Miracle-dz/UniFAR-FTUs huggingface dataset:
Endocrine-disrupting chemicals—Mechanisms of action on male reproductive system

Endocrine-disrupting chemicals (EDCs) are exogenous compounds that can cause disturbances in the endocrine system and have multiple harmful effects on health by targeting different organs and systems in the human body. Mass industrial production and widespread use of EDCs have resulted in worldwide contamination. Accumulating evidence suggest that human exposure to EDCs is related to the impairment of male reproductive function and can interrupt other hormonally regulated metabolic processes, particularly if exposure occurs during early development. Investigation of studies absent in previous reviews and meta-analysis of adverse effects of EDCs on functioning of the male reproductive system is the core of this work. Four main modes of action of EDCs on male fertility have been summarized in this review. First, studies describing estrogen- pathway disturbing chemicals are investigated. Second, androgen-signaling pathway alterations and influence on androgen sensitive tissues are examined. Third, evaluation of steroidogenesis dysfunction is discussed by focusing on the steroid hormone biosynthesis pathway, which is targeted by EDCs. Last, the reportedly destructive role of reactive oxygen species (ROS) on sperm function is discussed. Spermatogenesis is a remarkably complex process, hence multiple studies point out various dysfunctions depending on the development state at which the exposure occurred. Collected data show the need to account for critical windows of exposure such as fetal, perinatal and pubertal periods as well as effects of mixtures of several compounds in future research.
Pathogenesis of Lafora Disease: Transition of Soluble Glycogen to Insoluble Polyglucosan

Lafora disease (LD, OMIM #254780) is a rare, recessively inherited neurodegenerative disease with adolescent onset, resulting in progressive myoclonus epilepsy which is fatal usually within ten years of symptom onset. The disease is caused by loss-of-function mutations in either of the two genes EPM2A (laforin) or EPM2B (malin). It characteristically involves the accumulation of insoluble glycogen-derived particles, named Lafora bodies (LBs), which are considered neurotoxic and causative of the disease. The pathogenesis of LD is therefore centred on the question of how insoluble LBs emerge from soluble glycogen. Recent data clearly show that an abnormal glycogen chain length distribution, but neither hyperphosphorylation nor impairment of general autophagy, strictly correlates with glycogen accumulation and the presence of LBs. This review summarizes results obtained with patients, mouse models, and cell lines and consolidates apparent paradoxes in the LD literature. Based on the growing body of evidence, it proposes that LD is predominantly caused by an impairment in chain-length regulation affecting only a small proportion of the cellular glycogen. A better grasp of LD pathogenesis will further develop our understanding of glycogen metabolism and structure. It will also facilitate the development of clinical interventions that appropriately target the underlying cause of LD.
A diagnosis of dismobility--giving mobility clinical visibility: a Mobility Working Group recommendation.

Slow gait limits independence, decreases quality of life, and is associated with an increased risk of disability, hospitalization, placement in long-term care,1,2 and accelerated clinical progression of many chronic diseases, including chronic obstructive pulmonary disease, diabetes, congestive heart failure, and dementia. Slow gait speed is also a predictor of all-cause mortality.3 Measuring gait speed is simple, quick, reproducible, inexpensive, and feasible in clinical settings. These characteristics have led to the recommendation that gait speed be considered a vital sign for the care of older patients.
The Diagnostic Interview Schedule for Children-Revised Version (DISC-R): I. Preparation, field testing, interrater reliability, and acceptability.

OBJECTIVE To describe the history and assessment strategies used to investigate and revise the Diagnostic Interview Schedule for Children (DISC), a highly structured interview form used by lay interviewers to elicit diagnostic criteria for the common psychiatric disorders of childhood and adolescence. METHOD Revision was based on clinical and community data that identified unreliable and undiscriminating items in an earlier version of the instrument (DISC-1). A field study was carried out with 74 parent-child pairs. Interrater reliability and acceptability to patients was high. Accompanying papers describe the test-retest and construct validity of the instrument. CONCLUSIONS Taken together, the findings suggest that the DISC is an acceptable, brief, inexpensive, and convenient instrument for ascertaining a comprehensive range of child and adolescent diagnoses whose methodological properties are comparable with other child diagnostic instruments.
How do lesbian and gay people experience dementia?

