nils-herrmann/clean_scirepeval huggingface dataset:
Triple-class virologic failure in HIV-infected patients undergoing antiretroviral therapy for up to 10 years.

Life expectancy of people with human immunodeficiency virus (HIV) is now estimated to approach that of the general population in some successfully treated subgroups. However, to attain these life expectancies, viral suppression must be maintained for decades.



We studied the rate of triple-class virologic failure (TCVF) in patients within the Collaboration of Observational HIV Epidemiological Research Europe (COHERE) who started antiretroviral therapy (ART) that included a nonnucleoside reverse-transcriptase inhibitor (NNRTI) or a ritonavir-boosted protease inhibitor (PI/r) from 1998 onwards. We also focused on TCVF in patients who started a PI/r-containing regimen after a first-line NNRTI-containing regimen failed.



Of 45 937 patients followed up for a median (interquartile range) of 3.0 (1.5-5.0) years, 980 developed TCVF (2.1%). By 5 and 9 years after starting ART, an estimated 3.4% (95% confidence interval [CI], 3.1%-3.6%) and 8.6% (95% CI, 7.5%-9.8%) of patients, respectively, had developed TCVF. The incidence of TCVF rose during the first 3 to 4 years on ART but plateaued thereafter. There was no significant difference in the risk of TCVF according to whether the initial regimen was NNRTI or PI/r based (P = .11). By 5 years after starting a PI/r regimen as second-line therapy, 46% of patients had developed TCVF.



The rate of virologic failure of the 3 original drug classes is low, but not negligible, and does not appear to diminish over time from starting ART. If this trend continues, many patients are likely to need newer drugs to maintain viral suppression. The rate of TCVF from the start of a PI/r regimen after NNRTI failure provides a comparator for studies of response to second-line regimens in resource-limited settings.
Excellent cross-cultural validity, intra-test reliability and construct validity of the Dutch Rivermead Mobility Index in patients after stroke undergoing rehabilitation.

To investigate the cross-cultural validity of international Dutch-English comparisons when using the Dutch Rivermead Mobility Index (RMI), and the intra-test reliability and construct validity of the Dutch RMI.



Cross-cultural validity was studied in a combined data-set of Dutch and English patients undergoing rehabilitation after stroke, who were assessed with the Dutch version of the RMI and the original English RMI, respectively. Mokken scale analysis was used to investigate unidimensionality, monotone homogeneity model fit, and differential item functioning between the Dutch and the English RMI. Intra-test reliability and construct validity were studied in the Dutch patients by calculating the reliability coefficient and correlating the Dutch RMI and the Dutch Barthel Index.



The RMI was completed for Dutch (n = 200) and English (n = 420) patients after stroke. The unidimensionality and monotone homogeneity model fit of the RMI were excellent: combined Dutch-English data-set (coefficient H = 0.91); Dutch data-set (coefficient H = 0.93); English data-set (coefficient H = 0.89). No differential item functioning was found between the Dutch and the English RMI. The intra-test reliability of the Dutch RMI was excellent (coefficient rho = 0.97). In a sub-sample of patients (n = 91), the Dutch RMI correlated strongly with the Dutch Barthel Index (Spearman's correlation coefficient rho = 0.84).



The Dutch RMI allows valid international Dutch-English comparisons, and has excellent intra-test reliability and construct validity.
Clozapine's Effect on Recidivism Among Offenders with Mental Disorders.

Mental disorder is associated with criminal reoffending, especially violent acts of offending. Features of mental disorder, psychosocial stresses, substance use disorder, and personality disorder combine to increase the risk of criminal recidivism. Clozapine, an atypical antipsychotic, is indicated in the treatment of patients with psychotic disorders. This article is the report of a community follow-up study of a matched control of those treated with clozapine (n = 41) and those treated with other antipsychotics (n = 21). Rates of reoffending behavior in the general, nonviolent, violent, and sexual categories were calculated after two years of follow-up. Although not statistically significant, the two-year criminal conviction rates of those treated with other antipsychotics in all offense categories except sexual reoffending were two-fold higher than in those treated with clozapine. The time from release to the first offense and crime-free time in the community were significantly longer in the clozapine group. By prolonging the time it takes from release to first offense, clozapine confers additional crime-reduction advantages.
Short-term effectiveness of an online behavioral training in migraine self-management: a randomized controlled trial.

