Miracle-dz/UniFAR-FTUs huggingface dataset:
Prognostic indicators of secondary progression in a paediatric-onset multiple sclerosis cohort in Kuwait

Background: The frequency of paediatric-onset multiple sclerosis (POMS) and the precise risk of secondary progression of disease are largely unknown in the Middle East. This cross-sectional cohort study assessed the risk and examined prognostic factors for time to onset of secondary progressive multiple sclerosis (SPMS) in a cohort of POMS patients. Methods: The Kuwait National MS Registry database was used to identify a cohort of POMS cases (diagnosed at age <18 years) from 1994 to 2013. Data were abstracted from patients’ records. A Cox proportional hazards model was used to evaluate the prognostic significance of the variables considered. Results: Of 808 multiple sclerosis (MS) patients, 127 (15.7%) were POMS cases. The median age (years) at disease onset was 16.0 (range 6.5–17.9). Of 127 POMS cases, 20 (15.8%) developed SPMS. A multivariable Cox proportional hazards model showed that at MS onset, brainstem involvement (adjusted hazard ratio 5.71; 95% confidence interval 1.53–21.30; P=0.010), and POMS patient age at MS onset (adjusted hazard ratio 1.38; 95% confidence interval 1.01–1.88; P=0.042) were significantly associated with the increased risk of a secondary progressive disease course. Conclusions: This study showed that POMS patients with brainstem/cerebellar presentation and a relatively higher age at MS onset had disposition for SPMS and warrant an aggressive therapeutic approach.
Predicting naturalization of southern African Iridaceae in other regions

Summary 1 One of the major challenges in invasion biology is to predict the likelihood of naturalization, and ultimately invasiveness, of species from properties that can be assessed in the native range prior to a species’ introduction elsewhere. This is particularly relevant as intentional introduction for horticultural usage has been predicted to be the over-riding factor associated with naturalization. 2 We compiled a data set on 1036 species of Iridaceae native to southern Africa to test whether traits differ between horticulturally used and unused species, whether the likelihood of naturalization elsewhere is higher for horticulturally used species, and whether it differs according to species’ taxonomic affinities, geographical range size, altitudinal range, number of subtaxa and plant size. 3 Our results show that at least 306 southern African Iridaceae species are used in horticulture elsewhere. Of the 67 that have become naturalized elsewhere, no less than 62 are in horticulture, indicating horticultural trade as the main source of naturalized Iridaceae. 4 Global horticultural usage differs among the three subfamilies and among the genera. In addition, horticultural usage is more likely for species with a larger distributional range, a lower maximum altitude, more subtaxa and a taller height. This indicates that species introduced elsewhere for horticultural usage have a biased set of biogeographical and biological characteristics that should be corrected for in analyses of naturalization. 5 After correction for horticultural usage, naturalization differs between genera, and is more likely for species with lower maximum altitude, species with higher numbers of subtaxa and taller species. 6 Cross-validation of our predictive logistic regression model revealed a low kappa (0·279 ± 0·069, mean ± SE) that was significantly different from zero. This indicates that the estimates from our logistic regression model can be used to predict naturalization of Iridaceae but that the accuracy is relatively low. 7 Synthesis and applications. Our study shows that screening protocols for potential invasiveness of species of Iridaceae should include international horticultural usage, and taxonomic, biogeographical and biological characteristics in the native range, as predictors. Moreover, for the development of more accurate predictive models, experimental assessment of other plant characteristics associated with naturalization is still required.
Death Anxiety and Its Relationship With Obsessive-Compulsive Disorder

