Miracle-dz/UniFAR-FTUs huggingface dataset:
LSD2 - Joint Denoising and Deblurring of Short and Long Exposure Images with Convolutional Neural Networks

The paper addresses the problem of acquiring highquality photographs with handheld smartphone cameras in low-light imaging conditions. We propose an approach based on capturing pairs of short and long exposure images in rapid succession and fusing them into a single highquality photograph. Unlike existing methods, we take advantage of both images simultaneously and perform a joint denoising and deblurring using a convolutional neural network. The network is trained using a combination of real and simulated data. To that end, we introduce a novel approach for generating realistic short-long exposure image pairs. The evaluation shows that the method produces good images in extremely challenging conditions and outperforms existing denoising and deblurring methods. Furthermore, it enables exposure fusion even in the presence of motion blur.
An update on the latest chemical therapies for reflux esophagitis in children

ABSTRACT Introduction: Gastroesophageal reflux (GER), and its complicated form gastroesophageal reflux disease (GERD) is a common condition in infants and children. As GERD is often considered to cause extra-oesophageal symptoms in children and in the absence of standardized diagnostic and treatment algorithm, many children are inappropriately exposed to empirical anti-reflux treatments, with Acid-Suppressive Medications (ASM); mostly proton pump inhibitors (PPIs). Areas covered: The authors summarize the pharmacological management of pediatric GERD and discuss the efficacy of PPIs as randomized controlled trials have failed to demonstrate their clinical efficacy in the pediatric population. They consider the controversies surrounding the use of PPIs in the pediatric population as increasing evidence suggests of, although controversially, an increased risk of adverse events such as infection of the respiratory or gastrointestinal tract. Esophagitis is a complication that has a significant impact on weight gain and growth, as well as on the quality of life, and in such case, the benefit of treatment largely outweighs the risk. Expert opinion: Clinicians should reserve ASM use for infants and children with proven esophagitis and avoid their routine use in patients with merely symptoms of GER. Treatment need and options must be frequently re-evaluated to reduce the risks associated with ongoing therapy.
Prevalence of Clostridium perfringens netE and netF toxin genes in the feces of dogs with acute hemorrhagic diarrhea syndrome

Background Recently, novel pore‐forming toxin genes designated netE and netF were identified in a Clostridium perfringens type A strain isolated from a dog with acute hemorrhagic diarrhea. Objectives Pore‐forming toxins could play an important role in the disease pattern of acute hemorrhagic diarrhea syndrome (AHDS) in dogs. Thus, we aimed to determine the prevalence of C. perfringens genes encoding for netE and netF in the feces of dogs with AHDS and to evaluate any association between selected clinical variables and the presence of these toxin genes. Animals In total, 174 dogs were included in the study. Methods Fecal samples of all dogs were tested by real‐time polymerase chain reaction for netE and netF genes. Time to recovery, hospitalization time, and selected laboratory variables were compared between dogs with AHDS that were positive or negative for the toxin genes. Results A significant difference was found among the 3 groups in the prevalence of the pore‐forming toxin genes netE and netF: dogs with AHDS: 26 of 54 (48.1%); dogs with canine parvovirus (CPV) infection: 0 of 54 (0%); and healthy dogs: 8 of 66 (12.1%; P < .001). In dogs with AHDS, no significant difference was detected in any variables evaluated between netE‐positive and netF‐positive and netE‐negative and netF‐negative dogs. Conclusions and Clinical Importance The prevalence of C. perfringens encoding for netE and netF is significantly higher in dogs with AHDS compared to control dogs. Further studies are warranted to evaluate whether these toxins are an inciting cause for AHDS in dogs.
Effects of Acute Fluorene‐9‐Bisphenol Exposure on Mouse Oocyte in vitro Maturation and Its Possible Mechanisms

