Miracle-dz/UniFAR-FTUs huggingface dataset:
Reservoir‐host amplification of disease impact in an endangered amphibian

Emerging wildlife pathogens are an increasing threat to biodiversity. One of the most serious wildlife diseases is chytridiomycosis, caused by the fungal pathogen, Batrachochytrium dendrobatidis (Bd), which has been documented in over 500 amphibian species. Amphibians vary greatly in their susceptibility to Bd; some species tolerate infection, whereas others experience rapid mortality. Reservoir hosts—species that carry infection while maintaining high abundance but are rarely killed by disease—can increase extinction risk in highly susceptible, sympatric species. However, whether reservoir hosts amplify Bd in declining amphibian species has not been examined. We investigated the role of reservoir hosts in the decline of the threatened northern corroboree frog (Pseudophryne pengilleyi) in an amphibian community in southeastern Australia. In the laboratory, we characterized the response of a potential reservoir host, the (nondeclining) common eastern froglet (Crinia signifera), to Bd infection. In the field, we conducted frog abundance surveys and Bd sampling for both P. pengilleyi and C. signifera. We built multinomial logistic regression models to test whether Crinia signifera and environmental factors were associated with P. pengilleyi decline. C. signifera was a reservoir host for Bd. In the laboratory, many individuals maintained intense infections (>1000 zoospore equivalents) over 12 weeks without mortality, and 79% of individuals sampled in the wild also carried infections. The presence of C. signifera at a site was strongly associated with increased Bd prevalence in sympatric P. pengilleyi. Consistent with disease amplification by a reservoir host, P. pengilleyi declined at sites with high C. signifera abundance. Our results suggest that when reservoir hosts are present, population declines of susceptible species may continue long after the initial emergence of Bd, highlighting an urgent need to assess extinction risk in remnant populations of other declined amphibian species.
The Deployment Trauma Phenotype and Employment Status in Veterans of the Wars in Iraq and Afghanistan

Objectives: To determine the prevalence of comorbid mild traumatic brain injury (mTBI), posttraumatic stress disorder (PTSD), and depression, termed the deployment trauma phenotype (DTP), and its constituent diagnoses' impact on unemployment status in a national cohort of veterans. Setting: Retrospective analysis of the comprehensive TBI evaluation, a Veterans Affairs-wide protocol for assessing TBI, employment status, and psychiatric impressions. Participants: The final data set consisted of 48 821 veterans. Main Outcomes and Measures: Frequency of mTBI, PTSD, and depression in isolation and combinations and their association with unemployment status. Results: Age- and education-adjusted risk ratios (RRs) showed that the mTBI-only group was the least likely to be unemployed, RR = 0.65 (0.59–0.71). By contrast, the greatest likelihood of unemployment was associated with membership in the DTP group, RR = 1.45 (1.36–1.56), and the comorbid PTSD and depression group, RR = 1.39 (1.27–1.52). Furthermore, the DTP was nearly 3 times more prevalent (16.4%) in this sample compared with comorbid PTSD and depression (5.7%), indicating that the DTP conveys risk for unemployment to a significantly greater number of individuals. Conclusions and Relevance: The comorbid and interactive conditions of PTSD, depression, and mTBI, rather than mTBI in isolation, were linked to significant risk for unemployment in this veteran cohort. These findings suggest that multifaceted assessments and interventions to improve postdeployment reintegration are needed.
Metallomic Profiling and Linkage Map Analysis of Early Parkinson's Disease: A New Insight to Aluminum Marker for the Possible Diagnosis

Background Parkinson's disease (PD) is the most common neurodegenerative disorder. The diagnosis of PD is challenging and currently none of the biochemical tests have proven to help in diagnosis. Serum metallomic analysis may suggest the possibility of diagnosis of PD. Methodology/Results The metallomic analysis was targeted on 31 elements obtained from 42 healthy controls and 45 drug naive PD patients using ICP-AES and ICP-MS to determine the concentration variations of elements between PD and normal. The targeted metallomic analysis showed the significant variations in 19 elements of patients compared to healthy control (p<0.04). The partial least squares discriminant analysis (PLS-DA) showed aluminium, copper, iron, manganese and zinc are the key elements, contributes the separation of PD patients from control samples. The correlation coefficient analysis and element-element ratio confirm the imbalance of inter-elements relationship in PD patients' serum. Furthermore, elements linkage map analysis showed aluminium is a key element involved in triggering of phosphorus, which subsequently lead to imbalance of homeostatic in PD serum. The execution of neural network using elements concentrations provides 95% accuracy in detection of disease. Conclusions/Significance These results suggest that there is a disturbance in the elements homeostasis and inter-elements relationship in PD patients' serum. The analysis of serum elements helps in linking the underlying cellular processes such as oxidative stress, neuronal dysfunction and apoptosis, which are the dominating factors in PD. Also, these results increase the prospect of detection of early PD from serum through neural network algorithm.
Study of Carotid Intimal Medial Thickness in Essential Hypertension With or Without Left Ventricular Hypertrophy

