Miracle-dz/UniFAR-FTUs huggingface dataset:
ChEA: transcription factor regulation inferred from integrating genome-wide ChIP-X experiments

MOTIVATION Experiments such as ChIP-chip, ChIP-seq, ChIP-PET and DamID (the four methods referred herein as ChIP-X) are used to profile the binding of transcription factors to DNA at a genome-wide scale. Such experiments provide hundreds to thousands of potential binding sites for a given transcription factor in proximity to gene coding regions. RESULTS In order to integrate data from such studies and utilize it for further biological discovery, we collected interactions from such experiments to construct a mammalian ChIP-X database. The database contains 189,933 interactions, manually extracted from 87 publications, describing the binding of 92 transcription factors to 31,932 target genes. We used the database to analyze mRNA expression data where we perform gene-list enrichment analysis using the ChIP-X database as the prior biological knowledge gene-list library. The system is delivered as a web-based interactive application called ChIP Enrichment Analysis (ChEA). With ChEA, users can input lists of mammalian gene symbols for which the program computes over-representation of transcription factor targets from the ChIP-X database. The ChEA database allowed us to reconstruct an initial network of transcription factors connected based on shared overlapping targets and binding site proximity. To demonstrate the utility of ChEA we present three case studies. We show how by combining the Connectivity Map (CMAP) with ChEA, we can rank pairs of compounds to be used to target specific transcription factor activity in cancer cells. AVAILABILITY The ChEA software and ChIP-X database is freely available online at: http://amp.pharm. mssm.edu/lib/chea.jsp.
Resolving the Taxonomic Status of Chamelea gallina and C. striatula (Veneridae, Bivalvia): A Combined Molecular Cytogenetic and Phylogenetic Approach

The striped venus clams Chamelea gallina and C. striatula are commercially important bivalves inhabiting European and North African coastal waters. The taxonomic status of these taxa has been the subject of debate for decades. In order to elucidate this issue, we generated 5S and 28S ribosomal RNA and H3 histone gene probes and mapped them by fluorescent in situ hybridization to the chromosomes of morphologically identified striped venus clams, collected from four geographically distant Atlantic and Mediterranean populations. The nucleotide variation at the three DNA markers, that is, the nuclear internal transcribed spacer 2 (ITS2), the mitochondrial cytochrome c oxidase subunit I (COI), and the large ribosomal subunit rRNA (16S) fragments, was also studied and the resultant phylogenetic trees were evaluated. Striking differences in both the chromosome distribution of these genes and the clustering of the samples on the phylogenetic trees observed provide clear evidence that C. gallina and C. striatula are separated species.
Incidence and Predictors of Nonalcoholic Fatty Liver Disease by Serum Biomarkers in Patients with Inflammatory Bowel Disease

Background:Patients with inflammatory bowel disease (IBD) are at high risk for non-alcoholic fatty liver disease (NAFLD). Longitudinal data on incident NAFLD are lacking. We employed non-invasive methods to study incidence and predictors of NAFLD. Methods:This was a retrospective study of IBD patients without known liver disease followed at IBD clinic of McGill University. NAFLD was defined as Hepatic Steatosis Index (HSI) ≥36 and absence of alcohol intake. Advanced liver fibrosis was diagnosed by FIB-4 ≥2.67. Active IBD was defined as partial Mayo score ≥3 for ulcerative colitis, Harvey Bradshaw Index ≥ 5 or flare during follow-up. Kaplan-Meier and Cox regression analyses were used to investigate incidence and predictors of NAFLD development. Results:Three hundred twenty-one consecutive patients (median age 33.7 yr, 47% males) were observed for a median of 3.2 years (interquartile range 1.5–6). Over 1181.2 persons-year (PY), 108 (33.6%) patients developed NAFLD, accounting for an incidence rate of 9.1/100 PY (95% confidence interval [CI], 7.4–10.9). 7 (2.2%) patients developed advanced liver fibrosis, accounting for an incidence rate of 0.5/100 PY (95% CI, 0.2–1.1). Development of NAFLD was predicted by disease activity (adjusted hazard ratio [aHR] = 1.58; 95% CI, 1.08–2.33, P = 0.02), disease duration (aHR = 1.12; 95% CI, 1.03–1.23, P = 0.01), and prior surgery for IBD (aHR = 1.34; 95% CI, 1.04–1.74, P = 0.02). Conclusions:NAFLD is a frequent comorbidity in patients with IBD. These patients can also develop advanced liver fibrosis. Disease activity, duration of IBD and prior surgery are predictors of NAFLD development. This should represent one more incentive to achieve and maintain early clinical remission. Further prospective studies are of interest.
Family caregiving of individuals with traumatic brain injury in Botswana

