Miracle-dz/UniFAR-FTUs huggingface dataset:
The response of the melanized yeast Exophiala dermatitidis to gamma radiation exposure.

The melanized yeast Exophiala dermatitidis is resistant to many environmental stresses, and is used as a model for understanding the diverse roles of melanin in fungi. Here we describe the extent of resistance of E. dermatitidis to acute γ-radiation exposure and the major mechanisms it uses to recover from this stress. We find that melanin does not protect E. dermatitidis from γ-radiation. Instead, environmental factors such as nutrient availability, culture age, and culture density are much greater determinants of cell survival after exposure. We also observe a dramatic transcriptomic response to γ-radiation that mobilizes pathways involved in morphological development, protein degradation, and DNA repair, and is unaffected by the presence of melanin. Together, these results suggest that the ability of E. dermatitidis to survive γ-radiation exposure is determined by the prior and the current metabolic state of the cells as well as DNA repair mechanisms, and that small changes in these conditions can lead to large effects in radiation resistance, which should be taken into account when understanding how diverse fungi recover from this unique stress. This article is protected by copyright. All rights reserved.
Coenzyme Q10 Improves Sperm Parameters, Oxidative Stress Markers and Sperm DNA Fragmentation in Infertile Patients with Idiopathic Oligoasthenozoospermia

Purpose Oxidative stress and sperm DNA fragmentation (SDF) are potential contributing factors for idiopathic male infertility. Coenzyme Q10 (CoQ10) have been reported to be effective in the treatment of idiopathic male infertility, in general, owing to its antioxidant properties. Thus, the present study intends to investigate the effects of CoQ10 therapy on semen parameters, oxidative stress markers and SDF in infertile men, specifically with idiopathic oligoasthenozoospermia (OA). Materials and Methods In this case-control study, sixty-five infertile patients with idiopathic OA and forty fertile men (control) were included. All participants underwent semen analysis based on the World Health Organization guidelines (5th edition, 2010). Patients received CoQ10 at the dose of 200 mg/d orally for three months. Seminal plasma CoQ10, total antioxidant capacity (TAC), total reactive oxygen species (ROS), glutathione peroxidase (GPx), and SDF levels were measured in controls (baseline) and infertile patients pre- and post-CoQ10 treatment. Results CoQ10 treatment for three months significantly improved sperm concentration (p<0.05), progressive motility (p<0.05), total motility (p<0.01), seminal fluid CoQ10 concentration (p<0.001), TAC (p<0.001), and GPx (p<0.001) levels in infertile men with OA. Further, ROS level (p<0.05) and SDF percentage (p<0.001) were reduced in OA patients as compared to the baseline. CoQ10 levels also correlated positively with sperm concentration (r=0.48, p=0.01) and total motility (r=0.59, p=0.003) while a negative correlation was recorded between SDF and sperm motility (r=−0.54, p=0.006). Conclusions CoQ10 supplementation for three months could improve semen parameters, oxidative stress markers and reduce SDF in infertile men with idiopathic OA.
Into the wild: new yeast genomes from natural environments and new tools for their analysis.

Genomic studies of yeasts from the wild have increased considerably in the last few years. This revolution has been fueled by advances in high-throughput sequencing technologies and a better understanding of yeast ecology and phylogeography, especially for biotechnologically important species. The present review aims to first introduce new bioinformatic tools available for the generation and analysis of yeast genomes. We also assess the accumulated genomic data of wild isolates of industrially relevant species, such as Saccharomyces spp. , which provide unique opportunities to further investigate the domestication processes associated with the fermentation industry and opportunistic pathogenesis. The availability of genome sequences of other less conventional yeasts obtained from the wild has also increased substantially, including representatives of the phyla Ascomycota (e.g. Hanseniaspora) and Basidiomycota (e.g. Phaffia). Here we review salient examples of both fundamental and applied research that demonstrate the importance of continuing to sequence and analyze genomes of wild yeasts.
Characteristics and Behaviors Among a Representative Sample of New Jersey Adults Practicing Environmental Risk-Reduction Behaviors

