Miracle-dz/UniFAR-FTUs huggingface dataset:
Altered Red Blood Cell Membrane Fatty Acid Profile in Cancer Patients

The fatty acid (FA) composition of red blood cell (RBC) membrane phospholipids of cancer patients can reflect tumor status, dietary intakes, and cancer type or therapy. However, the characteristic membrane profiles have so far not yet defined as a potential biomarker to monitor disease evolution. The present work provides the first evidence of cancer metabolic signatures affecting cell membranes that are independent of nutritional habits. From the Oncology Outpatient Unit of the Onkologikoa hospital, two groups of cancer patients (n = 54) and healthy controls (n = 37) were recruited, and mature RBCs membrane phospholipids were analyzed for FA profiling (GC-MS). Dietary habits were evaluated using a validated food frequency questionnaire. The adjusted Analysis of Covariance Test (ANCOVA) model revealed cancer patients to have a lower relative percentage of saturated fatty acids (SFA) (C16:0 (5.7%); C18:0 (15.9%)), and higher monounsaturated fatty acids (MUFA) (9c-C18:1 (12.9%) and 11c-C18:1 (54.5%)), compared to controls. In line with this, we observe that the desaturase enzymatic index (delta-9 desaturase (Δ9D), +28.3%) and the membrane saturation index (SI = SFA/MUFA; −27.3%) were similarly modulated. Polyunsaturated fatty acids (PUFA) families showed an increase of n-6 C18:2 and C20:3 (15.7% and 22.2% respectively), with no differences in n-6 C20:4 and n-3 PUFA (docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA)). Importantly, these changes were found independent of foods and fat intakes from the diet. The membrane lipid profile in RBC was useful to ascertain the presence of two main metabolic signatures of increased desaturation activity and omega-6 in cancer patients, statistically independent from dietary habits.
Multiple matrix Gaussian graphs estimation

Matrix‐valued data, where the sampling unit is a matrix consisting of rows and columns of measurements, are emerging in numerous scientific and business applications. Matrix Gaussian graphical models are a useful tool to characterize the conditional dependence structure of rows and columns. We employ non‐convex penalization to tackle the estimation of multiple graphs from matrix‐valued data under a matrix normal distribution. We propose a highly efficient non‐convex optimization algorithm that can scale up for graphs with hundreds of nodes. We establish the asymptotic properties of the estimator, which requires less stringent conditions and has a sharper probability error bound than existing results. We demonstrate the efficacy of our proposed method through both simulations and real functional magnetic resonance imaging analyses.
Beryllium and lung cancer: A weight of evidence evaluation of the toxicological and epidemiological literature

The potential carcinogenicity of beryllium has been a topic of study since the mid-1940s. Since then, numerous scientific and regulatory bodies have assigned beryllium to various categories with respect to its carcinogenicity. Past epidemiologic and animal studies, however, have been marked with notable methodological shortcomings. Because it has been about 16 yr since IARC evaluated beryllium and approximately 50 relevant papers on the topic have been published since that time, we conducted a weight-of-evidence analysis of the historical as well as recent animal and human literature. We also assessed whether recently published studies improved upon methodological shortcomings or shed light upon uncertainties in prior studies. Thirty-three animal studies, principally designed to evaluate the cancer hazard or related mechanisms, and seventeen epidemiologic studies were considered in this assessment. Based on this analysis, the evidence for carcinogenicity of beryllium is not as clear as suggested by previous evaluations, because of the inadequacy of the available smoking history information, the lack of well-characterized historical occupational exposures and shortcomings in the animal studies. We concluded that the increase in potential risk of lung cancer was observed among those exposed to very high levels of beryllium and that beryllium’s carcinogenic potential in humans at exposure levels that exist in modern industrial settings should be considered either inadequate or marginally suggestive.
Comparison of the Allergenicity and Immunogenicity of Camel and Cow’s Milk—A Study in Brown Norway Rats