Introduction: Hypertension and atherosclerosis though separate entities, are interrelated as hypertension plays an important role in the pathogenesis of atherosclerosis. This study was undertaken to study the association of carotid intimal medial thickness with left ventricular hypertrophy (LVH) in hypertensive patients. Materials and Methods: Hundred hypertensives (JNC-7, Stage 1 and 2) between 30 and 55 years were enrolled in this prospective observational study conducted at a tertiary care teaching institute of Punjab, India. Electrocardiogram, Carotid Doppler, and Echocardiography were carried out in addition to routine biochemical investigations. Results: Increased carotid intimal medial thickness (CIMT) had statistically significant association with age, duration of hypertension, high systolic and diastolic blood pressure (BP), left ventricular hypertrophy and left ventricular mass index but was not associated with body mass index, low-density lipoproteins, and total cholesterol. Conclusions: LVH and arterial wall changes occur concurrently, and therefore, management of hypertension should not be limited just to control of BP but should also include therapy for carotid plaques and increased CIMT.
Association of NAFLD With Diabetes and the Impact of BMI Changes: A 5-Year Cohort Study Based on 18,507 Elderly

Context Previous studies about the relationship between nonalcoholic fatty liver disease (NAFLD) and diabetes are limited by inconsistent conclusions, mainly being cross-sectional and having a small sample size, no elderly people, or a lack of prediabetes. Objective This study sought to examine the relationship between NAFLD and diabetes and prediabetes in a large cohort based on Chinese male elderly. Design This was a retrospective cohort study that was followed up for ∼5 years. Setting This study was conducted in Beijing, China. Participants Chinese male elderly (n = 18,507). Participants with diabetes/prediabetes at baseline were excluded. Main Outcome Measures Ultrasound was used for diagnosis of NAFLD. Results Mean age of the 18,507 participants was 71.38 ± 14.15 years. The prevalence of NAFLD was 18.77% (3474/18,503), and participants with NAFLD had higher body mass index (BMI), blood pressure levels, blood lipid levels, and also higher alanine aminotransferase levels (P < 0.001). The total 5-year incidence was 2.448% for diabetes and 10.628% for prediabetes. Participants with NAFLD at baseline had a higher incidence of both diabetes and prediabetes. The adjusted relative risks (RRs) were 1.672 [95% confidence interval (CI), 1.361 to 2.052] and 1.336 (95% CI, 1.205 to 1.481). The RRs were closely related to BMI changes. The adjusted RRs for diabetes according to three BMI change groups (<-1.00 kg/m2, -1.00 to 1.00 kg/m2, >1.00 kg/m2) were 1.599 (95% CI, 1.054 to 2.426), 1.640 (95% CI, 1.241 to 2.167), and 1.918 (95% CI, 1.239 to 2.969), respectively. Similar results were obtained when prediabetes was used as the dependent variable. Conclusions There was a strong and independent association between NAFLD and both diabetes and prediabetes among Chinese male elderly, and this relationship was closely related to BMI changes.
Early life insults as determinants of chronic obstructive pulmonary disease in adult life

Background Early life events may predispose to the development of chronic lung disease in adulthood. Aim To provide an update on current knowledge of early nongenetic origins of COPD. Materials and methods Systematic literature review was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Results A total of 16 studies, comprising 69,365 individuals, met the predefined criteria and were included in the present review. Studies have shown that in utero tobacco exposure, low birth weight, preterm birth, and respiratory diseases, primarily asthma and pneumonia, in early childhood are associated with lung function impairment later in childhood, and by that predispose to subsequent development of COPD, although the causal association between childhood respiratory diseases and COPD has been questioned in one study. Environmental tobacco exposure has also been shown to have negative impact on lung function in childhood possibly leading to COPD in adulthood, although it is at present not possible to clearly distinguish between the impact of active and the environmental tobacco exposure on subsequent development of COPD. Conclusion Tobacco exposure in utero and early life is a risk factor for subsequent development of COPD. Furthermore, low birth weight, lower respiratory tract infections and asthma, including wheezy bronchitis, in childhood also seem to be important determinants for later development of COPD. Early life insults may, therefore, be crucial to COPD development.
Hospital-Acquired Respiratory Viral Infections: Incidence, Morbidity, and Mortality in Pediatric and Adult Patients

