Miracle-dz/UniFAR-FTUs huggingface dataset:
Common Genetic Variation and Breast Cancer Risk—Past, Present, and Future

Breast cancer is the most common cancer among women in the United States, with up to 30% of those diagnosed displaying a family history of breast cancer. To date, 18% of the familial risk of breast cancer can be explained by SNPs. This review summarizes the discovery of risk-associated SNPs using candidate gene and genome-wide association studies (GWAS), including discovery and replication in large collaborative efforts such as The Collaborative Oncologic Gene-environment Study and OncoArray. We discuss the evolution of GWAS studies, efforts to discover additional SNPs, and methods for identifying causal variants. We summarize findings associated with overall breast cancer, pathologic subtypes, and mutation carriers (BRCA1, BRCA2, and CHEK2). In addition, we summarize the development of polygenic risk scores (PRS) using the risk-associated SNPs and show how PRS can contribute to estimation of individual risks for developing breast cancer. Cancer Epidemiol Biomarkers Prev; 27(4); 380–94. ©2018 AACR. See all articles in this CEBP Focus section, “Genome-Wide Association Studies in Cancer. ”
The Effect of HIV-Hepatitis C Co-Infection on Bone Mineral Density and Fracture: A Meta-Analysis

Objective There is a variable body of evidence on adverse bone outcomes in HIV patients co-infected with hepatitis C virus (HCV). We examined the association of HIV/HCV co-infection on osteoporosis or osteopenia (reduced bone mineral density; BMD) and fracture. Design Systematic review and random effects meta-analyses. Methods A systematic literature search was conducted for articles published in English up to 1 April 2013. All studies reporting either BMD (g/cm2, or as a T-score) or incident fractures in HIV/HCV co-infected patients compared to either HIV mono-infected or HIV/HCV uninfected/seronegative controls were included. Random effects meta-analyses estimated the pooled odds ratio (OR) and the relative risk (RR) and associated 95% confidence intervals (CI). Results Thirteen eligible publications (BMD N = 6; Fracture = 7) of 2,064 identified were included with a total of 427,352 subjects. No publications reported data on HCV mono-infected controls. Meta-analysis of cross-sectional studies confirmed that low bone mineral density was increasingly prevalent among co-infected patients compared to HIV mono-infected controls (pooled OR 1.98, 95% CI 1.18, 3.31) but not those uninfected (pooled OR 1.47, 95% CI 0.78, 2.78). Significant association between co-infection and fracture was found compared to HIV mono-infected from cohort and case-control studies (pooled RR 1.57, 95% CI 1.33, 1.86) and compared to HIV/HCV uninfected from cohort (pooled RR 2.46, 95% CI 1.03, 3.88) and cross-sectional studies (pooled OR 2.30, 95% CI 2.09, 2.23). Conclusions The associations of co-infection with prevalent low BMD and risk of fracture are confirmed in this meta-analysis. Although the mechanisms of HIV/HCV co-infection’s effect on BMD and fracture are not well understood, there is evidence to suggest that adverse outcomes among HIV/HCV co-infected patients are substantial.
Inherited Inflammatory Response Genes Are Associated with B-Cell Non-Hodgkin’s Lymphoma Risk and Survival

