nils-herrmann/clean_scirepeval huggingface dataset:
Using pre-treatment EEG data to predict response to SSRI treatment for MDD

The problem of identifying in advance the most effective treatment agent for various psychiatric conditions remains an elusive goal. To address this challenge, we propose a machine learning (ML) methodology to predict the response to a selective serotonin reuptake inhibitor (SSRI) medication in subjects suffering from major depressive disorder (MDD), using pre-treatment electroencephalograph (EEG) measurements. The proposed feature selection technique is a modification of the method of Peng et al  that is based on a Kullback-Leibler (KL) distance measure. The classifier was realized as a kernelized partial least squares regression procedure, whose output is the predicted response. A low-dimensional kernelized principal component representation of the feature space was used for the purposes of visualization and clustering analysis. The overall method was evaluated using an 11-fold nested cross-validation procedure for which over 85% average prediction performance is obtained. The results indicate that ML methods hold considerable promise in predicting the efficacy of SSRI antidepressant therapy for major depression.
Simplification of the research diagnosis of HIV-associated sensory neuropathy.

Peripheral neuropathy (PN) is the most common neurological complication of HIV infection,affecting over one third of patients. The research diagnosis of PN is complicated by the need for expensive, time-consuming, and noxious diagnostic tests. We investigated whether nerve conduction studies (NSC) and quantitative sensory tests (QST) provide added value for the diagnosis of PN for research purposes or whether the easily obtainable clinical measures (sensory and motor symptoms, sensitivity to pain and vibration, tendon reflexes, motor function) are sufficient.
Visual impairment following stroke: do stroke patients require vision assessment?

the types of visual impairment followings stroke are wide ranging and encompass low vision, eye movement and visual field abnormalities, and visual perceptual difficulties.



the purpose of this paper is to present a 1-year data set and identify the types of visual impairment occurring following stroke and their prevalence.



a multi-centre prospective observation study was undertaken in 14 acute trust hospitals. Stroke survivors with a suspected visual difficulty were recruited. Standardised screening/referral and investigation forms were employed to document data on visual impairment specifically assessment of visual acuity, ocular pathology, eye alignment and movement, visual perception (including inattention) and visual field defects.



three hundred and twenty-three patients were recruited with a mean age of 69 years [standard deviation (SD) 15]. Sixty-eight per cent had eye alignment/movement impairment, 49% had visual field impairment, 26.5% had low vision and 20.5% had perceptual difficulties.



of patients referred with a suspected visual difficulty, only 8% had normal vision status confirmed on examination. Ninety-two per cent had visual impairment of some form confirmed which is considerably higher than previous publications and probably relates to the prospective, standardised investigation offered by specialist orthoptists. However, under-ascertainment of visual problems cannot be ruled out.
Genome-wide search for QTLs for apolipoprotein A-I level in elderly Swedish DZ twins: evidence of female-specific locus on 15q11–13

The effect of genetic variants underlying atherosclerosis is thought to be mediated through intermediate phenotypes such as serum cholesterol levels. Localization of quantitative trait loci influencing levels of serum lipids and (apo)lipoproteins may aid in the search for determinants of susceptibility to atherosclerotic diseases. Since apolipoprotein A-I is the primary protein constituent of high-density lipoprotein, it is considered to be critical for the antiatherogenic effect of high-density lipoproteins. We describe here an effort to map loci influencing apolipoprotein A-I levels. Measurements of apolipoprotein A-I levels and genome scans with more than 1000 microsatellite markers were successfully performed in both members of 501 pairs of fraternal twins from Sweden. Variance component linkage analysis was undertaken to map quantitative trait loci. In the total study sample, two loci showed comparable suggestive evidence of linkage, 6p21–12 (LOD=2.4) and 12q23 (LOD=2.4). Sex-limited analyses revealed significant female-specific linkage at marker D15S156 on 15q11–13 (LOD=4.1). The loci on 12q and 15q in the present study confirm previously reported loci for apolipoprotein A-I, while the peak on chromosome 6p lends further support to a locus influencing several phenotypes related to atherosclerosis. Intriguingly, the presence of genes belonging to the phospholipase A2 superfamily under three out of four observed linkage peaks would lend some support to the view that this group of genes might collectively represent candidates as apolipoprotein A-I level regulators.
Examining variation in depressive symptoms over the life course: a latent class analysis.

