Miracle-dz/UniFAR-FTUs huggingface dataset:
Biogeochemical Cycling by a Low-Diversity Microbial Community in Deep Groundwater

Olkiluoto, an island on the south-west coast of Finland, will host a deep geological repository for the storage of spent nuclear fuel. Microbially induced corrosion from the generation of sulphide is therefore a concern as it could potentially compromise the longevity of the copper waste canisters. Groundwater at Olkiluoto is geochemically stratified with depth and elevated concentrations of sulphide are observed when sulphate-rich and methane-rich groundwaters mix. Particularly high sulphide is observed in methane-rich groundwater from a fracture at 530.6 mbsl, where mixing with sulphate-rich groundwater occurred as the result of an open drill hole connecting two different fractures at different depths. To determine the electron donors fuelling sulphidogenesis, we combined geochemical, isotopic, metagenomic and metaproteomic analyses. This revealed a low diversity microbial community fuelled by hydrogen and organic carbon. Sulphur and carbon isotopes of sulphate and dissolved inorganic carbon, respectively, confirmed that sulphate reduction was ongoing and that CO2 came from the degradation of organic matter. The results demonstrate the impact of introducing sulphate to a methane-rich groundwater with limited electron acceptors and provide insight into extant metabolisms in the terrestrial subsurface.
Association between rs2278426 (C/T) and rs892066 (C/G) variants of ANGPTL8 (betatrophin) and susceptibility to type2 diabetes mellitus

Angiopoietin‐like protein 8 (ANGPTL8) is a hormone that mainly secreted from the liver and adipose tissue and plays an important role in the proliferation of pancreatic beta cells and lipid metabolism. Therefore, we studied the association of ANGPTL8 rs2278426 (C/T) and rs892066 (C/G) polymorphisms with the risk of type 2 diabetes mellitus (T2DM) and their association with biochemical parameters.
How Breath-Control Can Change Your Life: A Systematic Review on Psycho-Physiological Correlates of Slow Breathing

Background: The psycho-physiological changes in brain-body interaction observed in most of meditative and relaxing practices rely on voluntary slowing down of breath frequency. However, the identification of mechanisms linking breath control to its psychophysiological effects is still under debate. This systematic review is aimed at unveiling psychophysiological mechanisms underlying slow breathing techniques (<10 breaths/minute) and their effects on healthy subjects. Methods: A systematic search of MEDLINE and SCOPUS databases, using keywords related to both breathing techniques and to their psychophysiological outcomes, focusing on cardio-respiratory and central nervous system, has been conducted. From a pool of 2,461 abstracts only 15 articles met eligibility criteria and were included in the review. The present systematic review follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Results: The main effects of slow breathing techniques cover autonomic and central nervous systems activities as well as the psychological status. Slow breathing techniques promote autonomic changes increasing Heart Rate Variability and Respiratory Sinus Arrhythmia paralleled by Central Nervous System (CNS) activity modifications. EEG studies show an increase in alpha and a decrease in theta power. Anatomically, the only available fMRI study highlights increased activity in cortical (e.g., prefrontal, motor, and parietal cortices) and subcortical (e.g., pons, thalamus, sub-parabrachial nucleus, periaqueductal gray, and hypothalamus) structures. Psychological/behavioral outputs related to the abovementioned changes are increased comfort, relaxation, pleasantness, vigor and alertness, and reduced symptoms of arousal, anxiety, depression, anger, and confusion. Conclusions: Slow breathing techniques act enhancing autonomic, cerebral and psychological flexibility in a scenario of mutual interactions: we found evidence of links between parasympathetic activity (increased HRV and LF power), CNS activities (increased EEG alpha power and decreased EEG theta power) related to emotional control and psychological well-being in healthy subjects. Our hypothesis considers two different mechanisms for explaining psychophysiological changes induced by voluntary control of slow breathing: one is related to a voluntary regulation of internal bodily states (enteroception), the other is associated to the role of mechanoceptors within the nasal vault in translating slow breathing in a modulation of olfactory bulb activity, which in turn tunes the activity of the entire cortical mantle.
Standards of validity and the validity of standards in behavioral software engineering research: the perspective of psychological test theory