Background: When breastfeeding is impossible or insufficient, the use of cow’s milk-based hypoallergenic infant formulas is an option for infants suffering from or at risk of developing cow’s milk allergy. As the Camelidae family has a large evolutionary distance to the Bovidae family and as camel milk differs from cow’s milk protein composition, there is a growing interest in investigating the suitability of camel milk as an alternative to cow’s milk-based hypoallergenic infant formulas. Methods: The aim of the study was to compare the allergenicity and immunogenicity of camel and cow’s milk as well as investigating their cross-reactivity using a Brown Norway rat model. Rats were immunised intraperitoneally with one of four products: camel milk, cow’s milk, cow’s milk casein or cow’s milk whey fraction. Immunogenicity, sensitising capacity, antibody avidity and cross-reactivity were evaluated by means of different ELISAs. The eliciting capacity was evaluated by an ear swelling test. Results: Camel and cow’s milk showed similarity in their inherent immunogenicity, sensitising and eliciting capacity. Results show that there was a lower cross-reactivity between caseins than between whey proteins from camel and cow’s milk. Conclusions: The study showed that camel and cow’s milk have a low cross-reactivity, indicating a low protein similarity. Results demonstrate that camel milk could be a promising alternative to cow’s milk-based hypoallergenic infant formulas.
Density but not climate affects the population growth rate of guanacos ( Lama guanicoe) (Artiodactyla, Camelidae)

We analyzed the effects of population density and climatic variables on the rate of population growth in the guanaco ( Lama guanicoe), a wild camelid species in South America. We used a time series of 36 years (1977-2012) of population sampling in Tierra del Fuego, Chile. Individuals were grouped in three age-classes: newborns, juveniles, and adults; for each year a female population transition matrix was constructed, and the population growth rate (λ) was estimated for each year as the matrix highest positive eigenvalue. We applied a regression analysis with finite population growth rate (λ) as dependent variable, and total guanaco population, sheep population, annual mean precipitation, and winter mean temperature as independent variables, with and without time lags. The effect of guanaco population size was statistically significant, but the effects of the sheep population and the climatic variables on guanaco population growth rate were not statistically significant.
Automatic Graph-Based Modeling of Brain Microvessels Captured With Two-Photon Microscopy

Graph models of cerebral vasculature derived from two-photon microscopy have shown to be relevant to study brain microphysiology. Automatic graphing of these microvessels remain problematic due to the vascular network complexity and two-photon sensitivity limitations with depth. In this paper, we propose a fully automatic processing pipeline to address this issue. The modeling scheme consists of a fully-convolution neural network to segment microvessels, a three-dimensional surface model generator, and a geometry contraction algorithm to produce graphical models with a single connected component. Based on a quantitative assessment using NetMets metrics, at a tolerance of 60 $\mu$m, false negative and false positive geometric error 19 rates are 3.8% and 4.2%, respectively, whereas false nega- 20 tive and false positive topological error rates are 6.1% and 4.5%, respectively. Our qualitative evaluation confirms the efficiency of our scheme in generating useful and accurate graphical models.
Role of Telomeres and Telomerase in Aging and Cancer.

UNLABELLED Telomeres progressively shorten throughout life. A hallmark of advanced malignancies is the ability for continuous cell divisions that almost universally correlates with the stabilization of telomere length by the reactivation of telomerase. The repression of telomerase and shorter telomeres in humans may have evolved, in part, as an anticancer protection mechanism. Although there is still much we do not understand about the regulation of telomerase, it remains a very attractive and novel target for cancer therapeutics. This review focuses on the current state of advances in the telomerase area, identifies outstanding questions, and addresses areas and methods that need refinement. SIGNIFICANCE Despite many recent advances, telomerase remains a challenging target for cancer therapy. There are few telomerase-directed therapies, and many of the assays used to measure telomeres and telomerase have serious limitations. This review provides an overview of the current state of the field and how recent advances could affect future research and treatment approaches. Cancer Discov; 6(6); 584-93. ©2016 AACR.
An evaluation of the sociodemographic determinants of dental anxiety in patients scheduled for intra-alveolar extraction.