Older adults have the lowest prevalence and incidence of major depressive disorder, although it has been hypothesized that this finding is due in part to differences in expression of psychopathology in later life. The aim of this study was to examine variation in depressive symptomatology in the general population across the lifespan.



Data came from three sites of the Epidemiologic Catchment Area (ECA) Project (n=10 529). Depressive symptoms during the past 6 months were assessed using the Diagnostic Interview Schedule (DIS). Latent class analysis (LCA) was used to identify homogeneous groups of depressive symptomatology based on 16 individual symptoms, and to examine variation in the prevalence and composition of depression classes across age groups.



The DIS symptoms fit a four-class model composed of non-depressed (83.2%), mild depression (11.6%), severe depression (1.9%), and despondent (3.2%) groups. Relative to the non-depressed class, older age was inversely associated with being in the mild or severe depression class. The profile of the latent classes was similar across age groups with the exception of the despondent class, which was not well differentiated among the youngest adults and was not inversely associated with age.



The symptom profiles of depression are similar across age with the exception of the despondent class, which is more differentiated from severe depression among older adults. The findings demonstrate the benefit of examining individual symptoms rather than broad symptom groups for understanding the natural history of depression over the lifespan.
Reanalysis of a tailored web-based exercise programme for office workers with sub-acute low back pain: assessing the stage of change in behaviour.

To reanalyse a web-based intervention for physically untrained office workers with sub-acute non-specific low back pain in low back pain-related exercise behaviour terms.



Reanalysis of a randomized controlled trial.



Occupational Preventive Medicine of University.



Participants were randomized to an intervention group (proposed intervention plus standard care) or a control group (usual care only). The intervention exercise and education materials were developed as an online resource, and included video demonstrations recorded in a laboratory. Resources were loaded onto a dedicated section of the University Preventive Medicine Service website. All sessions included stretching, and exercises to improve postural stability (abdominal, lumbar, hip and thigh muscles) strength, flexibility and mobility. Outcome measures were self-reported health status (visual analogue scale (VAS) of the Euroquol-5D questionnaire); functional health status (Oswestry disability questionnaire); and the stage of change questionnaire. At nine months, outcomes in the intervention group were analysed and compared with baseline and outcomes in controls.



In the intervention group, significant positive effects were observed at nine-month follow up for stage of change in the behavioural domain as related with low back pain for all phases except for the contemplation phase. The positive change in the stage of change questionnaire correlated with the improvement observed in Oswestry (r = .388) and VAS (r = -.612).



The reanalysis of the trial suggests that exercise behaviour related to low back pain improve after the intervention period. This improvement correlates with changes in clinical low back pain-related outcomes.
Profiles of Cognitive Dysfunction in Chronic Amphetamine and Heroin Abusers

Groups of subjects whose primary drug of abuse was amphetamine or heroin were compared, together with age- and IQ-matched control subjects. The study consisted of a neuropsychological test battery which included both conventional tests and also computerised tests of recognition memory, spatial working memory, planning, sequence generation, visual discrimination learning, and attentional set-shifting. Many of these tests have previously been shown to be sensitive to cortical damage (including selective lesions of the temporal or frontal lobes) and to cognitive deficits in dementia, basal ganglia disease, and neuropsychiatric disorder. Qualitative differences, as well as some commonalities, were found in the profile of cognitive impairment between the two groups. The chronic amphetamine abusers were significantly impaired in performance on the extra-dimensional shift task (a core component of the Wisconsin Card Sort Test) whereas in contrast, the heroin abusers were impaired in learning the normally easier intra-dimensional shift component. Both groups were impaired in some of tests of spatial working memory. However, the amphetamine group, unlike the heroin group, were not deficient in an index of strategic performance on this test. The heroin group failed to show significant improvement between two blocks of a sequence generation task after training and additionally exhibited more perseverative behavior on this task. The two groups were profoundly, but equivalently impaired on a test of pattern recognition memory sensitive to temporal lobe dysfunction. These results indicate that chronic drug use may lead to distinct patterns of cognitive impairment that may be associated with dysfunction of different components of cortico-striatal circuitry.
Functional comparison of the HTLV-1 and HTLV-2 antisense viral proteins: implications for pathogenesis