Context: Environmental exposure to groundwater contamination from agricultural runoff, chemical pollution, or geology and indoor air hazards from misuse of consumer products or naturally occurring radon contributes to adverse health outcomes. Individuals can reduce exposure to environmental hazards by practicing risk-reduction behaviors. Objective: To characterize the demographic and behavioral characteristics of the population practicing environmental risk-reduction behaviors in order to identify gaps in current prevention outreach efforts. Design: The New Jersey Behavioral Risk Factor Survey captures data on self-reported environmental risk-reduction behaviors and health-promoting behaviors (cancer screenings, vaccinations, smoking). To account for complex survey data, weighted analyses were performed in SAS v9.4. Setting: New Jersey, 2014-2015. Participants: The New Jersey Behavioral Risk Factor Survey is an ongoing telephone health survey of NJ residents. About 1000 NJ residents are selected randomly each month to derive statewide representative prevalence estimates. Main Outcome Measures: Self-reported private well testing, radon screening, and carbon monoxide (CO) detector ownership. Results: Statewide prevalence of the practice of environmental risk-reduction practices includes 56.6% for private well testing, 44.3% for radon screening, and 86.1% for CO detector ownership. A larger percentage of individuals who are white or Asian, college-educated, earn more than $50 000, and own their homes reported CO detector ownership and radon screening. Age was the only demographic factor associated with private well testing. Screening for radon and CO detector ownership was positively associated with receiving an influenza shot, colonoscopy, aerobic exercise, and positive self-reported health and not smoking. Conclusions: There is a need to improve rates of environmental risk-reduction behaviors and reduce disparities in the practice of these behaviors through efforts to increase awareness. Public health officials should target outreach to specific populations that do not practice risk-reduction behaviors.
The Influence of Patients' Age on the Outcome of Treatment for Pancreatic Ductal Adenocarcinoma.

OBJECTIVE The aim of the study was to determine the impact of age on curative management and outcomes of patients with pancreatic ductal adenocarcinoma. METHODS Patients who underwent resection for pancreatic ductal adenocarcinoma at 2 units were retrospectively reviewed (between 2005 and 2017) and stratified by age (older patients ≥70 years). Regression analysis was used to explore factors impacting administration of adjuvant chemotherapy and survival. The Kaplan-Meier method was used to estimate overall survival (time from surgery to death). Statistical significance was set at P < 0.05. RESULTS From 2005 to 2014, 222 patients were identified (<70 years, n = 128; ≥70 years, n = 94). Elderly patients were less likely to receive adjuvant chemotherapy compared with younger patients (odds ratio, 0.57, P = 0.041). Tumor stage, margin, and year of surgery (post-2011 vs pre-2011) were not predictors for chemotherapy receipt (P > 0.05). Frailty was the commonest reason (36.8%) to decline chemotherapy in elderly patients. In patients receiving adjuvant chemotherapy, completion rates (P = 0.32) and overall survival (24 months vs 30 months, P = 0.50) were no different. CONCLUSIONS Elderly patients demonstrate similar outcomes to younger yet are less likely to commence chemotherapy because of frailty. Holistic preoperative assessment may improve selection for curative treatment.
Reversible Nontoxic Thermochromic Microcapsules.

Thermochromic materials exhibit colour change in response to a change in temperature. Creating nontoxic microcapsules containing thermochromic materials for applications in ink and film materials is historically challenging. In this study, we develop a nontoxic chlorophenol red (CPR)-water thermochromic system and its microcapsules with silicone shells via reaction between water and octadecyltrichlorosilane (OTS) at the interface of a w/o emulsion. The obtained microcapsules exhibit clear colour change with full reversibility and are successfully used as inks by screen printing and as additives in films. Nontoxicity of both microcapsules and films is demonstrated through cell cytotoxicity assays. These features make these novel materials applicable for the next generation of intelligent sensor, coating and food packaging materials.
Promiscuous Ribozymes and Their Proposed Role in Prebiotic Evolution