Background. There are some publications in software engineering research that aim at guiding researchers in assessing validity threats to their studies. Still, many researchers fail to address many aspects of validity that are essential to quantitative research on human factors. Goal. This paper has the goal of triggering a change of mindset in what types of studies are the most valuable to the behavioral software engineering field, and also provide more details of what construct validity is. Method. The approach is based on psychological test theory and draws upon methods used in psychology in relation to construct validity. Results. In this paper, I suggest a different approach to validity threats than what is commonplace in behavioral software engineering research. Conclusions. While this paper focuses on behavioral software engineering, I believe other types of software engineering research might also benefit from an increased focus on construct validity.
Effects of Multiple Forms of Information Bias on Estimated Prevalence of Suicide Attempts According to Sexual Orientation: An Application of a Bayesian Misclassification Correction Method to Data From a Systematic Review

Multiple epidemiologic studies demonstrate a disparity in suicide risk between sexual minority (lesbian, gay, bisexual) and heterosexual populations; however, both "exposure" (sexual minority status) and outcome (suicide attempts) may be affected by information bias related to errors in self-reporting. We therefore applied a Bayesian misclassification correction method to account for possible information biases. A systematic literature search identified studies of lifetime suicide attempts in sexual minority and heterosexual adults, and frequentist meta-analysis was used to generate unadjusted estimates of relative risk. A Bayesian model accounting for prior information about sensitivity and specificity of exposure and outcome measures was used to adjust for misclassification biases. In unadjusted frequentist analysis, the relative risk of lifetime suicide attempt comparing sexual minority with heterosexual groups was 3.38 (95% confidence interval: 2.65, 4.32). In Bayesian reanalysis, the estimated prevalence was slightly reduced in heterosexual adults and increased in sexual minority adults, yielding a relative risk of 4.67 (95% credible interval: 3.94, 5.73). The disparity in lifetime suicide attempts between sexual minority and heterosexual adults is greater than previously estimated, when accounting for multiple forms of information bias. Additional research on the impact of information bias in studies of sexual minority health should be pursued.
Variations in fatty acid composition of Laoshan goat milk from partum to 135 days postpartum.

The objective of this study was to characterize the variations in fatty acid (FA) profile during 7 days of colostrum production and 5 months of mature milk production in Laoshan goats. The individual FA profiles of each sample were investigated by gas chromatography-mass spectrometry. Significant differences in FAs were found between colostrum and mature milk. The contents of saturated fatty acids (SFA), unsaturated fatty acids (UFA), monounsaturated fatty acids (MUFA), and polyunsaturated fatty acids (PUFA), and sum of C6, C8, and C10 (SC6+C8+C10 ) were all significantly affected by lactation period. Furthermore, there was no significant difference in the ratio of UFA/SFA or C18:2 (cis9, cis12-octadecadienoic acid)/C18:3 (all cis-9,12,15-octadecatrienoic acid) during the lactation period. The highest concentrations of SC6+C8+C10 , UFA, MUFA, and PUFA appeared in colostrum, but the highest SFA content was in mature milk. The highest proportions of SC6+C8+C10 and SFA were 11.32% and 79.55% on 5th day and 135th day respectively. By contrast, the lowest proportion of UFA was 20.45% on the 135th day. C14:0 (10.93%-12.87%), C16:0 (27.54%-36.65%), C18:0 (10.47%-14.59%), and C18:1 (18.80%-30.61%) were the most predominant FAs in goat milk with significant differences during the 135 days lactation period except C18:0. In conclusion, the results of this study suggest that the lactation time has a pronounced effect on the FA compositions of goat milk.
Peroxisome proliferator-activated receptor gamma co-activator-1 alpha in depression and the response to electroconvulsive therapy