Behavioral training (BT) is recommended as a supplementary preventive treatment for migraine. Online interventions have been successful in promoting health behavior change, the evidence for online BT in migraine is limited, however. This randomized controlled trial aimed to determine the post-treatment effectiveness of online BT (n = 195) compared to a waitlist control group (WLC; n = 173) on migraine attack frequency (primary outcome), headache self-efficacy and locus of control (secondary outcomes). BT aims to counteract attacks in the prodromal stage through early detection of prodromal features and self-management via physical relaxation and cognitive behavioral regulation, and was offered with minimal e-mail support in eight online lessons. Results showed that 120 (62%) participants completed BT. A decrease of 20-25% in migraine attack frequency was found in both conditions without a between-group difference (ES = 0.02, p = .71). BT participants improved more than WLC participants on migraine related self-efficacy (ES = 0.86, p < .001), developed more internal (ES = 0.57, p < .001), and less external control (ES = 0.78, p < .001). To conclude, results at post-training did not corroborate that improvements in migraine attack frequency were due to online BT, the waitlist control group improved accordingly. However, positive effects of BT on self-efficacy and locus of control were established. We have to await the long term effects to see if improvements in psychological variables translate to a reduction in migraine headache.
Testosterone gel supplementation for men with refractory depression: a randomized, placebo-controlled trial.

Testosterone supplementation may produce antidepressant effects in men, but until recently it has required cumbersome parenteral administration. In an 8-week randomized, placebo-controlled trial, the authors administered a testosterone transdermal gel to men aged 30-65 who had refractory depression and low or borderline testosterone levels.



Of 56 men screened, 24 (42.9%) displayed morning serum total testosterone levels of 350 ng/dl or less (normal range=270-1070). Of these men, 23 entered the study. One responded to an initial 1-week single-blind placebo period, and 22 were subsequently randomly assigned: 12 to 1% testosterone gel, 10 g/day, and 10 to identical-appearing placebo. Each subject continued his existing antidepressant regimen. Ten subjects receiving testosterone and nine receiving placebo completed the 8-week trial.



The groups were closely matched on baseline demographic and psychiatric measures. Subjects receiving testosterone gel had significantly greater improvement in scores on the Hamilton Depression Rating Scale than subjects receiving placebo. These changes were noted on both the vegetative and affective subscales of the Hamilton Depression Rating Scale. A significant difference was also found on the Clinical Global Impression severity scale but not the Beck Depression Inventory. One subject assigned to testosterone reported increased difficulty with urination, suggesting an exacerbation of benign prostatic hyperplasia; no other subject reported adverse events apparently attributable to testosterone.



These preliminary findings suggest that testosterone gel may produce antidepressant effects in the large and probably underrecognized population of depressed men with low testosterone levels.
Age-related prevalence and morphological appearance of facial skin tumours: a prospective, cross-sectional, observational, multicentre study with special emphasis on melanocytic tumours.

The clinical and histopathological diagnosis of skin tumours arising on the face may be challenging.



An improved knowledge about the age-related patterns of facial skin tumours may aid the correct diagnosis and management.



We conducted a prospective, cross-sectional morphological study to investigate the age-related frequency and morphological variability in facial skin tumours in a cohort of consecutive subjects attending two skin lesion clinics in Italy between June and September 2011. A total of 454 consecutive subjects (249 women; 55.5%) presenting with a total of 1866 facial tumours were enrolled in the study. Of the entire cohort, 54 (11.9%) subjects had no facial lesion.



Total body naevus count correlated significantly with the mean number of facial lesions (ρ = 0.289, P < 0.001). The majority of flat lesions were pigmented (1056; 75.70%), compared to palpable (233; 17.40%) and raised lesions (93; 6.90%), the association being statistically significant (Pearson's chi square, P < 0.001. Considering melanocytic tumours only, the frequency of flat lesions significantly decreased with increasing age, while the number of palpable and raised lesions increased with increasing age (chi-square, P < 0.001). This trend was mainly due to naevi, whereby pigmented melanocytic naevi decreased with increasing age. Conversely, the percentage of non- pigmented naevi increased with increasing age (chi-square, P < 0.001).



The study was conducted in skin lesion clinics in Italy, thus any general conclusions with respect to common traits or features based on the phenotypic and genetic diversity within the European population cannot be stated.