The ability of enzymes, including ribozymes, to catalyze side reactions is believed to be essential to the evolution of novel biochemical activities. It has been speculated that the earliest ribozymes, whose emergence marked the origin of life, were low in activity but high in promiscuity, and that these early ribozymes gave rise to specialized descendants with higher activity and specificity. Here, we review the concepts related to promiscuity and examine several cases of highly promiscuous ribozymes. We consider the evidence bearing on the question of whether de novo ribozymes would be quantitatively more promiscuous than later evolved ribozymes or protein enzymes. We suggest that while de novo ribozymes appear to be promiscuous in general, they are not obviously more promiscuous than more highly evolved or active sequences. Promiscuity is a trait whose value would depend on selective pressures, even during prebiotic evolution.
Relevance of apparent diffusion coefficient features for a radiomics‐based prediction of response to induction chemotherapy in sinonasal cancer

In this paper, several radiomics‐based predictive models of response to induction chemotherapy (IC) in sinonasal cancers (SNCs) are built and tested. Models were built as a combination of radiomic features extracted from three types of MRI images: T1‐weighted images, T2‐weighted images and apparent diffusion coefficient (ADC) maps. Fifty patients (aged 54 ± 12 years, 41 men) were included in this study. Patients were classified according to their response to IC (25 responders and 25 nonresponders). Not all types of images were acquired for all of the patients: 49 had T1‐weighted images, 50 had T2‐weighted images and 34 had ADC maps. Only in a subset of 33 patients were all three types of image acquired.
A modified Fox pentagon technique performed using a polytetrafluoroethylene sling in frontalis suspension to treat blepharophimosis syndrome

The purpose of this study was to evaluate the functional and cosmetic outcomes of a new modified Fox pentagon technique performed using polytetrafluoroethylene in frontalis suspension surgery for blepharophimosis syndrome. This retrospective study enrolled 40 patients diagnosed with blepharophimosis syndrome from March 2016 to October 2018. All patients underwent frontalis suspension using a new modified Fox pentagon technique. The functional and cosmetic outcomes were evaluated. After the operation, the mean palpebral fissure height increased from 2.68 to 6.93 in right eyes and from 2.73 to 6.98 in left eyes. The mean MRD1 increased from 0.53 to 3.76 in right eyes and from 0.50 to 3.78 in left eyes. While preoperative to postoperative differences were statistically significant (p < 0.01), there were no significant differences between right and left eyes either before or after the surgery (p > 0.01). All patients achieved good cosmetic results with an average score of 0.6. We have experimentally created a modified Fox pentagon technique performed using a polytetrafluoroethylene sling in a frontalis suspension to treat BPES; this approach yielded favorable cosmetic and functional outcomes.
Deep learning-based clustering approaches for bioinformatics

Abstract Clustering is central to many data-driven bioinformatics research and serves a powerful computational method. In particular, clustering helps at analyzing unstructured and high-dimensional data in the form of sequences, expressions, texts and images. Further, clustering is used to gain insights into biological processes in the genomics level, e.g. clustering of gene expressions provides insights on the natural structure inherent in the data, understanding gene functions, cellular processes, subtypes of cells and understanding gene regulations. Subsequently, clustering approaches, including hierarchical, centroid-based, distribution-based, density-based and self-organizing maps, have long been studied and used in classical machine learning settings. In contrast, deep learning (DL)-based representation and feature learning for clustering have not been reviewed and employed extensively. Since the quality of clustering is not only dependent on the distribution of data points but also on the learned representation, deep neural networks can be effective means to transform mappings from a high-dimensional data space into a lower-dimensional feature space, leading to improved clustering results. In this paper, we review state-of-the-art DL-based approaches for cluster analysis that are based on representation learning, which we hope to be useful, particularly for bioinformatics research. Further, we explore in detail the training procedures of DL-based clustering algorithms, point out different clustering quality metrics and evaluate several DL-based approaches on three bioinformatics use cases, including bioimaging, cancer genomics and biomedical text mining. We believe this review and the evaluation results will provide valuable insights and serve a starting point for researchers wanting to apply DL-based unsupervised methods to solve emerging bioinformatics research problems.
Parent physical and mental health contributions to interpersonal fear avoidance processes in pediatric chronic pain.