HTLV-1 and HTLV-2 are highly related retroviruses that transform T-lymphocytes in cell culture, but display distinct pathobiology in vivo. HTLV-1 is the causative infectious agent of adult T-cell leukemia/lymphoma (ATL) and a neurodegenerative disease (HAM/TSP), whereas HTLV-2 is nonpathogenic. HTLV-1 encodes a protein on the antisense strand of its proviral genome called HTLV-1 basic leucine zipper (bZIP) factor (HBZ), which inhibits Tax-mediated viral transcription and is required for high proviral load and efficient viral persistence. Studies have shown that HBZ also modulates several cellular pathways that include activating protein-1 (AP-1), NFB, and innate immune responses. HTLV-2 also encodes a protein on the antisense genome strand named antisense protein of HTLV-2 (APH-2). Like HBZ, APH-2 also inhibits Tax-mediated viral transcription. However, we show that unlike HBZ, loss of APH-2 results in enhanced viral replication and viral persistence in infected rabbits. This led us to hypothesize that HBZ and APH-2 modulate cellular pathways differently, which translates to the distinct HTLV-1 and HTLV-2 pathobiology. In this study we directly compared APH-2 and HBZ biologic properties and functions on known HBZ-modulated pathways. We provide evidence that APH-2 protein is significantly less stable than HBZ protein (half-life approximately 30m vs. 6.5h). Despite the difference in protein half-life, HTLV-2 does not compensate for this instability by increasing APH-2 mRNA copy number. Additionally, APH-2 and HBZ share similar mRNA stability measurements. We further show that APH-2 inhibits the transforming growth factor b (TGF-b) signaling pathway in contrast to HBZ’s enhancement. Like HBZ, APH-2 is able to inhibit the cellular transcription factors p65 (NFB) and interferon response factor (IRF)-1. Taken together our results indicate that APH-2 is limited in some functions it shares with HBZ. Further studies should focus on distinct HBZ functions and interacting pathways to find new potential therapeutic targets for HTLV-1 disease.
Body composition in older acute stroke patients after treatment with individualized, nutritional supplementation while in hospital

Individualized, nutritional support reduced undernutrition among older stroke patients and improved quality of life in our recent randomized, controlled trial. Weight control thus seems to be important after stroke, and methods for monitoring nutritional status need to be simple and non-invasive. Here we aimed to assess if the nutritional intervention altered body composition in men and women in this study cohort, and also to examine the correlation between the methods for assessing body-, fat- and fat-free mass.



Acute stroke patients > 65 years at nutritional risk were randomized to either individualized, nutritional treatment with energy- and protein rich supplementation (intervention, n = 58) or routine, nutritional care (control, n = 66) while in hospital. Body composition was assessed with anthropometry and bioelectrical impedance. The follow-up period was three months.



During the first week while in hospital, weight loss was smaller in the intervention group compared with the controls (P = 0.013). After three months weight- and fat loss were significant in both men and women. Whereas no significant differences were found in changes in body composition between the male study groups, in the women both weight loss (P = 0.022) and fat loss (P = 0.005) was smaller in the intervention group compared with the controls. A high correlation (r = 0.87) between mid upper arm circumference (MUAC) and body mass index (BMI) was found.



Individualized nutritional support to older stroke patients in hospital was beneficial for maintaining an adequate body mass and body composition the first week and seemed to have a preventive effect on fat loss among women, but not among men after three months. Measurement of MUAC may be used in the assessment of nutritional status when BMI cannot be obtained.
Patient-centered disease management (PCDM) for heart failure: study protocol for a randomised controlled trial

Chronic heart failure (HF) disease management programs have reported inconsistent results and have not included comorbid depression management or specifically focused on improving patient-reported outcomes. The Patient Centered Disease Management (PCDM) trial was designed to test the effectiveness of collaborative care disease management in improving health status (symptoms, functioning, and quality of life) in patients with HF who reported poor HF-specific health status.