Background Malignant B-cell clones are affected by both acquired genetic alterations and by inherited genetic variations changing the inflammatory tumour microenvironment. Methods We investigated 50 inflammatory response gene polymorphisms in 355 B-cell non-Hodgkin’s lymphoma (B-NHL) samples encompassing 216 diffuse large B cell lymphoma (DLBCL) and 139 follicular lymphoma (FL) and 307 controls. The effect of single genes and haplotypes were investigated and gene-expression analysis was applied for selected genes. Since interaction between risk genes can have a large impact on phenotype, two-way gene-gene interaction analysis was included. Results We found inherited SNPs in genes critical for inflammatory pathways; TLR9, IL4, TAP2, IL2RA, FCGR2A, TNFA, IL10RB, GALNT12, IL12A and IL1B were significantly associated with disease risk and SELE, IL1RN, TNFA, TAP2, MBL2, IL5, CX3CR1, CHI3L1 and IL12A were, associated with overall survival (OS) in specific diagnostic entities of B-NHL. We discovered noteworthy interactions between DLBCL risk alleles on IL10 and IL4RA and FL risk alleles on IL4RA and IL4. In relation to OS, a highly significant interaction was observed in DLBCL for IL4RA (rs1805010) * IL10 (rs1800890) (HR = 0.11 (0.02–0.50)). Finally, we explored the expression of risk genes from the gene-gene interaction analysis in normal B-cell subtypes showing a different expression of IL4RA, IL10, IL10RB genes supporting a pathogenetic effect of these interactions in the germinal center. Conclusions The present findings support the importance of inflammatory genes in B-cell lymphomas. We found association between polymorphic sites in inflammatory response genes and risk as well as outcome in B-NHL and suggest an effect of gene-gene interactions during the stepwise oncogenesis.
Activity Enjoyment, Not Frequency, Is Associated With Alcohol-Related Problems and Heavy Episodic Drinking

Depression and alcohol use disorder (AUD) commonly co-occur, and this comorbidity is associated with greater impairment and higher likelihood of relapse compared to either disorder alone. Identifying shared vulnerability across depression and AUD may aid in developing more parsimonious treatment approaches. Low levels of positive reinforcement for healthy behaviors have been implicated as a shared vulnerability across both depression and AUD. However, prior research in this area has largely been conducted among college students and has rarely examined depression and AUD symptoms together. This study aims to extend prior literature by examining the association between both the frequency and enjoyment of activities and AUD symptoms in a national sample of adults (n = 609) while also accounting for depressive symptoms. Study results indicated that low levels of enjoyment were associated with greater alcohol-related problems and frequency of heavy episodic drinking, above and beyond depressive symptoms. The frequency of potentially pleasurable activities was unrelated to alcohol-related problems or heavy episodic drinking. Findings extend prior literature by providing evidence for the association between enjoyment of activities and alcohol use, above and beyond depressive symptoms, among a national sample of adults. These results suggest that prioritizing enjoyment of activities, rather than frequency, may be important for behavioral intervention efforts to address heavy drinking and associated problems. Future longitudinal research using observational methods of behavior is needed to identify causal relationships between activity enjoyment and AUD symptoms.
Effect of the spinal apelin-APJ system on the pathogenesis of chronic constriction injury-induced neuropathic pain in rats

Apelin is hypothesized to serve a dual function in pain processing. Spinal administration of apelin induces hyperalgesia, while opioid receptors are implicated in the antinociceptive effects of apelin in acute nociceptive models. However, whether the apelin-apelin receptor (APJ) system is involved in neuropathic pain remains to be elucidated. The present study aimed to evaluate the impact and mechanism of the spinal apelin-APJ system in neuropathic pain. Chronic constriction injury (CCI) of the sciatic nerve produced sustained spinal apelin and APJ upregulation, which was associated with mechanical allodynia and heat hyperalgesia development in the hind-paw plantar surface. Immunofluorescence demonstrated that apelin and APJ were localized to the superficial dorsal horns. In order to further clarify the function of the apelin-APJ system, a single intrathecal administration of ML221, an APJ antagonist, was used; this transiently reduced CCI-induced pain hypersensitivity. However, apelin-13 (the isoform which binds most strongly to APJ) exhibited no effect on the nociceptive response, suggesting an essential role for the spinal apelin-APJ system in neuropathic pain sensitization. The present study demonstrated that a single application of ML221 alleviated mechanical allodynia and heat hyperalgesia 7 days following CCI, in a dose-dependent manner. Intraspinal delivery of ML221, at the onset of and in fully-established neuropathic pain, persistently attenuated CCI-induced pain hypersensitivity, indicating that the apelin-APJ system was involved in initiating and maintaining pain. It was demonstrated, using immunoblotting, that intrathecal ML221 downregulated phosphorylated extracellular signal-related kinase (ERK) in the rat spinal cord dorsal horn, suggesting that the effect of apelin on neuropathic pain may be mediated via ERK signaling. The results of the present study suggested that the spinal apelin-APJ system may drive neuropathic pain. Inhibition of APJ may provide novel pharmacological interventions for neuropathic pain.
INFLUENCE OF SILICEOUS AND CALCAREOUS FLY-ASHES ON PROPERTIES OF CEMENT MORTARS