Theoretical models and evidence increasingly identify chronic pain as a family issue. To date, much of this work has focused on risk conferred by parental chronic pain status despite evidence suggesting parent mental illness and non-pain-related chronic illness may also contribute to poorer chronic pain outcomes in children. This study is the first to test interpersonal fear avoidance processes as possible mechanisms through which parent health (mental and physical) influences pediatric chronic pain functioning. We used structural equation models (SEM) to test such an integrative model using cross-sectional data from a large clinical registry of 448 dyads of patients 8-18 years old (M=14.57 years; SD=2.38; 327 females) with mixed chronic pain and their parents (403 mothers). As expected, poorer parent global health was indirectly related to greater child pain interference via higher parent pain catastrophizing, and then via greater parent protective behaviors, and child pain catastrophizing. The model demonstrated excellent fit to the data (χ[5] = 5.04, ns; χ/df = 1.01; CFI = 1.00, RMSEA = .004 [90% confidence interval (CI) = . 000-. 066]). Exploratory multiple-group comparison SEM revealed moderation of specific model paths based on child age group (8- to 12-year-olds versus 13- to 18-year-olds) and parent pain status (present versus absent). This study integrates family models of pain with the interpersonal fear avoidance model to extend our mechanistic understanding of parental physical and mental health contributors to pediatric chronic pain.
Comparison of Intralesional Hyaluronic Acid vs. Verapamil for the Treatment of Acute Phase Peyronie's Disease: A Prospective, Open-Label Non-Randomized Clinical Study

Purpose To compare the efficacy and safety of intralesional hyaluronic acid (HA) as compared with verapamil injection in patients with Peyronie's disease (PD). Materials and Methods Between January 2015 and December 2018, men in PD acute phase were prospectively recruited. This open-label, prospective study included 2 different protocols. Group A: 8-week cycle of weekly intraplaque injections with HA; Group B: 8-week cycle of weekly intraplaque injections with verapamil. Penile curvature, plaque size, International Index of Erectile Function (IIEF)-15 score and visual analogue scale (VAS) were assessed at baseline and after 3 months. Results Two-hundred forty-four patients were enrolled. Of these, 125 received intralesional HA (Group A), 119 received intralesional verapamil (Group B). At enrollment, median age was 56.0 years (interquartile range [IQR]=47.0–63.0 years), median curvature 35.0° (IQR=25.0°–45.0°), median IIEF-15 score 19.0 (IQR=16.0–23.0), median VAS 4.0 (IQR=4.0–5.0). Median difference for IIEF-15 was 1.0 (95% confidence interval [CI]=1.12–1.94) in Group A and 0.0 (95% CI=−0.04–0.14) in Group B (p<0.05) and median difference for VAS score was −4.0 (95% CI=−4.11–−3.65) in Group A and −1.0 (95% CI=−0.50–2.01) in Group B (p<0.05). Plaque size decreased by −1.50 mm (IQR=1.60–2.10 mm) in Group A and −1.20 in Group B (p=0.10), while penile curvature decreased by −9.50° (IQR=4.50°–13.00°) in group A and −4.50 (IQR=2.50–7.50) in Group B (p<0.01). Conclusions Intralesional HA injections could represent a reliable treatment option for the conservative management of patients with acute phase of PD.
Invasive pulmonary aspergillosis treatment duration in haematology patients in Europe: An EFISG, IDWP‐EBMT, EORTC‐IDG and SEIFEM survey