Introduction The subjective experience of dementia for lesbian and gay individuals is largely absent from the extant literature. This study aimed to explore what it means to experience dementia in this context given the documented psychosocial influences facing this population. A second aim was to develop understanding of these experiences within dyadic relationships. Method Ten semi-structured interviews were conducted with lesbian and gay individuals with dementia and people with whom they had a significant relationship and analysed using interpretative phenomenological analysis. Results Three superordinate themes, reflecting characteristics of participants’ experience, were identified: duality in managing dementia, giving yourself away vs. holding onto yourself and relationships as sheltered harbours. Ten subthemes indicated the processes that were adopted to adjust and make sense of the experience of dementia. These included decisions around concealment, ensuring safety and the promotion of personhood and couplehood. In line with findings for heterosexual couples, partners had an important role in maintaining the identity of the person with dementia. Conclusions Results suggest additional and distinct challenges, including experienced and perceived discrimination and heterosexism. In response to these conditions, interviewees worked to resist a ‘double stigma’ of dementia and sexuality. Findings indicated areas of improvement for dementia services, including training in inclusive practice.
Evidence for Extrinsic Exonucleolytic Proofreading

Exonucleolytic proofreading of DNA synthesis errors is one of the major determinants ofgenome stability. However, many DNA transactions that contribute to genome stability requiresynthesis by polymerases that naturally lack intrinsic 3´ exonuclease activity and some of whichare highly inaccurate. Here we discuss evidence that errors made by these polymerases may beedited by a separate 3´ exonuclease, and we consider how such extrinsic proofreading may differfrom proofreading by exonucleases that are intrinsic to replicative DNA polymerases.
The Interaction between IL-18 and IL-18 Receptor Limits the Magnitude of Protective Immunity and Enhances Pathogenic Responses following Infection with Intracellular Bacteria

The binding of IL-18 to IL-18Rα induces both proinflammatory and protective functions during infection, depending on the context in which it occurs. IL-18 is highly expressed in the liver of wild-type (WT) C57BL/6 mice following lethal infection with highly virulent Ixodes ovatus ehrlichia (IOE), an obligate intracellular bacterium that causes acute fatal toxic shock-like syndrome. In this study, we found that IOE infection of IL-18Rα−/− mice resulted in significantly less host cell apoptosis, decreased hepatic leukocyte recruitment, enhanced bacterial clearance, and prolonged survival compared with infected WT mice, suggesting a pathogenic role for IL-18/IL-18Rα in Ehrlichia-induced toxic shock. Although lack of IL-18R decreased the magnitude of IFN-γ producing type-1 immune response, enhanced resistance of IL-18Rα−/− mice against Ehrlichia correlated with increased proinflammatory cytokines at sites of infection, decreased systemic IL-10 production, increased frequency of protective NKT cells producing TNF-α and IFN-γ, and decreased frequency of pathogenic TNF-α–producing CD8+ T cells. Adoptive transfer of immune WT CD8+ T cells increased bacterial burden in IL-18Rα−/− mice following IOE infection. Furthermore, rIL-18 treatment of WT mice infected with mildly virulent Ehrlichia muris impaired bacterial clearance and enhanced liver injury. Finally, lack of IL-18R signal reduced dendritic cell maturation and their TNF-α production, suggesting that IL-18 might promote the adaptive pathogenic immune responses against Ehrlichia by influencing T cell priming functions of dendritic cells. Together, these results suggested that the presence or absence of IL-18R signals governs the pathogenic versus protective immunity in a model of Ehrlichia-induced immunopathology.
RENAL HOMOGRAFTS IN PATIENTS WITH MAJOR DONOR-RECIPIENT BLOOD GROUP INCOMPATIBILITIES.