Care of the environment in accordance with the principles of sustainable development introduces the possibility and need for waste recycling. Construction and building industries have the greatest potential for reuse of waste. The article presents the results of investigations of cement mortars – tests of compressive and tensile strength after 28 and 56 days of curing – for normative mortars and mortars containing fly ashes – calcareous and siliceous ash – in their composition. To make the samples, the Portland cement CEM I 32,5 R, 42,5R and natural aggregate with graining of 0–2 mm were used. Concrete with siliceous and calcareous admixtures was made in six lots where the ash was added in the quantity of 2%, 5%, 10% of the cement mass or the 2%, 5%, 10% of cement was replaced by ashes. After the tests, it was stated that the siliceous fly-ash admixture increases the compressive and bending strength in comparison to the mortars with the calcareous ash admixtures.
EPuL: An Enhanced Positive-Unlabeled Learning Algorithm for the Prediction of Pupylation Sites

Protein pupylation is a type of post-translation modification, which plays a crucial role in cellular function of bacterial organisms in prokaryotes. To have a better insight of the mechanisms underlying pupylation an initial, but important, step is to identify pupylation sites. To date, several computational methods have been established for the prediction of pupylation sites which usually artificially design the negative samples using the verified pupylation proteins to train the classifiers. However, if this process is not properly done it can affect the performance of the final predictor dramatically. In this work, different from previous computational methods, we proposed an enhanced positive-unlabeled learning algorithm (EPuL) to the pupylation site prediction problem, which uses only positive and unlabeled samples. Firstly, we separate the training dataset into the positive dataset and the unlabeled dataset which contains the remaining non-annotated lysine residues. Then, the EPuL algorithm is utilized to select the reliably negative initial dataset and then iteratively pick out the non-pupylation sites. The performance of the proposed method was measured with an accuracy of 90.24%, an Area Under Curve (AUC) of 0.93 and an MCC of 0.81 by 10-fold cross-validation. A user-friendly web server for predicting pupylation sites was developed and was freely available at http://59.73. 198.144:8080/EPuL.
Identification of the miRNA-mRNA regulatory network of small cell osteosarcoma based on RNA-seq

Small cell osteosarcoma (SCO) is a rare subtype of osteosarcoma characterized by highly aggressive progression and a poor prognosis. The miRNA and mRNA expression profiles of peripheral blood mononuclear cells (PBMCs) were obtained in 3 patients with SCO and 10 healthy individuals using high-throughput RNA-sequencing. We identified 37 dysregulated miRNAs and 1636 dysregulated mRNAs in patients with SCO compared to the healthy controls. Specifically, the 37 dysregulated miRNAs consisted of 27 up-regulated miRNAs and 10 down-regulated miRNAs; the 1636 dysregulated mRNAs consisted of 555 up-regulated mRNAs and 1081 down-regulated mRNAs. The target-genes of miRNAs were predicted, and 1334 negative correlations between miRNAs and mRNAs were used to construct an miRNA-mRNA regulatory network. Dysregulated genes were significantly enriched in pathways related to cancer, mTOR signaling and cell cycle signaling. Specifically, hsa-miR-26b-5p, hsa-miR-221-3p and hsa-miR-125b-2-3p were significantly dysregulated miRNAs and exhibited a high degree of connectivity with target genes. Overall, the expression of dysregulated genes in tumor tissues and peripheral blood samples of patients with SCO measured by quantitative real-time polymerase chain reaction corroborated with our bioinformatics analyses based on the expression profiles of PBMCs from patients with SCO. Thus, hsa-miR-26b-5p, hsa-miR-221-3p and hsa-miR-125b-2-3p may be involved in SCO tumorigenesis.
The bidirectional association between oral cancer and esophageal cancer: A population-based study in Taiwan over a 28-year period