Fluorene‐9‐bisphenol (BHPF), a substitute of bisphenol A (BPA) used in the production of the so‐called “BPA‐free” plastics, has now been shown to be released from commercial plastic bottles into drinking water and has strong anti‐estrogenic activity in mice, which suggests that BHPF is also an environmental toxin. However, whether BHPF exposure has effects on mouse oocyte development is unknown. In this study, the influence of acute exposure to BHPF (50–150 μM, 12 hr) on mouse oocyte maturation and its possible mechanisms were investigated. Of note, 50‐μM BHPF had no effects on the maturation of mouse oocytes, whereas 100‐ and 150‐μM BHPF significantly blocked germinal vesicle breakdown and led to the failure of first polar body extrusion. Particularly, 100‐μM BHPF exposure severely decreased the cellular adenosine triphosphate in a time‐dependent manner, which finally brought out the loss of spindles. In addition, the actin cytoskeleton was also impaired. The defective mitochondrial dynamics and decreased mitochondrial DNA implied the damage of mitochondria in BHPF‐treated oocytes. Increased PINK1, Beclin1, and LC3B protein level and decreased TOMM20 and TOMM17A protein level illustrated that mitophagy was induced, which also confirmed that BHPF exposure impaired the cellular mitochondria. Moreover, BHPF induced reactive oxygen species accumulation and early apoptosis. Oocyte quality was also impaired by BHPF exposure through altering histone modifications evidenced by increased H3K9me3 and H3K27me3 levels. Collectively, our results indicated that BHPF exposure disrupted mouse oocyte maturation and reduced oocyte quality through affecting cytoskeleton architecture, mitochondrial function, oxidative stress, apoptosis, and histone modifications. Environ. Mol. Mutagen. 60:243–253, 2019. © 2018 Wiley Periodicals, Inc.
Risk factors for permanent childhood hearing impairment

Objective While several perinatal risk factors for permanent childhood hearing impairment (PCHI) are known, association with gestational length remains unclear. We hypothesised that shorter gestational length predicts higher PCHI risk. Design 19 504 participants from the UK Millennium Cohort Study (born 2000–2002, prior to newborn screening). Methods Multivariable discrete-time survival analysis to examine associations between parent-reported PCHI by age 11 years and gestational length, plus other prespecified factors. Results PCHI affected 2.1 per 1000 children (95% CI 1.5 to 3.0) by age 11; however, gestational length did not predict PCHI risk (HR, 95% CI 1.00, 0.98 to 1.03 per day increase). Risk was increased in those with neonatal illness, with or without admission to neonatal care (6.33, 2.27 to 17.63 and 2.62, 1.15 to 5.97, respectively), of Bangladeshi or Pakistani ethnicity (2.78, 1.06 to 7.31) or born to younger mothers (0.92, 0.87 to 0.97 per year). Conclusion Neonatal illness, rather than gestational length, predicts PCHI risk. Further research should explore associations with ethnicity.
Adverse pregnancy and neonatal outcomes associated with Neisseria gonorrhoeae, Mycoplasma genitalium, M. hominis, Ureaplasma urealyticum and U. parvum: a systematic review and meta-analysis protocol

Introduction Several bacterial sexually transmitted and genital mycoplasma infections during pregnancy have been associated with poor pregnancy and perinatal outcomes. Comprehensive and systematic information about associations between sexually transmitted infections (STI) and genital infections in pregnancy and adverse perinatal outcomes is needed to improve understanding about the evidence for causal associations between these infections and adverse pregnancy and neonatal outcomes. Our primary objective is to systematically review the literature about associations between: (1) Neisseria gonorrhoeae in pregnancy and preterm birth; (2) Mycoplasma genitalium in pregnancy and preterm birth; (3) M. hominis, Ureaplasma urealyticum and/or U. parvum in pregnancy and preterm birth. Methods and analysis We will undertake a systematic search of Medline, Excerpta Medica database and the Cochrane Library and Cumulative Index to Nursing and Allied Health Literature. Following an initial screening of titles by one reviewer, abstracts will be independently assessed by two reviewers before screening of full-text articles. To exclude a manuscript, both reviewers need to agree on the decision. Any discrepancies will be resolved by discussion, or the adjudication of a third reviewer. Studies will be included if they report testing for one or more of N. gonorrhoeae, M. genitalium, M. hominis, U. urealyticum and/or U. parvum during pregnancy and report pregnancy and/or birth outcomes. In this review, the primary outcome is preterm birth. Secondary outcomes are premature rupture of membranes, low birth weight, spontaneous abortion, stillbirth, neonatal mortality and ophthalmia neonatorum. We will use standard definitions, or definitions reported by study authors. We will examine associations between exposure and outcome in forest plots, using the I2 statistic to examine between study heterogeneity. Where appropriate, we will use meta-analysis to combine results of individual studies. Ethics and dissemination This systematic review of published literature does not require ethical committee approval. Results of this review will be published in a peer reviewed, open access journal. PROSPERO registration number CRD42016050962.
Fungi infecting woody plants: emerging frontiers