Background Studies on anxiety in patients having intra-alveolar extraction as well as the effect of patient's sociodemographic characteristics influencing level of associated anxiety are few in our environment. The aim of this study was to statistically analyze the sociodemographic determinants of dental anxiety in patients scheduled for intra-alveolar extraction. Methods A cross-sectional study was conducted among 93 consecutive patients attending the outpatient clinic of the Department of Maxillofacial Surgery, University of Benin Teaching Hospital for intra-alveolar extraction in the months of November and December 2013. An interview-based questionnaire, Corah Dental Anxiety Scale Revised (DAS-R), was administered to evaluate levels of dental anxiety. Sociodemographic characteristics of the subjects were recorded. Descriptive statistics and regression models were done with the independent variables (sociodemographic factors) and the dependent variable being the DAS-R. A P<0.05 was considered significant. Results The internal consistency of the scale used as determined by Cronbach alpha was 0.76. Mean DAS score was 8.12±2.58. Dental anxiety and age of subjects showed significant inverse relationship. Females had a higher mean DAS score (8.76) than the males (7.37) (P=0.006). Residence (urban/rural) was not statistically significant. Singles reported the highest DAS score (9.41) (P=0.006). The educational level attained was significantly related to dental anxiety (P=0.005). Those with secondary school education had the highest DAS score (9.26). Class V social status had the highest mean anxiety score (P=0.012). Stepwise linear regression showed that the best predictors for dental anxiety were sex (P=0.008) and marital status (P=0.026). Conclusion This present study demonstrates that sex and marital status are the predictive factors for dental anxiety in the overall management of patients indicated for intra-alveolar extraction.
Opportunistic infections and AIDS malignancies early after initiating combination antiretroviral therapy in high-income countries

Background:There is little information on the incidence of AIDS-defining events which have been reported in the literature to be associated with immune reconstitution inflammatory syndrome (IRIS) after combined antiretroviral therapy (cART) initiation. These events include tuberculosis, mycobacterium avium complex (MAC), cytomegalovirus (CMV) retinitis, progressive multifocal leukoencephalopathy (PML), herpes simplex virus (HSV), Kaposi sarcoma, non-Hodgkin lymphoma (NHL), cryptococcosis and candidiasis. Methods:We identified individuals in the HIV-CAUSAL Collaboration, which includes data from six European countries and the US, who were HIV-positive between 1996 and 2013, antiretroviral therapy naive, aged at least 18 years, had CD4+ cell count and HIV-RNA measurements and had been AIDS-free for at least 1 month between those measurements and the start of follow-up. For each AIDS-defining event, we estimated the hazard ratio for no cART versus less than 3 and at least 3 months since cART initiation, adjusting for time-varying CD4+ cell count and HIV-RNA via inverse probability weighting. Results:Out of 96 562 eligible individuals (78% men) with median (interquantile range) follow-up of 31 [13,65] months, 55 144 initiated cART. The number of cases varied between 898 for tuberculosis and 113 for PML. Compared with non-cART initiation, the hazard ratio (95% confidence intervals) up to 3 months after cART initiation were 1.21 (0.90–1.63) for tuberculosis, 2.61 (1.05–6.49) for MAC, 1.17 (0.34–4.08) for CMV retinitis, 1.18 (0.62–2.26) for PML, 1.21 (0.83–1.75) for HSV, 1.18 (0.87–1.58) for Kaposi sarcoma, 1.56 (0.82–2.95) for NHL, 1.11 (0.56–2.18) for cryptococcosis and 0.77 (0.40–1.49) for candidiasis. Conclusion:With the potential exception of mycobacterial infections, unmasking IRIS does not appear to be a common complication of cART initiation in high-income countries.
Relationship between R1 resection, tumour rupture and recurrence in resected gastrointestinal stromal tumour

According to guidelines, adjuvant treatment or re‐excision should be considered after R1 resection of gastrointestinal stromal tumours (GISTs). However, the prognostic significance of R1 resection is uncertain and tumour rupture confounds its assessment. Here, the impact of positive margins was examined and related to rupture in a population‐based cohort.
Association of Serum Total Cholesterol with Pegylated Interferon-α Treatment in HBeAg-Positive Chronic Hepatitis B Patients