Previous studies have revealed that patients with oral or esophageal cancer are at higher risk for subsequently developing a second primary malignancy. However, it remains to be determined what association exists between oral cancer and esophageal cancer particularly in Asian countries where squamous cell carcinoma is the predominant type of esophageal cancer. A population-based study was carried out in Taiwan, where the incidence rates of both oral and esophageal squamous cell carcinomas are high, to test the hypothesis that oral cancer or esophageal cancer predisposes an individual to developing the other form of cancer. Our results showed that patients with primary oral cancer (n=45,859) had ten times the risk of second esophageal cancer compared to the general population. Within the same cohort, the reciprocal risk of oral cancer as a second primary in primary esophageal cancer patients (n=16,658) was also increased seven-fold. The bidirectional relationship suggests common risk factors between these two cancers. The present study is not only the first population-based study in Asia to validate the reciprocal relationship between oral and esophageal squamous cell carcinomas, but also will aid in the appropriate selection of high-risk patients for a future follow-up surveillance program.
The Dynamics of a Metapopulation: Changes in Life-History Traits in Resident Herring that Co-Occur with Oceanic Herring during Spawning

Different populations of Atlantic herring are regarded as forming a metapopulation, but we know little about the dynamics of the connectivity and degree of interbreeding between the populations. Based on data from three periods between 1962 and 2011, we identified the presence of two components of herring in a small semi-enclosed coastal marine ecosystem based on different somatic growth patterns and mean vertebrae sum (VS). The two components were interpreted as belonging to a resident herring population and the migratory, oceanic Norwegian spring spawning (NSS) herring population, and they co-occurred during spawning. In the 1960s, resident herring characterized by slow growth and low VS co-occurred with rapid growth, high VS oceanic NSS herring. Similar slow-growing resident and rapid-growing NSS herring were found in the 1970–80s, but both populations now had low VS suggesting similar origins. Finally, in the 2000s both populations showed rapid growth. The changes coincided with the NSS herring going from a state of high abundance and oceanic distribution to a collapse in the late 1960s that resulted in a coastal distribution closer to resident herring populations, before full recovery and resumption of the migratory, oceanic pattern in the 1990s. During all three periods, NSS herring were only present in the local system up to an age of about five years, but the synchronous spawning of the populations supports mixed spawning and interbreeding. During the investigation period both longevity, length at age (growth) and length-at-first maturity increased markedly for the resident herring, which then became more similar to the NSS herring. Genetic and/or cultural factors are believed to be the main causes of the observed changes in life history traits, although some effect of changes in environmental factors cannot be excluded. Our study suggests that relationships among populations in a metapopulation can be highly dynamic.
IL13RA2 targeted alpha particle therapy against glioblastomas

Glioblastoma (GBM) is the most aggressive primary malignant brain cancer that invariably results in a dismal prognosis. Chemotherapy and radiotherapy have not been completely effective as standard treatment options for patients due to recurrent disease. We and others have therefore developed molecular strategies to specifically target interleukin 13 receptor alpha 2 (IL13RA2), a GBM restricted receptor expressed abundantly on over 75% of GBM patients. In this work, we evaluated the potential of Pep-1L, a novel IL13RA2 targeted peptide, as a platform to deliver targeted lethal therapies to GBM. To demonstrate GBM-specificity, we radiolabeled Pep-1L with Copper-64 and performed in vitro cell binding studies, which demonstrated specific binding that was blocked by unlabeled Pep-1L. Furthermore, we demonstrated real-time GBM localization of [64Cu]Pep-1L to orthotopic GBMs using small animal PET imaging. Based on these targeting data, we performed an initial in vivo safety and therapeutic study using Pep-1L conjugated to Actinium-225, an alpha particle emitter that has been shown to potently and irreversibly kill targeted cells. We infused [225Ac]Pep-1L into orthotopic GBMs using convection-enhanced delivery and found no significant adverse events at injected doses. Furthermore, our initial data also demonstrated significantly greater overall, median and mean survival in treated mice when compared to those in control groups (p < 0.05). GBM tissue extracted from mice treated with [225Ac]Pep-1L showed double stranded DNA breaks, lower Ki67 expression and greater propidium iodide internalization, indicating anti-GBM therapeutic effects of [225Ac]Pep-1L. Based on our results, Pep-1L warrants further investigation as a potential targeted platform to deliver anti-cancer agents.
Increasing availability of illicit and prescription opioids among people who inject drugs in a Canadian setting, 2010–2014