Patients with a HF diagnosis at four VA Medical Centers were identified through population-based sampling. Patients with a Kansas City Cardiomyopathy Questionnaire (KCCQ, a measure of HF-specific health status) score of < 60 (heavy symptom burden and impaired quality of life) were invited to enroll in the PCDM trial. Enrolled patients were randomized to receive usual care or the PCDM intervention, which included: (1) collaborative care management by VA clinicians including a nurse, cardiologist, internist, and psychiatrist, who worked with patients and their primary care providers to provide guideline-concordant care management, (2) home telemonitoring and guided patient self-management support, and (3) screening and treatment for comorbid depression. The primary study outcome is change in overall KCCQ score. Secondary outcomes include depression, medication adherence, guideline-based care, hospitalizations, and mortality.



The PCDM trial builds on previous studies of HF disease management by prioritizing patient health status, implementing a collaborative care model of health care delivery, and addressing depression, a key barrier to optimal disease management. The study has been designed as an 'effectiveness trial' to support broader implementation in the healthcare system if it is successful.
Comparison of pegfilgrastim on day 2 vs. day 4 as primary prophylaxis of intense dose-dense chemotherapy in patients with node-positive primary breast cancer within the prospective, multi-center GAIN study: (GBG 33)

Preliminary data suggest that pegfilgrastim given on day 4 (P4) might be superior to pegfilgrastim on day 2 (P2) in reducing grade 4 leucopenia. Patients with node-positive primary breast cancer receiving epirubicin–paclitaxel–cyclophosphamide chemotherapy were randomized to receive P2 versus P4. Primary endpoint was leucopenia grade 4, assuming a risk reduction of 50% with P4 from 50% in P2 to 25% with P4. Three-hundred fifty-one patients were randomized to P2 (n = 174) versus P4 (n = 177). The rate of leucopenia (grade 4) was 47.1% with P2 and 42.0% with P4 (p = 0.387), neutropenia (grade 3 + 4) was 47.9% versus 40.8% (p = 0.337), FN was 4.7% versus 8.0% (p = 0.271), and infections was 29.9% versus 25.4% (p = 0.404), respectively. This study failed to demonstrate that pegfilgrastim on day 4 was more efficacious than on day 2 with respect to grade 4 leucopenia (the primary endpoint), febrile neutropenia, or infections.
Potentials of Plasma NGAL and MIC-1 as Biomarker(s) in the Diagnosis of Lethal Pancreatic Cancer

Pancreatic cancer (PC) is lethal malignancy with very high mortality rate. Absence of sensitive and specific marker(s) is one of the major factors for poor prognosis of PC patients. In pilot studies using small set of patients, secreted acute phase proteins neutrophil gelatinase associated lipocalin (NGAL) and TGF-β family member macrophage inhibitory cytokine-1 (MIC-1) are proposed as most potential biomarkers specifically elevated in the blood of PC patients. However, their performance as diagnostic markers for PC, particularly in pre-treatment patients, remains unknown. In order to evaluate the diagnostic efficacy of NGAL and MIC-1, their levels were measured in plasma samples from patients with pre-treatment PC patients (n = 91) and compared it with those in healthy control (HC) individuals (n = 24) and patients with chronic pancreatitis (CP, n = 23). The diagnostic performance of these two proteins was further compared with that of CA19-9, a tumor marker commonly used to follow PC progression. The levels of all three biomarkers were significantly higher in PC compared to HCs. The mean (± standard deviation, SD) plasma NGAL, CA19-9 and MIC-1 levels in PC patients was 111.1 ng/mL (2.2), 219.2 U/mL (7.8) and 4.5 ng/mL (4.1), respectively. In comparing resectable PC to healthy patients, all three biomarkers were found to have comparable sensitivities (between 64%-81%) but CA19-9 and NGAL had a higher specificity (92% and 88%, respectively). For distinguishing resectable PC from CP patients, CA19-9 and MIC-1 were most specific (74% and 78% respectively). CA19-9 at an optimal cut-off of 54.1 U/ml is highly specific in differentiating resectable (stage 1/2) pancreatic cancer patients from controls in comparison to its clinical cut-off (37.1 U/ml). Notably, the addition of MIC-1 to CA19-9 significantly improved the ability to distinguish resectable PC cases from CP (p = 0.029). Overall, MIC-1 in combination with CA19-9 improved the diagnostic accuracy of differentiating PC from CP and HCs.
Amoxicillin plus temocillin as an alternative empiric therapy for the treatment of severe hospital-acquired pneumonia: results from a retrospective audit

