenient tool to analyze or monitor gene expression targeting this event. However, there are no reports of isolated gene promoters that can direct gene expression in petal or petal limb during the rapid cell wall dynamics when the flower opens. Xyloglucan endotransglucosylase/hydrolase 7 (XTH7), a cell wall modifying enzyme, was reported having up-regulated gene expression in the petal of Arabidopsis thaliana and Petunia hybrida. In this study, we fused a 1,904 bp length P. hybrida XTH7 promoter with a gene encoding a bright bioluminescent protein (Green enhanced Nano-lantern) to report gene expression and observed petal up-regulated bioluminescence activity by means of a consumer-grade camera. More importantly, this novel promoter demonstrated up-regulated activity in the petal limb of P. hybrida matured flower during flower opening. P. hybrida XTH7 promoter would be a useful tool for flowering study, especially for petal expansion research during flower opening.
Prevalence of POC5 Coding Variants in French-Canadian and British AIS Cohort

Adolescent idiopathic scoliosis (AIS) is a complex common disorder of multifactorial etiology defined by a deviation of the spine in three dimensions that affects approximately 2% to 4% of adolescents. Risk factors include other affected family members, suggesting a genetic component to the disease. The POC5 gene was identified as one of the first ciliary candidate genes for AIS, as three variants were identified in large families with multiple members affected with idiopathic scoliosis. To assess the prevalence of p.(A429V), p.(A446T), and p.(A455P) POC5 variants in patients with AIS, we used next-generation sequencing in our cohort of French-Canadian and British families and sporadic cases. Our study highlighted a prevalence of 13% for POC5 variants, 7.5% for p.(A429V), and 6.4% for p.(A446T). These results suggest a higher prevalence of the aforementioned POC5 coding variants in patients with AIS compared to the general population.
Optimization of Protein Isolation and Label-Free Quantitative Proteomic Analysis in Four Different Tissues of Korean Ginseng

Korean ginseng is one of the most valuable medicinal plants worldwide. However, our understanding of ginseng proteomics is largely limited due to difficulties in the extraction and resolution of ginseng proteins because of the presence of natural contaminants such as polysaccharides, phenols, and glycosides. Here, we compared four different protein extraction methods, namely, TCA/acetone, TCA/acetone–MeOH/chloroform, phenol–TCA/acetone, and phenol–MeOH/chloroform methods. The TCA/acetone–MeOH/chloroform method displayed the highest extraction efficiency, and thus it was used for the comparative proteome profiling of leaf, root, shoot, and fruit by a label-free quantitative proteomics approach. This approach led to the identification of 2604 significantly modulated proteins among four tissues. We could pinpoint differential pathways and proteins associated with ginsenoside biosynthesis, including the methylerythritol 4–phosphate (MEP) pathway, the mevalonate (MVA) pathway, UDP-glycosyltransferases (UGTs), and oxidoreductases (CYP450s). The current study reports an efficient and reproducible method for the isolation of proteins from a wide range of ginseng tissues and provides a detailed organ-based proteome map and a more comprehensive view of enzymatic alterations in ginsenoside biosynthesis.
Multi-technique characterization of various artefacts and raw materials from Old

A multitechnique (SEM-EDX, XRD, TGA) characterization was performed on several materials and artefacts from Old Nisa excavated during the recent Italian-Turkmen archaeological expedition, which involved a large building in the SW corner of the citadel, formed by rooms utilized as warehouses and workshops. Polygenic conglomerates archaeologically classified as anhydrites were examined and proved to be highly compatible with all the studied architectural artefacts (a plaster, a mortar, and a mould), making strongly plausible their identification as raw materials. Besides, several pigments at different stages of the manufacturing process were examined. A very complex situation emerged, suggesting the existence of different productive processes. At last, a black cylindrical object, identified as a seal, but almost completely devoid of engravings, turned out to be made of graphite and obtained by turning. The results of the analyses on these materials shed a new light on the complexity of the manufaturing processes carried out in Old Nisa in connection with the production of decorative elements for the monumental complex located inside the citadel.