Background Recent studies suggest that serum lipids are associated with pegylated interferon-alpha (PEG-IFN-α) treatment response in chronic hepatitis C patients. However, the role of serum lipids in influencing the outcome of HBV treatment is not well understood. This study aims to investigate the association of serum lipids with the response to interferon-alpha treatment for chronic hepatitis B (CHB) patients. Methods We dynamically measured 11 clinical serum lipid parameters of 119 hepatitis B e antigen (HBeAg)-positive CHB patients, including 53 patients who achieved sustained response (SR) and 66 patients who achieved non-response (NR) induced by PEG-IFN-α treatment for 48 weeks. Results The dynamic analysis showed that the baseline serum total cholesterol (TCHO) level was higher in the NR group than that in the SR group (P=0.004). Moreover, the correlation analysis demonstrated a significant positive correlation between TCHO and hepatitis B surface antigen (HBsAg) at baseline (P=0.009). In addition, CHB patients with high baseline TCHO levels exhibited higher HBV DNA, HBsAg, HBeAg and hepatitis B e antibody (HBeAb) levels during early treatment periods (weeks 0, 4, 12 and 24) than those with the low TCHO levels. Furthermore, the logistic regression analysis identified that baseline serum TCHO was a risk factor for NR achievement (OR=4.94; P=0.047). Conclusions: Our results indicated that serum TCHO was associated with PEG-IFN-α therapeutic response in HBeAg-positive CHB patients which suggested that serum TCHO could be useful as an auxiliary clinical factor to predict poor efficacy of PEG-IFN-α therapy.
CONSORT 2010 Explanation and Elaboration: updated guidelines for reporting parallel group randomised trials

Overwhelming evidence shows the quality of reporting of randomised controlled trials (RCTs) is not optimal. Without transparent reporting, readers cannot judge the reliability and validity of trial findings nor extract information for systematic reviews. Recent methodological analyses indicate that inadequate reporting and design are associated with biased estimates of treatment effects. Such systematic error is seriously damaging to RCTs, which are considered the gold standard for evaluating interventions because of their ability to minimise or avoid bias. A group of scientists and editors developed the CONSORT (Consolidated Standards of Reporting Trials) statement to improve the quality of reporting of RCTs. It was first published in 1996 and updated in 2001. The statement consists of a checklist and flow diagram that authors can use for reporting an RCT. Many leading medical journals and major international editorial groups have endorsed the CONSORT statement. The statement facilitates critical appraisal and interpretation of RCTs. During the 2001 CONSORT revision, it became clear that explanation and elaboration of the principles underlying the CONSORT statement would help investigators and others to write or appraise trial reports. A CONSORT explanation and elaboration article was published in 2001 alongside the 2001 version of the CONSORT statement. After an expert meeting in January 2007, the CONSORT statement has been further revised and is published as the CONSORT 2010 Statement. This update improves the wording and clarity of the previous checklist and incorporates recommendations related to topics that have only recently received recognition, such as selective outcome reporting bias. This explanatory and elaboration document-intended to enhance the use, understanding, and dissemination of the CONSORT statement-has also been extensively revised. It presents the meaning and rationale for each new and updated checklist item providing examples of good reporting and, where possible, references to relevant empirical studies. Several examples of flow diagrams are included. The CONSORT 2010 Statement, this revised explanatory and elaboration document, and the associated website (www.consort-statement.org) should be helpful resources to improve reporting of randomised trials.
Mobile Phone Use and Mental Health. A Review of the Research That Takes a Psychological Perspective on Exposure