Abstract Background The impairments that affect survivors of TBI impact the person’s independence, and family members frequently have to take on a caregiver role. This study examined the experience of caregiving for individuals with TBI in Botswana and its impact on psychological distress in caregivers. Methods Using a mixed methods study design, qualitative data from semi-structured interviews were thematically analyzed and triangulated with data regarding functional status from the Structured Head Injury Outcome Questionnaire and the Hospital Anxiety and Depression Scale (HADS). Results The study included 26 participants with moderate to severe TBI, and a total of 18 caregivers were recruited. Caregivers commonly reported receiving limited information regarding their relatives’ injuries and management methods. Heavy caregiving demands were placed on them, with little support from the healthcare system. A significant proportion of caregivers experienced anxiety and depression, which was associated with lower functional independence in their injured relative. Somewhat more spouses than parents reported clinically significant anxiety levels. Other consequences of caregiving included social isolation and limited support from the wider community as well as financial difficulties. Despite these stresses caregivers tended to accept their caregiving role. Cultural factors such devotion to their families and faith and belief in God moderated burden and distress. Conclusions Carers of individuals with TBI in Botswana face significant challenges. Rehabilitation efforts need to take these into account. Specifically, more information and support needs to be provided to survivors and their families. Psychological, economic and health needs of the care providers also should be addressed in the planning of rehabilitation interventions. Implications for Rehabilitation Caregivers of individuals with TBI in under-resourced countries carry much of the burden of care, face many challenges and experience significant stress. More information and support needs to be provided to survivors of TBI and their families in countries such as Botswana in a culturally sensitive manner. Psychological, economic and health needs also need to be addressed in the planning of rehabilitation interventions, which are currently non-existent in Botswana.
The progress and potential of proteomic biomarkers for type 1 diabetes in children

ABSTRACT Introduction: Although it is possible to identify the genetic risk for type 1 diabetes (T1D), it is not possible to predict who will develop the disease. New biomarkers are needed that would help understand the mechanisms of disease onset and when to administer targeted therapies and interventions. Areas covered: An overview is presented of international study efforts towards understanding the cause of T1D, including the collection of several extensive temporal sample series that follow the development of T1D in at risk children. The results of the proteomics analysis of these materials are presented, which have included bodily fluids, such as serum or plasma and urine, as well as tissue samples from the pancreas. Expert commentary: Promising recent reports have indicated detection of early proteomic changes in the serum of patients prior to diagnosis, potentially providing new measures for risk assessment. Similarly, there has been evidence that post-translational modification (PTM) may result in the recognition of islet cell proteins as autoantigens; modified proteins could thus be used as targets for immunomodulation to overcome the threat of the autoimmune response.
Randomized Trial of Interventions for Smoking Cessation Among Medicaid Beneficiaries With Mental Illness.

OBJECTIVE Medicaid beneficiaries with severe mental illnesses are a financially disadvantaged group with high rates of smoking and poor cessation outcomes. This study examined whether abstinence-contingent monetary incentives improved outcomes when added to cessation treatments at community mental health centers: prescriber visit for pharmacotherapy only (PV only), prescriber visit and facilitated quitline (PV+Q), and prescriber visit and telephone cognitive-behavioral therapy (PV+CBT). METHODS During 2012-2015, a total of 1,468 adult, daily smoking Medicaid beneficiaries with mental illnesses received Web-based motivational tobacco education. Eligible participants who wanted cessation treatment (N=661) were randomly assigned to treatment with or without abstinence-contingent incentives for four weeks after a quit attempt and assessed for biologically verified abstinence at three, six, nine, and 12 months. To examine intervention effect on abstinence over time, logistic generalized linear models estimated with generalized estimating equations were used, with missing observations imputed as smoking. RESULTS Participants included smokers with schizophrenia disorders (N=148), bipolar disorder (N=150), major depressive disorder (N=158), and anxiety and other disorders (N=205). There was no significant effect of intervention (PV only, PV+Q, and PV+CBT). However, participants who received monetary incentives were more likely to be abstinent from smoking over time (adjusted odds ratio [AOR]=1.77, p=.009). Post hoc comparisons indicated greater abstinence at 12 months in PV+Q with incentives than in PV+Q without incentives (14% versus 4% abstinent, AOR=3.94, p=.014). Treatment participation and cessation outcomes did not differ significantly between diagnostic groups. CONCLUSIONS Abstinence-contingent incentives improved cessation outcomes among financially disadvantaged smokers with mental illness receiving tobacco treatment at community mental health centers.
Ieee Projects 100% Working Code + Documentation+ Explaination – Best Price a Novel Sensory Data Processing Framework to Integrate Sensor Networks with Mobile Cloud