The studies presented in this article explored the relevance of death fears to Obsessive Compulsive Disorder (OCD). In Study 1, the relationships between death anxiety and a variety of markers of psychopathology were examined in 171 treatment-seeking participants with OCD. Moderate to large correlations between Collett-Lester Fear of Death scale scores, taken at initial assessment, and clinical ratings of OCD severity, number of hospitalizations, number of medications, and total number of lifetime anxiety-related diagnoses identified in structured diagnostic interviews were obtained. Study 2 used the mortality salience (MS) paradigm to examine whether experimentally manipulated death cognitions exacerbate compulsive cleaning behaviors among OCD washers. Treatment-seeking participants with OCD (66 washers and 66 nonwashers) were randomly allocated to either a MS or dental pain priming condition. Following priming, participants completed a series of distraction tasks involving skin conductance recording, before being offered an opportunity to wash conductive gel off their hands. As hypothesized, washers went to greater efforts in cleaning (as measured by washing duration and soap and paper towel use) than nonwashers. Similarly, participants in the MS condition showed greater cleaning than those in the dental pain salience condition. However, these main effects were qualified by significant interactions for both washing duration and soap use. As expected, simple effect contrasts revealed that the effect of MS on cleaning behaviors was significant for washers but not for nonwashers. Clinical implications and directions for future research are discussed.
Automated Text Messaging as an Adjunct to Cognitive Behavioral Therapy for Depression: A Clinical Trial

Background Cognitive Behavioral Therapy (CBT) for depression is efficacious, but effectiveness is limited when implemented in low-income settings due to engagement difficulties including nonadherence with skill-building homework and early discontinuation of treatment. Automated messaging can be used in clinical settings to increase dosage of depression treatment and encourage sustained engagement with psychotherapy. Objectives The aim of this study was to test whether a text messaging adjunct (mood monitoring text messages, treatment-related text messages, and a clinician dashboard to display patient data) increases engagement and improves clinical outcomes in a group CBT treatment for depression. Specifically, we aim to assess whether the text messaging adjunct led to an increase in group therapy sessions attended, an increase in duration of therapy attended, and reductions in Patient Health Questionnaire-9 item (PHQ-9) symptoms compared with the control condition of standard group CBT in a sample of low-income Spanish speaking Latino patients. Methods Patients in an outpatient behavioral health clinic were assigned to standard group CBT for depression (control condition; n=40) or the same treatment with the addition of a text messaging adjunct (n=45). The adjunct consisted of a daily mood monitoring message, a daily message reiterating the theme of that week’s content, and medication and appointment reminders. Mood data and qualitative responses were sent to a Web-based platform (HealthySMS) for review by the therapist and displayed in session as a tool for teaching CBT skills. Results Intent-to-treat analyses on therapy attendance during 16 sessions of weekly therapy found that patients assigned to the text messaging adjunct stayed in therapy significantly longer (median of 13.5 weeks before dropping out) than patients assigned to the control condition (median of 3 weeks before dropping out; Wilcoxon-Mann-Whitney z=−2.21, P=.03). Patients assigned to the text messaging adjunct also generally attended more sessions (median=6 sessions) during this period than patients assigned to the control condition (median =2.5 sessions), but the effect was not significant (Wilcoxon-Mann-Whitney z=−1.65, P=.10). Both patients assigned to the text messaging adjunct (B=−.29, 95% CI −0.38 to −0.19, z=−5.80, P<.001) and patients assigned to the control conditions (B=−.20, 95% CI −0.32 to −0.07, z=−3.12, P=.002) experienced significant decreases in depressive symptom severity over the course of treatment; however, the conditions did not significantly differ in their degree of symptom reduction. Conclusions This study provides support for automated text messaging as a tool to sustain engagement in CBT for depression over time. There were no differences in depression outcomes between conditions, but this may be influenced by low follow-up rates of patients who dropped out of treatment.
Trends of caesarean section rates in Turkey