Abstract Background The transcriptional coactivator peroxisome proliferator-activated receptor-γ coactivator (PGC-1α), termed the ‘master regulator of mitochondrial biogenesis’, has been implicated in stress and resilience to stress-induced depressive-like behaviours in animal models. However, there has been no study conducted to date to examine PGC-1α levels in patients with depression or in response to antidepressant treatment. Our aim was to assess PGC-1α mRNA levels in blood from healthy controls and patients with depression pre-/post-electroconvulsive therapy (ECT), and to examine the relationship between blood PGC-1α mRNA levels and clinical symptoms and outcomes with ECT. Methods Whole blood PGC-1α mRNA levels were analysed in samples from 67 patients with a major depressive episode and 70 healthy controls, and in patient samples following a course of ECT using quantitative real-time polymerase chain reaction (qRT-PCR). Exploratory subgroup correlational analyses were carried out to determine the relationship between PGC-1α and mood scores. Results PGC-1α levels were lower in patients with depression compared with healthy controls (p = 0.03). This lower level was predominantly accounted for by patients with psychotic unipolar depression (p = 0.004). ECT did not alter PGC-1α levels in the depressed group as a whole, though exploratory analyses revealed a significant increase in PGC-1α in patients with psychotic unipolar depression post-ECT (p = 0.045). We found no relationship between PGC-1α mRNA levels and depression severity or the clinical response to ECT. Conclusions PGC-1α may represent a novel therapeutic target for the treatment of depression, and be a common link between various pathophysiological processes implicated in depression.
Clinical Characteristics of Functional Movement Disorders: A Clinic-based Study

Background Functional movement disorders are recognized as a “crisis” in neurology. We aimed to determine the rate of incidence of functional movement disorder patients at a university outpatient neurology clinic in South Korea, and highlight the clinical and phenomenological characteristics. Methods Patients who were assessed by a movement disorders neurologist at a university hospital between March 2016 and May 2017 were screened for functional movement disorders. Demographic and clinical data were reviewed, and the phenomenology of movements was studied. Results Of 321 patients evaluated for the chief complaint of a movement abnormality, approximately 10% (31 patients) were diagnosed with a functional movement disorder. The female to male ratio was 7:1 (27 females to four males). The mean age at presentation was 53 years (standard error 3.6 years), and the mean disease duration was 5 years (standard error 1.4 years). Sixty-one percent (19 out of 31 patients) had a past medical history of depression, anxiety, or other psychiatric illnesses. Tremor and speech abnormalities were most prevalent (19 and 12 patients, respectively). Onset was reported to be abrupt in 14 patients (45%). Thirteen (42%) patients were found to have improvement at a follow-up visit, 10 (32%) had no improvement, and eight (26%) were lost to follow-up. Discussion Functional movement disorders are not uncommon in the outpatient neurology clinic. Our results confirm that tremor is the most frequent movement occurring in functional movement disorders, and the most commonly affected body parts were found to be the upper and lower extremities. Speech was also found to be frequently involved (39%). Patients with no improvement at follow-up had longer mean disease duration (6.2 years), consistent with previous observations that prolonged symptom duration is associated with poor clinical outcome. Our study results obtained from a Korean population suggest that previous observations on functional movement disorders from other regions hold true in Eastern Asia.
Cascaded Mutual Modulation for Visual Reasoning

Visual reasoning is a special visual question answering problem that is multi-step and compositional by nature, and also requires intensive text-vision interactions. We propose CMM: Cascaded Mutual Modulation as a novel end-to-end visual reasoning model. CMM includes a multi-step comprehension process for both question and image. In each step, we use a Feature-wise Linear Modulation (FiLM) technique to enable textual/visual pipeline to mutually control each other. Experiments show that CMM significantly outperforms most related models, and reach state-of-the-arts on two visual reasoning benchmarks: CLEVR and NLVR, collected from both synthetic and natural languages. Ablation studies confirm the effectiveness of CMM to comprehend natural language logics under the guidence of images. Our code is available at https://github.com/FlamingHorizon/CMM-VR.
Paediatric psychotropic prescribing practices in Ireland