ABSTRACT Background: Nonmedical use of prescription opioid and illicit opioid has been increasing at an alarming rate in North America over the past decade. Objective: We sought to examine the temporal trends and correlates of the availability of illicit and prescription opioids among people who inject drugs (PWID) in Vancouver, Canada. Methods: Data were derived from three prospective cohort studies of PWID in Vancouver between 2010 and 2014. In semiannual interviews, participants reported the availability of five sets of illicit and prescription opioids: (1) heroin; (2) Percocet (oxycodone/acetaminophen), Vicodin (hydrocodone/acetaminophen), or Demerol (meperidine); (3) Dilaudid (hydromorphone); (4) Morphine; (5) oxycontin/OxyNEO (controlled-release oxycodone). We defined perceived availability as immediate (e.g., available within 10 minutes) versus no availability/available after 10 minutes. The trend and correlation of immediate availability were identified by multivariable generalized estimating equations logistic regression. Results: Among 1584 participants, of which 564 (35.6%) were female, the immediate availability of all illicit and prescribed opioids (except for oxycontin/OxyNEO) increased over time, independent of potential confounders. The Adjusted Odds Ratios of immediate availability associated with every calendar year increase were between 1.09 (95% confidence interval 1.05–1.12) (morphine and Dilaudid) and 1.13 (95% confidence interval 1.09–1.17) (Percocet/Vicodin/Demerol) (all p-values <0.05). Conclusion: The availability of most prescription opioids had continued to increase in recent years among our sample of PWID in Vancouver. Concurrent increases in the availability of heroin were also observed, raising concerns regarding combination of both illicit and prescription opioid use among PWID that could potentially increase the risk of overdose.
Impact of form factors and input conditions on absolute indirect-touch pointing tasks

Absolute indirect interaction maps the absolute position of a device's end-effector to the absolute position of a remote on-screen object.Despite its long-time use with graphics tablets and growing use in research prototypes, little is known on the influence of form factors and input conditions on pointing performance with such a mapping. The input and display can have different sizes and aspect ratios, for example. The on-screen targets can vary in size. Users can look solely at the display or at the input device as well. They can also hold the input device in certain cases, or let it rest on a table. This paper reports on two experiments designed to investigate the influence of all these factors on absolute indirect-touch pointing performance. We also provide design guidelines for interaction in these situations based on the observed impacting factors.
Population Structure of the Chagas Disease Vector Triatoma infestans in an Urban Environment

Chagas disease is a vector-borne disease endemic in Latin America. Triatoma infestans, a common vector of this disease, has recently expanded its range into rapidly developing cities of Latin America. We aim to identify the environmental features that affect the colonization and dispersal of T. infestans in an urban environment. We amplified 13 commonly used microsatellites from 180 T. infestans samples collected from a sampled transect in the city of Arequipa, Peru, in 2007 and 2011. We assessed the clustering of subpopulations and the effect of distance, sampling year, and city block location on genetic distance among pairs of insects. Despite evidence of genetic similarity, the majority of city blocks are characterized by one dominant insect genotype, suggesting the existence of barriers to dispersal. Our analyses show that streets represent an important barrier to the colonization and dispersion of T. infestans in Arequipa. The genetic data describe a T. infestans infestation history characterized by persistent local dispersal and occasional long-distance migration events that partially parallels the history of urban development.