Abstract The aims of this study was to determine the trends in rates of caesarean sections in Turkey. The data source for this study was the Turkey Demographic and Health Survey (TDHS) 1993–1998–2003–2008–2013 conducted by Hacettepe University, Institute of Population Studies. Cross tables and binary logistic regression were used for analysis. It was found that the caesarean section rate, which was 14.3% in 1993, increased to 51.9% in 2013. The rate increased with maternal age and educational level at childbirth. The Caesarean section rate was higher in women who were under health insurance coverage, first time mothers, childbirth in the private health institutions, those staying in the Western region and urban areas, and having the highest level of wealth. This study aims to contribute to the literature of caesarean sections especially in developing countries, in which caesarean section has become a major healthcare issue. Impact Statement What is already known on this subject: Caesarean section is among the most widely practiced obstetric surgery worldwide. Previous studies have suggested that the rates of caesarean section were affected by the biological, genetic and medical factors. What the results of this study add: Besides the biological, genetic and medical factors, it is believed that social factors (income and social status, education, employment, etc.) play an important role on the caesarean section in developing countries. Although the laws on caesarean sections have been enforced since 2012 in Turkey, this study shows that there has been a significant increase in caesarean section between the 1993 and 2013 periods. The study also reveals that prohibiting caesarean sections, except in cases of medical necessity, is a problematic issue in the health system despite all efforts. What the implications are of these findings for clinical practice and/or further research: This study may be of interest for authorities and researchers in terms of showing the social factors associated with the caesarean section.
Genome-wide methylation analysis of a large population sample shows neurological pathways involvement in chronic widespread musculoskeletal pain

Abstract Chronic widespread musculoskeletal pain (CWP), has a considerable heritable component, which remains to be explained. Epigenetic factors may contribute to and account for some of the heritability estimate. We analysed epigenome-wide methylation using MeDIPseq in whole blood DNA from 1708 monozygotic and dizygotic Caucasian twins having CWP prevalence of 19.9%. Longitudinally stable methylation bins (lsBINs), were established by testing repeated measurements conducted ≥3 years apart, n = 292. DNA methylation variation at lsBINs was tested for association with CWP in a discovery set of 50 monozygotic twin pairs discordant for CWP, and in an independent dataset (n = 1608 twins), and the results from the 2 samples were combined using Fisher method. Functional interpretation of the most associated signals was based on functional genomic annotations, gene ontology, and pathway analyses. Of 723,029 signals identified as lsBINs, 26,399 lsBINs demonstrated the same direction of association in both discovery and replication datasets at nominal significance (P ⩽ 0.05). In the combined analysis across 1708 individuals, whereas no lsBINs showed genome-wide significance (P < 10-8), 24 signals reached p⩽9E-5, and these included association signals mapping in or near to IL17A, ADIPOR2, and TNFRSF13B. Bioinformatics analyses of the associated methylation bins showed enrichment for neurological pathways in CWP. We estimate that the variance explained by epigenetic factors in CWP is 6%. This, the largest study to date of DNA methylation in CWP, points towards epigenetic modification of neurological pathways in CWP and provides proof of principle of this method in teasing apart the complex risk factors for CWP.
Mineral metabolism factors predict accelerated progression of common carotid intima-media thickness in chronic kidney disease: the NEFRONA study

Background The leading cause of premature death in chronic kidney disease (CKD) is cardiovascular disease (CVD), but risk assessment in renal patients is challenging. The aim of the study was to analyse the factors that predict accelerated progression of common carotid intima-media thickness (CCIMT) in a CKD cohort after 2 years of follow-up (2010-12). Methods The study included 1152 patients from the NEFRONA cohort with CKD stages 3-5D and without a clinical history of CVD. CCIMT was measured at the far wall on both common carotids. CCIMT progression was defined as the change between CCIMT at baseline and at 24 months for each side, averaged and normalized as change per year. Accelerated progressors were defined as those with a CCIMT change ≥75th percentile. Results The median CCIMT progression rate was 0.0125 mm/year, without significant differences between CKD stages. The cut-off value for defining accelerated progression was 0.0425 mm/year. After adjustment, age was a common factor among all CKD stages. Traditional cardiovascular risk factors, such as diabetes and systolic blood pressure, were predictors of progression in CKD stages 4-5, whereas high-density lipoprotein and low-density lipoprotein cholesterol predicted progression in women in stage 3. Mineral metabolism factors predicting accelerated progression were serum phosphorus in stages 3 and 5D; low 25-hydroxyvitamin D and parathyroid hormone levels >110 pg/mL in stages 4-5 and intact parathyroid hormone levels out of the recommended range in stage 5D. Conclusions Mineral metabolism parameters might predict accelerated CCIMT progression from early CKD stages.
Predicting Rotator Cuff Tears Using Data Mining and Bayesian Likelihood Ratios