Taking advantage of the data gathering capability of wireless sensor networks (WSNs) as well as the data storage and processing ability of mobile cloud computing (MCC), WSN–MCC integration is attracting significant attention from both academia and industry. This paper focuses on processing of the sensory data in WSN–MCC integration, by identifying the critical issues concerning WSN– MCC integration and proposing a novel sensory data processing framework, which aims at transmitting desirable sensory data to the mobile users in a fast, reliable, and secure manner. The proposed framework could prolong the WSN lifetime, decrease the storage requirements of the sensors and the WSN gateway, and reduce the traffic load and bandwidth requirement of sensory data transmissions. In addition, the framework is capable of monitoring and predicting the future trend of the sensory data traffic, as well as improving its security. The framework further decreases the storage and processing overhead of the cloud, while enabling mobile users to securely obtain their desired sensory data faster. Analytical and experimental results are presented to demonstrate the effectiveness of the proposed framework.
An Introduction to Programming for Bioscientists: A Python-Based Primer

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in molecular biology, biochemistry, and other biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language’s usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a “variable,” the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.
The role of dietary coconut for the prevention and treatment of Alzheimer's disease: potential mechanisms of action

Coconut, Cocos nucifera L. , is a tree that is cultivated to provide a large number of products, although it is mainly grown for its nutritional and medicinal values. Coconut oil, derived from the coconut fruit, has been recognised historically as containing high levels of saturated fat; however, closer scrutiny suggests that coconut should be regarded more favourably. Unlike most other dietary fats that are high in long-chain fatty acids, coconut oil comprises medium-chain fatty acids (MCFA). MCFA are unique in that they are easily absorbed and metabolised by the liver, and can be converted to ketones. Ketone bodies are an important alternative energy source in the brain, and may be beneficial to people developing or already with memory impairment, as in Alzheimer's disease (AD). Coconut is classified as a highly nutritious ‘functional food’. It is rich in dietary fibre, vitamins and minerals; however, notably, evidence is mounting to support the concept that coconut may be beneficial in the treatment of obesity, dyslipidaemia, elevated LDL, insulin resistance and hypertension – these are the risk factors for CVD and type 2 diabetes, and also for AD. In addition, phenolic compounds and hormones (cytokinins) found in coconut may assist in preventing the aggregation of amyloid-β peptide, potentially inhibiting a key step in the pathogenesis of AD. The purpose of the present review was to explore the literature related to coconut, outlining the known mechanistic physiology, and to discuss the potential role of coconut supplementation as a therapeutic option in the prevention and management of AD.
Variation in body temperature response of naked neck and normally feathered chickens to heat stress.

Abstract The effect of the naked neck (Na) gene on basal body temperature (BT) in a 21 C (control) or in a 32 C (chronic heat stress) environment and on change in BT when exposed to acute heat stress conditions (40.5 C) was examined in small and large BW populations. Birds grown at 32 C had a significantly lower basal BT, 8-wk BW, and a significantly smaller change in BT when exposed to 40.5 C than birds grown in 21 C. The small BW birds had a higher basal BT and a smaller change in BT when exposed to acute heat stress than large BW birds. There was no difference in basal BT between naked neck and normal birds in either the small BW (Athens-Canadian randombred) population, or in the large BW broiler population. The Na/Na birds in the small BW population had a significantly greater change in BT when exposed to acute heat stress than Na/na or na/na birds, but no differences were seen among genotypes in the large BW population. In the 21 C environment, naked neck birds seemed to have a greater change in BT than normal birds when exposed to 40.5 C. The difference in BT change was significant in the large BW population but was not significant in the small BW population. Few significant correlations were found between basal BT and 8-wk BW or between change in BT and 8-wk BW. A consistent negative correlation was found between basal BT and change in BT for both populations.
The effect of various aluminum compounds on chick performance.