Objectives This study describes the attitudes, knowledge and prescribing of psychotropic medication in children. Method A study-specific questionnaire was mailed to all child psychiatrists, paediatricians and a group of registered general practitioners (GPs) from a selected Child and Adolescent Mental Health Services catchment area. Results In the 116 respondents who replied (39% response rate), psychotropic medication was generally valued and used by all groups (70.1%). Respondents believed that the majority (61.9%) of their non-medical colleagues would also value/support the use of medication and this endorsement influenced the respondents’ prescribing rates. Initiating medication was viewed as the province of child psychiatry (78.6%). Medication is felt to be justified in a wide variety of mental health disorders, their use being reserved for severe presentations, with psychostimulants and selective serotonin reuptake inhibitors being most used. A significant number of GPs (60.9%) and paediatricians (63.4%) were felt to be lacking in competence in psychotropic prescribing, with a general request for more seminars in this area (61.5%) with almost half (45%) of them believing that they would prescribe more often. Conclusion The use of psychotropic medication in children remains a valued and common practice in Ireland. Attitudinal and practice differences across professional groups exist, and although the experience is one of relative safety there was a strong desire for further education leading to a perceived increase in utilisation. The impact of perceived public opinion regarding psychotropic prescribing along with a lack of competence may represent a major barrier to effective prescribing, thus highlighting the importance of ongoing professional development and increased public health initiatives to increase knowledge and understanding in this increasingly important area.
Immunopathological Features of Severe Chronic Atopic Keratoconjunctivitis and Effects of Topical Cyclosporine Treatment

ABSTRACT Purpose: To assess differential roles of inflammatory cells in pathophysiology of severe atopic keratoconjunctivitis (AKC) and evaluate immunomodulatory effects of topical cyclosporine A (CsA). Methods: A total of 10 patients with severe, steroid-dependent/resistant chronic active AKC were treated using frequent topical CsA 0.05% as monotherapy for 2 months. Conjunctival biopsy specimens before and after treatment were examined using immunohistochemistry. A total of 10 healthy age-matched adults served as the control group. Results: Baseline AKC samples revealed greater cluster of differentiation 4 (CD4), interferon gamma (IFNγ), human leukocyte antigen–D-related (HLA-DR) positive cell densities compared with healthy controls (P < 0.05), as well as interleukin (IL)-17 (P = 0.08). Topical CsA treatment induced a significant reduction in CD4 and IL-17 expressions (P < 0.05); post-treatment levels were same as normals (P > 0.05). Despite reduction after treatment (P = 0.06), HLA-DR expression remained higher than controls (P < 0.05). Conclusions: AKC-related conjunctival inflammation appears to be mediated by delayed hypersensitivity. In this short-term trial, frequent topical CsA improved conjunctival inflammation.
Pore detection in high-resolution fingerprint images using Deep Residual Network

This letter presents a residual learning-based convolutional neural network, referred to as DeepResPore, for detection of pores in high-resolution fingerprint images. Specifically, the proposed DeepResPore model generates a pore intensity map from the input fingerprint image. Subsequently, the local maxima filter is operated on the pore intensity map to identify the pore coordinates. The results of our experiments indicate that the proposed approach is effective in extracting pores with a true detection rate of 94:49% on Test set I and 93:78% on Test set II of the publicly available PolyU HRF dataset. Most importantly, the proposed approach achieves state-of-the-art performance on both test sets.
Novel film-forming formulations of the biocontrol agent Candida sake CPA-1: biocontrol efficacy and performance at field conditions in organic wine grapes.

BACKGROUND The biocontrol agent (BCA) Candida sake CPA-1 has previously effectively reduced Botrytis bunch rot (BBR) and it was also suggested as a promising strategy to control sour rot in grapes under field conditions. However, biocontrol efficacy of solid formulations of CPA-1 has never been tested in field trials. The present study aims to confirm the efficacy against BBR and sour rot in grapes under field conditions of two novel formulations recently developed by the addition of biodegradable coatings using a fluidized-bed spray-drying system. RESULTS Novel film-forming formulations of the BCA C. sake CPA-1 controlled B. cinerea as well as liquid formulation. Sour rot control resulted better in the second season and severity reductions were more satisfactory than incidence control. Visual and cryoSEM observations revealed that film-forming treatments were uniformly distributed on plant surfaces. CPA-1 coating could be observed on grapes at harvest time. CONCLUSION The results of this work suggest that solid formulations would be a competitive alternative to conventional fungicides because they were easy to package and transport, and cell viability could be maintained for a long period of time. © 2018 Society of Chemical Industry.
The Effect of Ambulance Response Time on Survival Following Out-of-Hospital Cardiac Arrest.