Objectives Rotator cuff tear is a common cause of shoulder diseases. Correct diagnosis of rotator cuff tears can save patients from further invasive, costly and painful tests. This study used predictive data mining and Bayesian theory to improve the accuracy of diagnosing rotator cuff tears by clinical examination alone. Methods In this retrospective study, 169 patients who had a preliminary diagnosis of rotator cuff tear on the basis of clinical evaluation followed by confirmatory MRI between 2007 and 2011 were identified. MRI was used as a reference standard to classify rotator cuff tears. The predictor variable was the clinical assessment results, which consisted of 16 attributes. This study employed 2 data mining methods (ANN and the decision tree) and a statistical method (logistic regression) to classify the rotator cuff diagnosis into “tear” and “no tear” groups. Likelihood ratio and Bayesian theory were applied to estimate the probability of rotator cuff tears based on the results of the prediction models. Results Our proposed data mining procedures outperformed the classic statistical method. The correction rate, sensitivity, specificity and area under the ROC curve of predicting a rotator cuff tear were statistical better in the ANN and decision tree models compared to logistic regression. Based on likelihood ratios derived from our prediction models, Fagan's nomogram could be constructed to assess the probability of a patient who has a rotator cuff tear using a pretest probability and a prediction result (tear or no tear). Conclusions Our predictive data mining models, combined with likelihood ratios and Bayesian theory, appear to be good tools to classify rotator cuff tears as well as determine the probability of the presence of the disease to enhance diagnostic decision making for rotator cuff tears.
Fertility outcomes in women experiencing severe complications after surgery for colorectal endometriosis

STUDY QUESTION What are the fertility outcomes in women wishing to conceive after experiencing a severe complication from surgical removal of colorectal endometriosis? SUMMARY ANSWER The pregnancy rate (PR) among women who wished to conceive after a severe complication of surgery for colorectal endometriosis was 41.2% (spontaneously for 80%, after ART procedure for 20%). WHAT IS KNOWN ALREADY While the long-term benefit of surgery on pain and quality of life is well documented for women with colorectal endometriosis, it exposes women to the risk of severe complications. However, little is known about fertility outcomes in women experiencing such severe postoperative complications. STUDY DESIGN, SIZE, DURATION This retrospective cohort study included women who experienced a severe complication after surgery for colorectal endometriosis between January 2004 and June 2014, and who wished to conceive. A total of 53 patients met the inclusion criteria. The fertility outcome was available for 48 women, who were therefore included in the analysis. The median follow-up was 5 years. PARTICIPANTS/MATERIALS, SETTING, METHODS All the women underwent complete removal of colorectal endometriosis. Postoperative severe complications were defined as grades III-IV of the Clavien-Dindo classification. Fertility outcomes, PR and cumulative pregnancy rate (CPR), were estimated. MAIN RESULTS AND THE ROLE OF CHANCE Most women experienced a grade IIIb complication (83.3%). Of 48 women, 20 became pregnant (overall PR: 41.2%); spontaneously for 16 (80%) and after ART procedure for 4 (20%). The median interval between surgery and first pregnancy was 3 years. The live birth rate was 14/48 (29.2%). The 5-year CPR was 46%. A lower CPR was found for women who experienced anastomotic leakage (with or without rectovaginal fistula) (P = 0.02) or deep pelvic abscess (with or without anastomotic leakage) (P = 0.04). LIMITATIONS REASONS FOR CAUTION Due to a lack of information, no sub-analysis was done to investigate other parameters potentially impacting fertility outcomes. WIDER IMPLICATIONS OF THE FINDINGS The PR for our population was slightly lower to that observed in the literature for women who experience such surgery without consideration for the occurrence of complications. However, 'severe complications' covers a range of conditions which are likely to have a very different impacts on fertility. Even if the PR and CPR appear satisfactory, septic complications can negatively impact fertility outcomes. Rapid ART may be a good option for these patients. STUDY FUNDING/COMPETING INTEREST(S) No funding was required for the current study. Pr H. Roman reported personal fees from Plasma Surgical Inc. (Roswell, GA, USA) for participating in a symposium and a masterclass, in which he presented his experience in the use of PlasmaJet®. None of the other authors declared any conflict of interest. TRIAL REGISTRATION NUMBER N/A.
Predicting Response to Repetitive Transcranial Magnetic Stimulation in Patients With Schizophrenia Using Structural Magnetic Resonance Imaging: A Multisite Machine Learning Analysis