A formulary decision was made at a large provider of acute hospital services in Surrey to replace piperacillin/tazobactam with amoxicillin+temocillin for the empiric treatment of severe hospital-acquired pneumonia. This decision was made because the use of broad-spectrum-β-lactam antibiotics is a known risk factor for Clostridium difficile infection (CDI) and for the selection of resistance. After the antibiotic formulary was changed, a retrospective audit was conducted to assess the effect of this change. Data from patients hospitalised between January 2011 and July 2012 for severe hospital-acquired pneumonia and treated empirically with piperacillin/tazobactam or amoxicillin+temocillin were reviewed retrospectively. Clinical characteristics of patients, data related to the episode of pneumonia, clinical success and incidence of significant diarrhoea and CDI were analysed. One hundred ninety-two episodes of severe hospital-acquired pneumonia in 188 patients were identified from hospital records. Ninety-eight patients received piperacillin/tazobactam and 94 amoxicillin+temocillin. At baseline, the two treatment groups were comparable, except that more patients with renal insufficiency were treated with piperacillin/tazobactam. Clinical success was comparable (80 versus 82 %; P = 0.86), but differences were observed between piperacillin/tazobactam and amoxicillin+temocillin for the rates of significant diarrhoea (34 versus 4 %, respectively; P < 0.0001) and for CDI (7 versus 0 %, respectively; P < 0.0028). This preliminary study suggests that the combination amoxicillin+temocillin is a viable alternative to piperacillin/tazobactam for the treatment of severe hospital-acquired pneumonia. This combination appears to be associated with fewer gastrointestinal adverse events. Further studies are needed to evaluate the place of amoxicillin+temocillin as empiric treatment of severe hospital-acquired pneumonia.
Effect of Global Posture Reeducation and of Static Stretching on Pain, Range of Motion, and Quality of Life in Women with Chronic Neck Pain: A Randomized Clinical Trial

Compare the effect of conventional static stretching and muscle chain stretching, as proposed by the global posture reeducation method, in the manual therapy of patients with chronic neck pain.



Thirty-three female patients aged 35 to 60 years old, 31 of whom completed the program, were randomly divided into two groups: The global posture reeducation group (n=15) performed muscle chain stretching, while the conventional stretching group (n=16) performed conventional static muscle stretching. Both groups also underwent manual therapy. Patients were evaluated before and after treatment and at a six-week follow-up appointment and tested for pain intensity (by means of visual analog scale), range of motion (by goniometry), and health-related quality of life (by the SF-36 questionnaire). The treatment program consisted of two 1-hour individual sessions per week for six weeks. Data were statistically analyzed at a significance level of p<0.05.



Significant pain relief and range of motion improvement were observed after treatment in both groups, with a slight reduction at follow-up time. Quality of life also improved after treatment, except for the global posture reeducation group in one domain; at follow-up, there was improvement in all domains, except that both groups reported increased pain. There were no significant differences between groups



Conventional stretching and muscle chain stretching in association with manual therapy were equally effective in reducing pain and improving the range of motion and quality of life of female patients with chronic neck pain, both immediately after treatment and at a six-week follow-up, suggesting that stretching exercises should be prescribed to chronic neck pain patients.