You are free to share to copy, distribute and transmit the work, under the following conditions: Attribution: You must attribute the work in the manner specified by the author or licensor (but not in any way that suggests that they endorse you or your use of the work). Non-commercial: You may not use this work for commercial purposes. No derivative works: You may not alter, transform, or build upon this work. For any reuse or distribution, you must make clear to others the license terms of this work, which can be found at http://creativecommons.org/licenses/by-nc-nd/3.0/legalcode. Any of the above conditions can be waived if you get permission from the copyright holder. Nothing in this license impairs or restricts the author’s moral rights. Persoonia 40, 2018: i– iii ISSN (Online) 1878-9080 www.ingentaconnect. com/content/nhn/pimj https://doi.org/10.3767/persoonia.2018. 40.00 EDITORIAL
Evaluation of the psychometric properties of the Brazilian version of the Oral Health Literacy Assessment in Spanish and development of a shortened form of the instrument

Objective The objective of this study was to investigate the psychometric properties of the Oral Health Literacy Assessment in Spanish (OHLA-S) for the Brazilian-Portuguese language using robust analysis and with the results disclose possibilities to develop a shorter and more valid instrument. Methods OHLA-S is an oral health literacy instrument comprising a word recognition section and a comprehension section. It consists of 24 dental words. It was translated into the Brazilian-Portuguese language (OHLA-B) and its psychometric properties were evaluated in a random sample of 250 adults aged 20–59 years. To assess the dimensionality and factor structure were tested by means of Exploratory Factor Analysis (EFA) and Confirmatory Factor Analysis (CFA). Reliability was assessed using two indicators: Cronbach's alpha and McDonald’s Omega. Results EFA and CFA demonstrated that the OHLA-B with 24 items did not present an adequate adjustment of the model, compromising its validity. In addition, reliability values at 0.50 for Cronbach's alpha and 0.67 for McDonald's omega were below the minimum acceptable rate of 0.70. As no support was found for the original structure, we decided to proceed with the withdrawal of individual items and successive reanalysis of the model until the indicators were adjusted in a shorter instrument. A new structure with 15 items produced an instrument with two dimensions and a better goodness of fit than the original instrument. The Alpha and Omega reliability index values increased to 0.83 and 0.80, respectively, and all scores were better in the OLHA-B with 15 items than in the instrument with 24 items. Conclusion OLHA-B with the original structure composed by 24 items did not show acceptable construct validity. The shorter version with 15 items showed more promising results for assessing oral health literacy levels in the Brazilian population.
The biological embedding of neonatal stress exposure: A conceptual model describing the mechanisms of stress‐induced neurodevelopmental impairment in preterm infants

The biological embedding of early life stress exposure may result in life-long neurodevelopmental impairment in preterm infants. Infants hospitalized in the neonatal intensive care unit are exposed to significant experiential, environmental, and physiologic stressors over the course of their extended hospitalization. Stress exposure during the sensitive period of brain development may alter biological processes, including functioning of the immune system, the autonomic nervous system, and the hypothalamic-pituitary-adrenal axis as well as gene expression. These alterations may subsequently affect brain structure and function. Changes to these processes may mediate the relationship between neonatal stress exposure and neurodevelopment in preterm infants and represent potential therapeutic targets to improve long-term outcomes. The purpose of this paper is to introduce a conceptual model, based on published research, that describes the mechanisms mediating stress exposure and neurodevelopment impairment in preterm infants and to provide the theoretical foundation on which to base future descriptive research, intervention studies, and clinical care.
Protein variability in cerebrospinal fluid and its possible implications for neurological protein biomarker research