BACKGROUND Out of hospital cardiac arrest (OHCA) is one of the more common causes of death in Germany. Ambulance response time is an important planning parameter for emergency medical services (EMS) systems. We studied the effect of ambulance response time on survival after resuscitation from OHCA. METHODS We analyzed data from the German Resuscitation Registry for the years 2010-2016. First, we used a multivariate logistic regression analysis to determine the effect of ambulance response time (defined as the interval from the alarm to the arrival of the first rescue vehicle) on the hospital-discharge rate (in percent), depending on various factors, including resuscitation by bystanders. Second, we compared faster and slower EMS systems (defined as those arriving on the scene within 8 minutes in more than 75% of cases or in ≤ 75% of cases) with respect to the frequency of resuscitation and the number of surviving patients. RESULTS Our analysis of data from a total of 10 853 patients in the logistical regression model revealed that the rate of hospital discharge was significantly affected by the ambulance response time, bystander resuscitation, past medical history, age, witnessed vs. unwitnessed collapse, the initial heart rhythm, and the site of the collapse. The success of resuscitation was inversely related to the ambulance response time; thus, among patients who did not receive bystander resuscitation, the discharge rate declined from 12.9% at a mean response time of 1 minute and 10 seconds to 6.4% at a mean response time of 9 minutes and 47 seconds. Twelve faster EMS systems and 13 slower ones were identified, with a total of 9669 and 7865 resuscitated patients, respectively. The faster EMS systems initiated resuscitation more frequently and also had a higher discharge rate with good neurological outcome in proportion to the population of the catchment area (7.7 versus 5.6 persons per 100 000 population per year, odds ratio [OR] 0.72, 95% confidence interval [0.66; 0.79], p<0.001). CONCLUSION Rapid ambulance response is associated with a higher rate of survival from OHCA with good neurological outcome. The response time, independently of whether bystander resuscitation measures are provided, ha^ a significant independent effect on the survival rate. In drawing conclusions from these findings, one should bear in mind that this was a retrospective registry study, with the corresponding limitations.
Plasma surfactant protein-A levels in apparently healthy smokers, stable and exacerbation COPD patients

Objective: To compare the plasma level of surfactant protein-A in apparently healthy smokers, stable and exacerbation Chronic Obstructive Pulmonary Disease (COPD) patients. Methods: This was a comparative study conducted from January, 2015 to March, 2016. This study was conducted on 87 subjects of both gender and age between 30-70 years. Of the total 87 subjects; 29 subjects were “healthy smokers” selected from general population as control group. Another 29 were “stable COPD” patients free of exacerbation since last six weeks. Lastly, another 29 subjects were “exacerbated COPD” patients with 7-10 days of exacerbation. COPD was diagnosed on the basis of relevant history and spirometry showing post bronchodilator FEV1/FVC <0.70. Surfactant Protein-A level (ng/ml) was estimated by a specific solid phase enzyme linked immunosorbent assay (ELISA) using automated EIA analyzer. Results: The SP-A levels, determined by competitive ELISA, was significantly higher (P<0.025) in healthy smokers (44.19±39.17 ng/ml) and exacerbated (43.86±40.17) than the stable COPD (25.89±18.85) patients. The lung function parameters (FEV1, FVC and FEV1/ FVC) were lower in COPD patients compared to healthy smokers and were related to the duration of smoking. Conclusion: Current smokers and exacerbated patients had higher values of SP-A protein than stable COPD patients since they had stopped smoking.