Three documented cases of clinical renal transplantation in which the donor and recipient patients had different major blood types have been presented. The relationship of the donor-recipient pairs ranged from that of sister-to-brother to that of totally unrelated patients of different races. The renal homografts were obtained from living donors in 2 cases and from a recently dead cadaver in the third. Renal function was prompt and excellent when living donors were used, and more indolent when a cadaver kidney subjected to a long period of ischemia was employed. Two of the patients have normal renal function after 74 and 49 days. The third patient died with rejection and sepsis 24 days after transplantation. This study demonstrates the feasibility of obtaining both immediate and prolonged renal function despite the presence of major blood group incompatibilities between donor and recipient patients. This knowledge should expand the donor pool, making it possible to transfer renal homografts under much less stringent requirements than has been the case in the past. © 1964.
Integrative modeling of gene and genome evolution roots the archaeal tree of life

Significance The Archaea represent a primary domain of cellular life, play major roles in modern-day biogeochemical cycles, and are central to debates about the origin of eukaryotic cells. However, understanding their origins and evolutionary history is challenging because of the immense time spans involved. Here we apply a new approach that harnesses the information in patterns of gene family evolution to find the root of the archaeal tree and to resolve the metabolism of the earliest archaeal cells. Our approach robustly distinguishes between published rooting hypotheses, suggests that the first Archaea were anaerobes that may have fixed carbon via the Wood–Ljungdahl pathway, and quantifies the cumulative impact of horizontal transfer on archaeal genome evolution. A root for the archaeal tree is essential for reconstructing the metabolism and ecology of early cells and for testing hypotheses that propose that the eukaryotic nuclear lineage originated from within the Archaea; however, published studies based on outgroup rooting disagree regarding the position of the archaeal root. Here we constructed a consensus unrooted archaeal topology using protein concatenation and a multigene supertree method based on 3,242 single gene trees, and then rooted this tree using a recently developed model of genome evolution. This model uses evidence from gene duplications, horizontal transfers, and gene losses contained in 31,236 archaeal gene families to identify the most likely root for the tree. Our analyses support the monophyly of DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, Nanohaloarchaea), a recently discovered cosmopolitan and genetically diverse lineage, and, in contrast to previous work, place the tree root between DPANN and all other Archaea. The sister group to DPANN comprises the Euryarchaeota and the TACK Archaea, including Lokiarchaeum, which our analyses suggest are monophyletic sister lineages. Metabolic reconstructions on the rooted tree suggest that early Archaea were anaerobes that may have had the ability to reduce CO2 to acetate via the Wood–Ljungdahl pathway. In contrast to proposals suggesting that genome reduction has been the predominant mode of archaeal evolution, our analyses infer a relatively small-genomed archaeal ancestor that subsequently increased in complexity via gene duplication and horizontal gene transfer.
Well-Being and Chronic Disease Incidence: The English Longitudinal Study of Ageing

Background Previous research suggests that greater well-being may protect against onset of chronic disease. However, it is unclear whether this association is similar across different types of disease. Method We used Cox proportional hazards regression to examine the prospective relationship between well-being (measured using the CASP-19 quality of life questionnaire) and incidence of arthritis, cancer, stroke, diabetes, myocardial infarction, and chronic lung disease over 8 years. The sample consisted of 8182 participants 50 years or older from the English Longitudinal Study of Ageing. Results After adjustments for established risk factors, a standard deviation increase in CASP-19 score was associated with a decrease in arthritis risk (hazard ratio [HR] = 0.89, 95% confidence interval [CI] = 0.83–0.96) and, in those younger than 65 years, a decrease in diabetes risk (HR = 0.82, 95% CI = 0.70–0.95) and chronic lung disease risk (HR = 0.80, 95% CI = 0.66–0.97). Higher CASP-19 scores were associated with reduced risk for stroke and myocardial infarction; however, these associations were no longer significant after adjustments for established risk factors. No association was observed for cancer incidence. An age interaction was observed for diabetes, myocardial infarction, and chronic lung disease, with a stronger association between CASP-19 score and disease incidence at younger ages. Conclusions The extent of association between well-being and incident disease risk is not consistent across different chronic diseases. Future studies should examine the cause of this variation.
No Sex Differences in the Frequencies of Common Single Nucleotide Polymorphisms Associated with Age-Related Macular Degeneration