Invasive pulmonary aspergillosis (IPA) optimal duration of antifungal treatment is not known. In a joint effort, four international scientific societies/groups performed a survey to capture current practices in European haematology centres regarding management of IPA. We conducted a cross‐sectional internet‐based questionnaire survey in 2017 to assess practices in sixteen European countries concerning IPA management in haematology patients including tools to evaluate treatment response, duration and discontinuation. The following four groups/societies were involved in the project: European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Fungal Infection Study Group (EFISG), Infectious Diseases Working Party‐European Society for Blood and Bone Marrow Transplantation (IDWP‐EBMT), European Organisation for Research and Treatment‐Infectious Disease group (EORTC‐IDG) and Sorveglianza Epidemiologica Infezioni nelle Emopatie (SEIFEM). A total of 112 physicians from 14/16 countries answered the survey. Galactomannan antigen was available in serum and bronchoalveolar lavage in most centres (106/112 [95%] and 97/112 [87%], respectively), quantitative Aspergillus PCR in 27/112 (24%) centres, β‐D‐glucan in 24/112 (21%) and positron emission tomography in 50/112 (45%). Treatment duration differed between haematological malignancies, with a median duration of 6 weeks [IQR 3‐12] for patients with AML, 11 [4‐12] for patients with allogenic stem cell transplantation and GvHD and 6 [3‐12] for patients with lymphoproliferative disease. Treatment duration significantly differed according to country. Essential IPA biomarkers are not available in all European countries, and treatment duration is highly variable according to country. It will be important to provide guidelines to help with IPA treatment cessation with algorithms according to biomarker availability.
Association study of candidate genes with obesity and metabolic traits in antipsychotic-treated patients with first-episode psychosis over a 2-year period

Aims: Patients with a first episode of psychosis (FEP) often display different metabolic disturbances even independently of drug therapy. However, antipsychotic (AP) treatment, especially with second-generation APs, is strongly linked to weight gain, which increases patients’ risk of developing obesity and other metabolic diseases. There is an important genetic risk component that can contribute to the appearance of these disturbances. The aim of the present study was to evaluate the effect of polymorphisms in selected candidate genes on obesity and other anthropometric and metabolic traits in 320 AP-treated FEP patients over the course of a 2-year follow-up. Methods: These patients were recruited in the multicentre PEPs study (Phenotype−genotype and environmental interaction; Application of a predictive model in first psychotic episodes). A total of 127 validated single nucleotide polymorphisms (SNPs) in 18 candidate genes were included in the genetic analysis. Results: After Bonferroni correction, SNPs in ADRA2A, FTO, CNR1, DRD2, DRD3, LEPR and BDNF were associated with obesity, abdominal circumference, triglycerides, HDL cholesterol, and/or percentage of glycated haemoglobin. Conclusions: Although our results should be interpreted as exploratory, they support previous evidence of the impact of these candidate genes on obesity and metabolic status. Further research is required to gain a better knowledge of the genetic variants that can be considered relevant metabolic risk factors. The ability to identify FEP patients at higher risk for these metabolic disturbances would enable clinicians to better select and control their AP treatment.
Molecular Aberrations Associated with Seizure Control in Diffuse Astrocytic and Oligodendroglial Tumors

Diffuse astrocytic and oligodendroglial tumors are frequently associated with symptomatic epilepsy, and predictive seizure control is important for the improvement of patient quality of life. To elucidate the factors related to drug resistance of brain tumor-associated epilepsy from a pathological perspective. From January 2012 to October 2017, 36 patients diagnosed with diffuse astrocytic or oligodendroglial tumors were included. Assessment for seizure control was performed according to the Engel classification of seizures. Patient clinical, radiological, and pathological data were stratified based on the following 16 variables: age, sex, location of tumor, existence of the preoperative seizure, extent of resection, administration of temozolomide, radiation therapy, recurrence, Karnofsky performance scale, isocitrate dehydrogenase 1, 1p/19q co-deletion, Olig2, platelet-derived growth factor receptor alpha, p53, ATRX, and Ki67. These factors were compared between the well-controlled group and drug-resistant seizure group. Twenty-seven patients experienced seizures; of these, 14 cases were well-controlled, and 13 cases were drug-resistant. Neither clinical nor radiological characteristics were significantly different between these two groups, though p53 immunodetection levels were significantly higher, and the frequency of 1p/19q co-deletion was significantly lower in the group with drug-resistant seizures than in the well-controlled group. In the multivariate analysis, only one item was selected according to stepwise methods, and a significant difference was observed for p53 (OR, 21.600; 95% CI, 2.135–218.579; P = 0.009). Upregulation of p53 may be a molecular mechanism underlying drug resistant epilepsy associated with diffuse astrocytic and oligodendroglial tumors.