Cerebrospinal fluid is investigated in biomarker studies for various neurological disorders of the central nervous system due to its proximity to the brain. Currently, only a limited number of biomarkers have been validated in independent studies. The high variability in the protein composition and protein abundance of cerebrospinal fluid between as well as within individuals might be an important reason for this phenomenon. To evaluate this possibility, we investigated the inter- and intraindividual variability in the cerebrospinal fluid proteome globally, with a specific focus on disease biomarkers described in the literature. Cerebrospinal fluid from a longitudinal study group including 12 healthy control subjects was analyzed by label-free quantification (LFQ) via LC-MS/MS. Data were quantified via MaxQuant. Then, the intra- and interindividual variability and the reference change value were calculated for every protein. We identified and quantified 791 proteins, and 216 of these proteins were abundant in all samples and were selected for further analysis. For these proteins, we found an interindividual coefficient of variation of up to 101.5% and an intraindividual coefficient of variation of up to 29.3%. Remarkably, these values were comparably high for both proteins that were published as disease biomarkers and other proteins. Our results support the hypothesis that natural variability greatly impacts cerebrospinal fluid protein biomarkers because high variability can lead to unreliable results. Thus, we suggest controlling the variability of each protein to distinguish between good and bad biomarker candidates, e.g., by utilizing reference change values to improve the process of evaluating potential biomarkers in future studies.
Self-organising coordinate transformation with peaked and monotonic gain modulation in the primate dorsal visual pathway

We study a self-organising neural network model of how visual representations in the primate dorsal visual pathway are transformed from an eye-centred to head-centred frame of reference. The model has previously been shown to robustly develop head-centred output neurons with a standard trace learning rule [1], but only under limited conditions. Specifically it fails when incorporating visual input neurons with monotonic gain modulation by eye-position. Since eye-centred neurons with monotonic gain modulation are so common in the dorsal visual pathway, it is an important challenge to show how efferent synaptic connections from these neurons may self-organise to produce head-centred responses in a subpopulation of postsynaptic neurons. We show for the first time how a variety of modified, yet still biologically plausible, versions of the standard trace learning rule enable the model to perform a coordinate transformation from eye-centred to head-centred reference frames when the visual input neurons have monotonic gain modulation by eye-position.
Unsupervised speech recognition through spike-timing-dependent plasticity in a convolutional spiking neural network

Speech recognition (SR) has been improved significantly by artificial neural networks (ANNs), but ANNs have the drawbacks of biologically implausibility and excessive power consumption because of the nonlocal transfer of real-valued errors and weights. While spiking neural networks (SNNs) have the potential to solve these drawbacks of ANNs due to their efficient spike communication and their natural way to utilize kinds of synaptic plasticity rules found in brain for weight modification. However, existing SNN models for SR either had bad performance, or were trained in biologically implausible ways. In this paper, we present a biologically inspired convolutional SNN model for SR. The network adopts the time-to-first-spike coding scheme for fast and efficient information processing. A biological learning rule, spike-timing-dependent plasticity (STDP), is used to adjust the synaptic weights of convolutional neurons to form receptive fields in an unsupervised way. In the convolutional structure, the strategy of local weight sharing is introduced and could lead to better feature extraction of speech signals than global weight sharing. We first evaluated the SNN model with a linear support vector machine (SVM) on the TIDIGITS dataset and it got the performance of 97.5%, comparable to the best results of ANNs. Deep analysis on network outputs showed that, not only are the output data more linearly separable, but they also have fewer dimensions and become sparse. To further confirm the validity of our model, we trained it on a more difficult recognition task based on the TIMIT dataset, and it got a high performance of 93.8%. Moreover, a linear spike-based classifier—tempotron—can also achieve high accuracies very close to that of SVM on both the two tasks. These demonstrate that an STDP-based convolutional SNN model equipped with local weight sharing and temporal coding is capable of solving the SR task accurately and efficiently.
Genomic Reduction at TTC Repeats in the Bacterial Genome of Treated Cases of Hansen's Disease: A Possible Survival Mechanism of Mycobacterium leprae