Background The variability of responses to plasticity-inducing repetitive transcranial magnetic stimulation (rTMS) challenges its successful application in psychiatric care. No objective means currently exists to individually predict the patients' response to rTMS. Methods We used machine learning to develop and validate such tools using the pre-treatment structural Magnetic Resonance Images (sMRI) of 92 patients with schizophrenia enrolled in the multisite RESIS trial (http://clinicaltrials.gov, NCT00783120): patients were randomized to either active (N = 45) or sham (N = 47) 10-Hz rTMS applied to the left dorsolateral prefrontal cortex 5 days per week for 21 days. The prediction target was nonresponse vs response defined by a ≥20% pre-post Positive and Negative Syndrome Scale (PANSS) negative score reduction. Results Our models predicted this endpoint with a cross-validated balanced accuracy (BAC) of 85% (nonresponse/response: 79%/90%) in patients receiving active rTMS, but only with 51% (48%/55%) in the sham-treated sample. Leave-site-out cross-validation demonstrated cross-site generalizability of the active rTMS predictor despite smaller training samples (BAC: 71%). The predictive pre-treatment pattern involved gray matter density reductions in prefrontal, insular, medio-temporal, and cerebellar cortices, and increments in parietal and thalamic structures. The low BAC of 58% produced by the active rTMS predictor in sham-treated patients, as well as its poor performance in predicting positive symptom courses supported the therapeutic specificity of this brain pattern. Conclusions Individual responses to active rTMS in patients with predominant negative schizophrenia may be accurately predicted using structural neuromarkers. Further multisite studies are needed to externally validate the proposed treatment stratifier and develop more personalized and biologically informed rTMS interventions.
Functional non-synonymous variants of ABCG2 and gout risk

Objectives Common dysfunctional variants of ATP binding cassette subfamily G member 2 (Junior blood group) (ABCG2), a high-capacity urate transporter gene, that result in decreased urate excretion are major causes of hyperuricemia and gout. In the present study, our objective was to determine the frequency and effect on gout of common and rare non-synonymous and other functional allelic variants in the ABCG2 gene. Methods The main cohort recruited from the Czech Republic consisted of 145 gout patients; 115 normouricaemic controls were used for comparison. We amplified, directly sequenced and analysed 15 ABCG2 exons. The associations between genetic variants and clinical phenotype were analysed using the t-test, Fisher's exact test and a logistic and linear regression approach. Data from a New Zealand Polynesian sample set and the UK Biobank were included for the p.V12M analysis. Results In the ABCG2 gene, 18 intronic (one dysfunctional splicing) and 11 exonic variants were detected: 9 were non-synonymous (2 common, 7 rare including 1 novel), namely p.V12M, p.Q141K, p.R147W, p.T153M, p.F373C, p.T434M, p.S476P, p.D620N and p.K360del. The p.Q141K (rs2231142) variant had a significantly higher minor allele frequency (0.23) in the gout patients compared with the European-origin population (0.09) and was significantly more common among gout patients than among normouricaemic controls (odds ratio = 3.26, P < 0.0001). Patients with non-synonymous allelic variants had an earlier onset of gout (42 vs 48 years, P = 0.0143) and a greater likelihood of a familial history of gout (41% vs 27%, odds ratio = 1.96, P = 0.053). In a meta-analysis p.V12M exerted a protective effect from gout (P < 0.0001). Conclusion Genetic variants of ABCG2, common and rare, increased the risk of gout. Non-synonymous allelic variants of ABCG2 had a significant effect on earlier onset of gout and the presence of a familial gout history. ABCG2 should thus be considered a common and significant risk factor for gout.