ABSTRACT Purpose: Since some studies have reported differences in the association of age-related macular degeneration (AMD) with biological sex, we set out to determine whether the difference in the disease susceptibility is afforded by common single nucleotide polymorphisms (SNPs) associated with AMD. Methods: We genotyped 2067 Caucasian subjects from the Age-Related Eye Disease Study cohort for commonly associated AMD SNPs, including those in CFH (rs1061170, rs1410996, and rs3766404), ARMS2 (rs10490924), and C3 (rs2230199) using either a Sequenom MassARRAY MALDI-TOF mass spectrometer or using Taqman genotyping reagents. A Cox proportional hazards model was used to determine the effect of genotype, age, sex, and smoking status on the development of AMD. Results: All tested SNPs genotyped are associated strongly with AMD (p < 0.0001), in concordance with previous studies. However, we found no observable differences in any of the SNPs studied when categorized by sex. Interactions between SNPs and sex were found to be not statistically significant (p = 0.38–0.79). Conclusions: The difference between male and female incidence of AMD is not explained by the most commonly AMD-associated SNPs, though it does not exclude the possibility that other, less common SNPs contribute to this difference.
Negotiation, Mediation and Communication between Cultures: End-of-Life Care for South Asian Immigrants in Canada from the Perspective of Family Caregivers

In the present study, we explored family caregivers' experiences in providing end-of-life care for terminally ill South Asian immigrants. We employed qualitative methods and. in-depth interviews were conducted with seven family caregivers living in Nova Scotia, Canada. Interview data were validated, coded and organized for themes. Three major themes identified in the data illustrated (a) how South Asian caregivers experienced clashes between biomedical and ethno-cultural realms of care that led to cultural insensitivity, (b) how family members acted as mediators, and (c) how communication issues that challenged cultural sensitivity were handled. Findings provide directions for culturally sensitive end-of-life care planning.
Using HRD to Support Repatriates

A systematic review of repatriation literature in human resource development (HRD) journals reveals common themes of low motivation to repatriate among expatriates and high rates of repatriation failure in organizations. In addition, there is a gap in the published research regarding organization development (OD), suggesting that there is a need to look more closely at managing the changes for individuals, teams, and organizations associated with repatriation. In this article, we addressed this literature gap by proposing a framework for creating an OD strategy for repatriation. This framework is useful for HRD instructors, trainers, and other practitioners who are tasked with creating and instructing others on how to create an OD strategy for repatriation. Such a strategy could help improve repatriation motivation and decrease repatriation failure, ultimately improving organizational performance. The proposed framework was adapted from a positive model of planned change and focuses on discovering, examining, and capitalizing on previous organizational successes to positively impact the repatriation process.
Tumor Progression Can Occur despite the Induction of Very High Levels of Self/Tumor Antigen-Specific CD8+ T Cells in Patients with Melanoma

The identification of many tumor-associated epitopes as nonmutated “self” Ags led to the hypothesis that the induction of large numbers of self/tumor Ag-specific T cells would be prevented because of central and peripheral tolerance. We report in this study on vaccination efforts in 95 HLA-A*0201 patients at high risk for recurrence of malignant melanoma who received prolonged immunization with the “anchor-modified” synthetic peptide, gp100209–217(210M). Vaccination using this altered peptide immunogen was highly effective at inducing large numbers of self/tumor-Ag reactive T cells in virtually every patient tested, with levels as high as 42% of all CD8+ T cells assessed by tetramer analysis. From 1 to 10% of all CD8+ cells were tumor-Ag reactive in 44% of patients and levels >10% were generated in 17% of patients. These studies were substantiated using the ELISPOT assay and a bulk cytokine release assay. Although our data regarding “tumor escape” were inconclusive, some patients had growing tumors that expressed Ag and HLA-A*0201 in the presence of high levels of antitumor T cells. There was no difference in the levels of antitumor Ag-specific T cells in patients who recurred compared with those that remained disease-free. Thus, the mere presence of profoundly expanded numbers of vaccine-induced, self/tumor Ag-specific T cells cannot by themselves be used as a “surrogate marker” for vaccine efficacy. Further, the induction of even high levels of antitumor T cells may be insufficient to alter tumor progression.
On the Mismanagement and Maliciousness of Networks