Abstract Background Hospital-acquired respiratory viral infections can result in morbidity and mortality of hospitalized patients. This study was undertaken to better understand the magnitude of the problem of nosocomial respiratory viral infections in adult and pediatric patients. Methods This was a retrospective study at a tertiary care adult and pediatric teaching hospital. Study patients met a priori criteria for definite or possible nosocomial respiratory viral infection. Results From April 1, 2015 to April 1, 2016, we identified 40 nosocomial respiratory viral infections in 38 patients involving 14 definite and 3 possible cases in our adult hospital and 18 definite and 5 possible cases in our pediatric hospital. The incidence was 5 cases/10 000 admissions and 44 cases/10 000 admissions to our adult and pediatric hospitals, respectively. Only 6.8% of cases were due to influenza. Although 63% of cases occurred during the fall and winter, such infections were identified throughout the year. Five (13%) nosocomial respiratory viral infections occurred in 2 adult and 3 pediatric patients who died during the hospitalization. Conclusions Nosocomial respiratory viral infections are an underappreciated cause of morbidity and mortality in hospitalized adult and pediatric patients. The incidence was nearly 10-fold higher in our pediatric hospital. We estimate there are approximately 18 955 pediatric and adult cases of nosocomial respiratory viral infections in US acute care hospitals each year.
More Drinking, More Problems—Stable Association Between Alcohol Consumption and Harm Among Swedish Youth 1995–2012

Aims Alcohol consumption among Swedish youth increased during the 1990s. In the following decade, levels declined coinciding with a reduction in the prevalence of self-reported alcohol-related harm. We examine how the trend in self-reported alcohol-related problems among young Swedish alcohol consumers has followed the trend in alcohol consumption during 1995-2012, and test whether the strength of the association between self-reported alcohol consumption and alcohol-related problems within individuals is inversely proportional to the overall level of consumption among youth. Methods The study was based on a representative survey on alcohol and drug habits among ninth-year students, consisting of current alcohol consumers (n = 68 863), 1995-2012. Negative binominal regression models were used to estimate the relationship between three consumption variables (average volume of consumption, binge drinking and heavy drinking) and self-reported alcohol-related problems. Results The prevalence of binge drinking showed a greater association with self-reported alcohol-related problems than did overall mean consumption. No noticeable variation in the strength of the individual-level alcohol and harm relationship was found over the study period. We found no significant interaction between the individual alcohol use measures and overall mean youth consumption. Conclusion We found no signs of normalization; on the contrary, young alcohol consumers suffer about the same number of self-reported negative consequences from their drinking, regardless of the level of overall youth consumption. The study also suggests that binge drinking rather than overall consumption is the main factor that influences the development of self-reported problems experienced among young alcohol consumers. Short summary Young alcohol consumers suffer about the same number of self-reported negative consequences from their drinking, regardless of the level of overall mean consumption in the youth population. Binge drinking consumption appears to be the main factor influencing the development of self-reported alcohol-related problems among young alcohol consumers.
Can’t Take My Eyes Off of You: Eye Tracking Reveals How Ruminating Young Adolescents Get Stuck

Rumination, a cognitive process that involves passively, repetitively focusing on negative feelings and their meaning, is a transdiagnostic risk factor for psychopathology. Research with adults has suggested that attentional control difficulties may underlie rumination, but questions remain about the nature of these processes. Furthermore, the relationship between attentional control and rumination in youth has received little empirical examination. In the present study, 92 youth (ages 9–14; 72% girls; 74% Caucasian) reported on their trait rumination and internalizing symptoms. They also completed a 1,500 ms emotional-faces dot-probe task while their eye movements were measured to examine overt visual attention with high temporal precision. Youth’s rumination was associated with greater dwell on emotional faces but not with initial orientation. These findings suggest that rumination is associated with increased attention to emotional information during the later stages of selective attention rather than earlier orienting to emotional cues. Implications for prevention and treatment of psychopathology are discussed.
Equivalent lumped element models for various n-port Through Silicon Vias networks

This paper proposes an equivalent lumped element model for various multi-TSV arrangements and introduces closed form expressions for the capacitive, resistive, and inductive coupling between those arrangements. The closed form expressions are in terms of physical dimensions and material properties and are driven based on the dimensional analysis method. The model's compactness and compatibility with SPICE simulators allows the electrical modeling of various TSV arrangements without the need for computationally expensive field-solvers and the fast investigation of a TSV impact on a 3-D circuit performance. The proposed model accuracy is tested versus a detailed electromagnetic simulation and showed less than 6% difference. Finally, the proposed model can be a possible solution to the industrial need for broadband electrical modeling of TSVs interconnections arising in 3-D integration. Also, our presented work provides valuable insight into creating guidelines for TSV macro-modeling.
Oncologic and functional outcomes of patients treated with transoral CO2 laser microsurgery or radiotherapy for T2 glottic carcinoma: a systematic review of the literature