Abstract ALUMINUM is usually present in most types of animal diets. The phosphate supplement can be a primary contributor of this element because the aluminum content of different sources may vary from trace amounts to as much as 3.5%. Some of the other dietary ingredients also contain aluminum (Williams et al., 1942). Cox et al. (1931), Deobald and Elvehjem (1935), Insko et al. (1938) and Street (1942) reported on the adverse effects of aluminum to various types of animals. The cause of this effect probably originates in the digestive tract because little, if any, aluminum is absorbed (McCollum et al., 1928; MacKenzie, 1931). It has been attributed to the interference with phosphorus absorption by the formation of insoluble aluminum phosphate. This appears to be a logical explanation because Jones (1938) found that aluminum sulfate decreased serum phosphatase and bone mineral. This report describes experiments studying the effects of various aluminum compounds .
Neighborhood change and the role of environmental stewardship: a case study of green infrastructure for stormwater in the City of Portland, Oregon, USA

Throughout the history of cities, the ecological landscape has often been buried, removed, or taken for granted. A recent recognition that humans are part of the global ecosystem, and that human actions both cause and are affected by ecological change, brings with it an awareness of the value of nature in cities and of natural systems on which cities depend. The feedbacks between humans and their environment within an urban context can have profound implications for the growth of and change in cities, yet there is a limited understanding of the interactions between biophysical changes in cities and the implications of these changes on the quality of life for residents. The application of a coupled human and natural systems (CHANS) framework provides a timely and fruitful opportunity to enrich the theory, methods, and understanding of these feedbacks and interconnections. Here, I integrated biophysical and social dimensions relevant to managing urban stormwater by examining a case study of Portland, Oregon, USA. I used empirical data from a pre-post survey (2-yr span) of residents in eight urban neighborhoods to describe feedbacks and interactions between a localized biophysical change in the form of a large-scale decentralized stormwater program and the resulting changes in resident’s perceptions in neighborhoods undergoing rapid change. My findings corroborate earlier findings suggesting that people with higher income and education levels are more likely to participate in stewardship actions. The results also suggest an overall and initial negative perception of neighborhoods facilities and services immediately following the construction of decentralized stormwater facilities, but conversely, high levels of anticipation for their construction. By describing these findings through a CHANS framework, I make explicit the importance of integrating scientific understanding, governance efforts, and human behaviors to address acute urban environmental challenges.
A Benamou-Brenier Approach to Branched Transport

The problem of branched transportation aims to describe the movement of masses when, due to concavity effects, they have the interest to travel together as much as possible, because the cost for a path of length l covered by a mass m is proportional to a concave power m^a l. The optimization of this criterion let branched structures appear and is suitable to applications like road systems, blood vessels, river networks\dots Several models have been employed in the literature to present this transport problem, and the present paper looks at a dynamical one, similar to the celebrated Benamou-Brenier formulation of Kantorovitch optimal transport. The movement is represented by a path of probabilities, satisfying the continuity equation together with a velocity field v. The transportation cost to be minimized is non-convex and finite only on atomic measures.
The Normalization of Cannabis Use Among Bangladeshi and Pakistani Youth: A New Frontier for the Normalization Thesis?

ABSTRACT Background: The Asian population in Britain has grown, representing the second largest ethnic group; Bangladeshi, Pakistani, and Indian nationalities are prevalent (Jivraj, 2012; Office for National Statistics, 2013). Yet, we know relatively little about the nature and extent of their substance use. Jayakody et al. (2006) argue ethnic minority groups may be influenced by the norms and values of the dominant culture. Given recreational drug use has undergone a process of normalization in Britain (Aldridge et al., 2011; Parker et al., 1998, 2002), we explore the degree to which this is occurring in a Bangladeshi and Pakistani community of Muslim faith in Northern England; a group typically assumed to reject substance use because of robust religious and cultural values. Objectives: To examine the extent, frequency, and nature of substance use, and associated attitudes. Methods: A cross-sectional study collecting qualitative data from a sample (N = 43) of adolescents accessing a drug service and a range of professionals working with them during 2014. We also present analyses of routinely collected quantitative client data. Results: Adolescent interviewees reported extensive personal experience smoking skunk cannabis, and professionals working in the community confirmed many young Asians smoked it. Its consumption appeared to be accommodated into the daily lives of young people and the supply of it also showed signs of acceptance. Conclusions: Skunk cannabis may be undergoing a process of normalization within some Asian communities in Britain. Our study has significant implications for the normalization thesis, finding evidence for normalization within a subpopulation that is typically perceived to resist this trend.
A regularized sequential dictionary learning algorithm for fmri data analysis

Sequential dictionary learning algorithms have been successfully applied to a number of image processing problems. In a number of these problems however, the data used for dictionary learning are structured matrices with notions of smoothness in the column direction. This prior information which can be traduced as a smoothness constraint on the learned dictionary atoms has not been included in existing dictionary learning algorithms. In this paper, we remedy to this situation by proposing a regularized sequential dictionary learning algorithm. The proposed algorithm differs from the existing ones in their dictionary update stage. The proposed algorithm generates smooth dictionary atoms via the solution of a regularized rank-one matrix approximation problem where regularization is introduced via penalization in the dictionary update stage. Experimental results on synthetic and real data illustrating the performance of the proposed algorithm are provided.