In this paper, we systematically explore the widely held, anecdotal belief that mismanaged networks are responsible for a wide range of security incidents. Utilizing Internet-scale measurements of DNS resolvers, BGP routers, and SMTP, HTTP, and DNS-name servers, we find there are thousands of networks where a large fraction of network services are misconfigured. Combining global feeds of malicious activities including spam, phishing, malware, and scanning, we find a statistically significant correlation between networks that are mismanaged and networks that are responsible for maliciousness.
Treatment of chronic myeloid leukemia: assessing risk, monitoring response, and optimizing outcome

Abstract Over the past two decades, tyrosine kinase inhibitors have become the foundation of chronic myeloid leukemia (CML) treatment. The choice between imatinib and newer tyrosine kinase inhibitors (TKIs) needs to be balanced against the known toxicity and efficacy data for each drug, the therapeutic goal being to maximize molecular response assessed by BCR-ABL RQ-PCR assay. There is accumulating evidence that the early achievement of molecular targets is a strong predictor of superior long-term outcomes. Early response assessment provides the opportunity to intervene early with the aim of ensuring an optimal response. Failure to achieve milestones or loss of response can have diverse causes. We describe how clinical and laboratory monitoring can be used to ensure that each patient is achieving an optimal response and, in patients who do not reach optimal response milestones, how the monitoring results can be used to detect resistance and understand its origins.
RDF Sketch Maps - Knowledge Complexity Reduction for Precision Medicine Analytics

Realization of precision medicine ideas requires significant research effort to be able to spot subtle differences in complex diseases at the molecular level to develop personalized therapies. It is especially important in many cases of highly heterogeneous cancers. Precision diagnostics and therapeutics of such diseases demands interrogation of vast amounts of biological knowledge coupled with novel analytic methodologies. For instance, pathway-based approaches can shed light on the way tumorigenesis takes place in individual patient cases and pinpoint to novel drug targets. However, comprehensive analysis of hundreds of pathways and thousands of genes creates a combinatorial explosion, that is challenging for medical practitioners to handle at the point of care. Here we extend our previous work on mapping clinical omics data to curated Resource Description Framework (RDF) knowledge bases to derive influence diagrams of interrelationships of biomarker proteins, diseases and signal transduction pathways for personalized theranostics. We present RDF Sketch Maps - a computational method to reduce knowledge complexity for precision medicine analytics. The method of RDF Sketch Maps is inspired by the way a sketch artist conveys only important visual information and discards other unnecessary details. In our case, we compute and retain only so-called RDF Edges - places with highly important diagnostic and therapeutic information. To do this we utilize 35 maps of human signal transduction pathways by transforming 300 KEGG maps into highly processable RDF knowledge base. We have demonstrated potential clinical utility of RDF Sketch Maps in hematopoietic cancers, including analysis of pathways associated with Hairy Cell Leukemia (HCL) and Chronic Myeloid Leukemia (CML) where we achieved up to 20-fold reduction in the number of biological entities to be analyzed, while retaining most likely important entities. In experiments with pathways associated with HCL a generated RDF Sketch Map of the top 30% paths retained important information about signaling cascades leading to activation of proto-oncogene BRAF, which is usually associated with a different cancer, melanoma. Recent reports of successful treatments of HCL patients by the BRAF-targeted drug vemurafenib support the validity of the RDF Sketch Maps findings. We therefore believe that RDF Sketch Maps will be invaluable for hypothesis generation for precision diagnostics and therapeutics as well as drug repurposing studies.