Purpose of review To give an overview of the laryngeal preservation and functional outcomes of patients treated with transoral CO2 laser microsurgery (TLM) or radiotherapy for T2 glottic carcinoma. This information supports physicians and patients in treatment counselling and choices. Recent findings A recent systematic review showed that local control rates at 5-year did not differ between radiotherapy and TLM for T2 glottic tumours. However, there is a lack of comparative data on laryngeal preservation as well as functional outcomes in T2 glottic carcinoma. Summary Laryngeal preservation for T2 tumours in this review is higher for patients treated primarily with TLM (88.8 vs. 79.0%). It is important to differentiate between tumours with normal and impaired mobility (T2a and T2b) because the latter showed poorer prognosis for both TLM and radiotherapy. Involvement of the anterior commissure does not result in significantly lower oncological results, if adequately staged and treated. More studies are needed to support these data and to compare the functional outcomes between TLM and radiotherapy for T2 glottic carcinoma.
Iterative h‐minima‐based marker‐controlled watershed for cell nucleus segmentation

Automated microscopy imaging systems facilitate high‐throughput screening in molecular cellular biology research. The first step of these systems is cell nucleus segmentation, which has a great impact on the success of the overall system. The marker‐controlled watershed is a technique commonly used by the previous studies for nucleus segmentation. These studies define their markers finding regional minima on the intensity/gradient and/or distance transform maps. They typically use the h‐minima transform beforehand to suppress noise on these maps. The selection of the h value is critical; unnecessarily small values do not sufficiently suppress the noise, resulting in false and oversegmented markers, and unnecessarily large ones suppress too many pixels, causing missing and undersegmented markers. Because cell nuclei show different characteristics within an image, the same h value may not work to define correct markers for all the nuclei. To address this issue, in this work, we propose a new watershed algorithm that iteratively identifies its markers, considering a set of different h values. In each iteration, the proposed algorithm defines a set of candidates using a particular h value and selects the markers from those candidates provided that they fulfill the size requirement. Working with widefield fluorescence microscopy images, our experiments reveal that the use of multiple h values in our iterative algorithm leads to better segmentation results, compared to its counterparts. © 2016 International Society for Advancement of Cytometry
SHP-2 phosphatase contributes to KRAS-driven intestinal oncogenesis but prevents colitis-associated cancer development

A major risk factor of developing colorectal cancer (CRC) is the presence of chronic inflammation in the colon. In order to understand how inflammation contributes to CRC development, the present study focused on SHP-2, a tyrosine phosphatase encoded by PTPN11 gene in which polymorphisms have been shown to be markers of colitis susceptibility. Conversely, gain-of-function mutations in PTPN11 gene (E76 residue) have been found in certain sporadic CRC. Results shown herein demonstrate that SHP-2 expression was markedly increased in sporadic human adenomas but not in advanced colorectal tumors. SHP-2 silencing inhibited proliferative, invasive and tumoral properties of both intestinal epithelial cells (IECs) transformed by oncogenic KRAS and of human CRC cells. IEC-specific expression of a SHP-2E76K activated mutant in mice was not sufficient to induce tumorigenesis but markedly promoted tumor growth under the ApcMin/+ background. Conversely, mice with a conditional deletion of SHP-2 in IECs developed colitis-associated adenocarcinomas with age, associated with sustained activation of Wnt/β-catenin, NFκB and STAT3 signalings in the colonic mucosae. Moreover, SHP-2 epithelial deficiency considerably increased tumor load in ApcMin/+ mice, shifting tumor incidence toward the colon. Overall, these results reveal that SHP-2 can exert opposing functions in the large intestine: it can promote or inhibit tumorigenesis depending of the inflammatory context.
Influence of interferon-gamma Receptor 1 gene polymorphisms on the susceptibility to pulmonary tuberculosis among sudanese population

Background: A variety of genetic mutations are thought to be responsible for acquisition of different infections such as tuberculosis (TB). An obvious example for these variations is the link between pulmonary TB and polymorphisms within interferon-gamma receptor 1 (IFN-γ R1) gene. This project is designed to identify the role of IFN-γR1 gene polymorphism in the development of pulmonary TB among Sudanese patients attending several hospitals in Khartoum State. Methods: One hundred (n = 100) patients with active TB and fifty (n = 50) matched healthy controls were investigated for the association of two genetic polymorphisms within IFN-γR1 gene and their risk of developing pulmonary tuberculosis. Polymerase chain reaction (PCR) assay and PCR-restriction fragment length polymorphism were performed. Results: Migrated IFN-γR1 DNA bands representing genotypes and polymorphic alleles were identified. Molecular findings revealed that two genetic variants, namely, −56C and +295C deletion 12 within IFN-γR1 gene, were nonsignificantly linked with increased risk of development of pulmonary TB, P = 0.771 and 0.343, respectively. Two genetic variants within IFN-γR1 gene were examined for suggested role in inducing development of TB. Conclusion: The two genetic variants were found to have potential risk in association with active disease development among Sudanese patients. Further intensive research work involving use of large collection of samples should be conducted to verify these findings.