Introduction: Mycobacterium leprae has a small genome and a tendency of persisting as a very low-grade infection. The authors have shown earlier, that the changes in TTC repeats, in M. leprae genome may contribute to the restriction of the pathogenicity of the bacterium and its survival strategy in case of pure neural Hansen's disease. We suspect, that a similar genomic reduction if happens in treated cases of Hansen's disease, can be a determining factor for developing persisters and relapse. Aim: The present study aimed to find out if there was any evidence of genomic reduction in treated cases of Hansen's disease that showed microbiological nonresponse. Methods: Skin biopsies were taken from treated cases of Hansen's disease at tertiary centers in Kolkata and at Raipur who had bacterial index (BI) unchanged or increased compared to their pretreatment BI. Analysis for the mutation in rpoB gene and folP1 gene were done to rule out rifampicin and dapsone resistance, respectively. The entire TTC repeat region of the bacteria was amplified by polymerase chain reaction and was subjected to sequencing. The obtained sequences were then analyzed by CLUSTALW. Results: A total of 127 patients were included in the study of which in 52 the BI remained same and 75 had an increase in BI, even after 6 months of completion of multidrug therapy. Among the samples, 2 had positive rpoB gene mutation. No mutation was found in the folP1 gene. The TTC repeat of both the rpoB-resistant samples was found to have 17 copies, which matched their pretreatment copy number. In other 125 cases, 60 cases showed no change from their pretreatment TTC number. Of those 65 samples that showed evidence of genomic reduction, 11 samples showed one copy, 41 showed 2 copies, and 13 showed 3 copies deletion. We also observed a significant regional variation. Conclusion: We concluded that there was evidence of genomic reduction, which might lead to microbiological nonresponse in treated cases of Hansen's disease. This indicated a possibility of future persistence and relapse.
Frontotemporal dementia causative CHMP2B impairs neuronal endolysosomal traffic-rescue by TMEM106B knockdown

See Bechek and Gitler (doi:10.1093/brain/awy294) for a scientific commentary on this article. Mutations in the endosome-associated protein CHMP2B cause frontotemporal dementia (FTD). Clayton et al. report a mechanism for CHMP2B-mediated neuronal dysfunction and a potential therapeutic strategy targeting the TMEM106B gene, a major risk factor for FTD. Targeting TMEM106B may be relevant to a broad range of FTDs.
Development of actionable quality indicators and an action implementation toolbox for appropriate antibiotic use at intensive care units: A modified-RAND Delphi study

Introduction Extensive antibiotic use makes the intensive care unit (ICU) an important focus for antibiotic stewardship programs. The aim of this study was to develop a set of actionable quality indicators for appropriate antibiotic use at ICUs and an implementation toolbox, which can be used to assess and improve the appropriateness of antibiotic use in the treatment of adult patients at an ICU. Methods A four round modified-RAND Delphi procedure was used. Potential indicators were identified by a multidisciplinary panel of 15 Dutch experts, from international literature and guidelines. Using an online survey, the identified indicators were rated on three criteria: relevance, actionability and feasibility. Experts discussed and rated the indicators for the second time during a face-to-face consensus meeting. During a final consensus meeting the toolbox was developed, containing potential barriers and improvement strategies which were identified using a validated checklist by Flottorp et al., and if available also containing supporting material. Results The first round resulted in 24 potential indicators. After the final meeting a set of three process indicators, one structure indicator and one quantity metric remained: 1) perform at least two sets of blood cultures before start of empirical systemic therapy; 2) perform therapeutic drug monitoring in patients treated with vancomycin or aminoglycosides; 3) perform surveillance cultures if selective digestive or oropharyngeal decontamination is applied at the ICU; 4) biannual face-to-face meetings between ICU and microbiology staff in which local resistance rates are discussed; and 5) quantitative antibiotic use at the ICU expressed in days of therapy (DOT). The toolbox contains 24 unique barriers and 37 improvement strategies. Conclusions Our study identified a set of four actionable quality indicators and one quantity metric, together with an implementation toolbox, to improve appropriate antibiotic use at ICUs.