The purpose of this study was to carry out a review of observational studies that consider links between mobile phone use and mental health from a psychological or behavioral perspective. Systematic literature searches in PubMed and PsycINFO for articles published until 2017 were done. Exclusion criteria included: papers that considered radiofrequency fields, attention, safety, relational consequences, sexual behavior, cyberbullying, and reviews, qualitative, and case or experimental studies. A total of 4738 papers were screened by title and abstract, 404 were retrieved in full text, and 290 were included. Only 5% had any longitudinal design. Self-reporting was the dominating method of measurement. One third of the studies included children or youth. A majority of adult populations consisted of university students and/or self-selected participants. The main research results included associations between frequent mobile phone use and mental health outcomes, such as depressive symptoms and sleep problems. Mobile phone use at bedtime was associated with, e.g., shorter sleep duration and lower sleep quality. “Problematic use” (dependency) was associated with several negative outcomes. In conclusion, associations between mobile phone use and adverse mental health outcomes are found in studies that take a psychological or behavioral perspective on the exposure. However, more studies of high quality are needed in order to draw valid conclusions about the mechanisms and causal directions of associations.
Predictors of enacted, internal, and anticipated stigma among PLHIV in New Jersey

ABSTRACT This article describes findings from the first statewide implementation of the People Living with HIV (PLHIV) Stigma Index in the United States. The goals of the study were to identify sources of stigma and contributing factors as a means of developing stigma-reduction interventions in New Jersey. Based on a sample of 371 PLHIV, the study found high levels of internal and anticipated stigma, particularly feelings of self-blame, anger, low self-esteem, fear of gossip, and fear of lack of sexual intimacy. Forty-nine percent of participants stated that they had experienced gossip in the past year, which was the most common type of enacted stigma. Current use of antiretroviral medications was the factor most strongly associated with enacted stigma, while self-rated health had the strongest association with internal and anticipated stigma. These findings were consistent with studies implementing the Stigma Index in other countries and locations within the United States. In New Jersey, people who were unemployed or homeless and those who identified as someone diagnosed with a mental illness or as a sex worker, most frequently reported experiencing all three types of stigma. The study’s findings suggest the need to invest in interventions to address needs for job training, mental health services, and housing supports for PLHIV. One result of the study was the formation of a new advocacy group, the Coalition to End Discrimination, which seeks to develop new policies and interventions to reduce HIV-related stigma in New Jersey.
Impact of Tetracationic Calix[4]arene Conformation—from Conic Structure to Expanded Bolaform—on Their Antibacterial and Antimycobacterial Activities

The four possible conformers of a new tetrakisguanidino calix[4]arene thought to interact deleteriously with bacterial membranes have been synthesized, characterized, and evaluated for their in vitro cytotoxicity and antibacterial activity against various reference Gram‐negative and Gram‐positive bacteria, as well as Mycobacterium tuberculosis. It appears that reversal of at least one phenolic unit results in clear increases in their activities. This can be attributed to the evolution towards bolaform structures, which are able to interact more deeply with the bacterial membrane. Indeed, the 1,3‐alternate conformer 16 exhibits the best antibacterial activity (MIC<1.0 μg mL−1 on Staphylococcus aureus). Moreover, 16 displays very good antibacterial activities against an isoniazid‐resistant strain of M. tuberculosis (MIC=1.2 μg mL−1), associated with the lowest cytotoxicity, thus making it the most potent compound of the series; this could open new ways of research in the field of anti‐infective drug development to meet the huge current demand.
Network proteomics of human dermal wound healing

Objective: The healing of wounds is critical in protecting the human body against environmental factors. The mechanisms involving protein expression during this complex physiological process have not been fully elucidated. Approach: Here, we use reverse-phase protein microarrays (RPPA) involving 94 phosphoproteins to study tissue samples from tubes implanted in healing dermal wounds in seven human subjects tracked over two weeks. We compare the proteomic profiles to proteomes of controls obtained from skin biopsies from the same subjects. Main results: Compared to previous proteomic studies of wound healing, our approach focuses on wound tissue instead of wound fluid, and has the sensitivity to go beyond measuring only highly abundant proteins. To study the temporal dynamics of networks involved in wound healing, we applied two network analysis methods that integrate the experimental results with prior knowledge about protein–protein physical and regulatory interactions, as well as higher-level biological processes and associated pathways. Significance: We uncovered densely connected networks of proteins that are up- or down-regulated during human wound healing, as well as their relationships to microRNAs and to proteins outside of our set of targets that we measured with proteomic microarrays.