Our study suggests that a high number of facial naevi could predict a high total naevus count. Moreover, naevi present a different morphological appearance during lifetime being initially flat, small and pigmented and becoming later raised, large and hypopigmented. Instead, lentigo maligna is an intraepidermal proliferation that typically presents as flat, large pigmented macule. A given histopathological diagnosis of a junctional naevus of a flat, facial pigmented macule of an elderly should be critically reviewed and treated with caution.
Tri-length laser therapy associated to tecar therapy in the treatment of low-back pain in adults: a preliminary report of a prospective case series

Low-back pain is very frequent, especially in active adult population. There are several different orthopaedic condition that can cause low-back pain, and the pain worsen the quality of life significantly. The treatments vary from drugs, physical therapies, kinesiology, local infiltrations, and so on. Laser therapy has an important role in the treatment of the inflammatory causes of pain, with several studies that demonstrate the efficacy of low and high energy laser therapy in the treatment of low-back pain. Sixty-six consecutive patients with low-back pain with or without leg pain were treated using a combination of Tri-length laser I-Triax® (Mectronic Medicale, Bergamo, Italy) and Pharon® tecar therapy (Mectronic Medicale, Bergamo, Italy). The patients were treated three times a week, every other day, for a total of 10 sessions. Clinical results were evaluated using visual analogic scale for individual pain (0 to 10) and the Oswestry disability scale (ODS). Tests started before the beginning of therapies and 8 weeks after the end of the therapies. Visual analogic scale (VAS) score significantly improved from an average value of 8.1 ± 1.58 pre-treatment to an average value 8-weeks post-treatment of 2.63 ± 2.74 (P < .01). ODS values start from a pre-treatment average value of 53.0 ± 13.0 to a post-treatment average value of 23.5 ± 19.8 (P < .01). A higher improvement both in VAS and in ODS was denoted in the group of patient with low-back pain and leg pain (respectively, VAS from 8.66 ± 1.58 to 2.86 ± 2.94 and ODS from 57.8 ± 15.5 to 23.7 ± 19.5). Low-back pain, associated or not with leg pain, is a very common clinical situation. The treatments of this condition are different, and an important role can be given to the laser therapy. The conclusion of this study is that the association between laser therapy iLux-Triax® and tecar therapy Pharon® in the treatment of low-back pain, with or without leg pain, can significantly reduce pain and improve the quality of life in patients with degenerative and inflammatory problems.
Tracking the neurodegeneration of parkinsonian disorders – a pilot study

The purpose of the study was to explore the possibilities of using diffusion tensor imaging (DTI) and tractography (DTT) for the differential diagnosis and monitoring of disease progression in idiopathic Parkinson’s disease (IPD), compared with the atypical parkinsonian disorders multiple system atrophy (MSA) and progressive supranuclear palsy (PSP). A 3.0-T MR scanner was used. DTI was acquired using a single-shot EPI sequence with diffusion encoding in 32 directions and a voxel size of 2 × 2 × 2 mm3. DTI data were analysed and DTT was performed using the PRIDE fibre tracking tool supplied by the manufacturer. The fractional anisotropy (FA) and apparent diffusion coefficient (ADC) within each tract were determined. DTI and DTT images in patients with moderate to advanced MSA demonstrated degeneration of the middle cerebellar peduncles and pontine crossing tracts, with decreased FA and increased ADC. This accounted for most of the pontine and cerebellar atrophy characteristic of this disease. In contrast, patients with PSP showed a selective degeneration of the superior cerebellar peduncle. Three-dimensional images of whole-brain white matter tracts demonstrated a reduction of cortical projection fibres in all patients with PSP. Visualization of the selective degeneration of individual fibre tracts, using DTI and DTT, adds qualitative data facilitating the differential diagnosis of parkinsonian disorders. Repeated measurements of FA and ADC values in a whole fibre tract might be used for monitoring disease progression and studying the effect of treatment in neuroprotective trials. The results are preliminary considering the small number of subjects in the study.
On the platform specificity of STM instrumentation mechanisms

Supporting atomic blocks (e.g., Transactional Memory (TM)) can have far-reaching effects on language design and implementation. While much is known about the language-level semantics of TM and the performance of algorithms for implementing TM, little is known about how platform characteristics affect the manner in which a compiler should instrument code to achieve efficient transactional behavior. We explore the interaction between compiler instrumentation and the performance of transactions. Through evaluation on ARM/Android, SPARC/Solaris, IA32/Linux and IA32/MacOS, we show that the compiler must consider the platform when determining which analyses, transformations, and optimizations to perform. Implementation issues include how TM library code is reached, how per-thread TM metadata is stored and accessed, and how a library switches between modes of operation. We also show that different platforms favor different TM algorithms, through the introduction of a new TM algorithm for the ARM processor. Our findings will affect compiler and TM library designers: to achieve peak performance for transactions, the compiler must perform platform-dependent analysis, transformation, and optimization, and the interface to the TM library must differ according to platform.
Targeted association mapping demonstrating the complex molecular genetics of fatty acid formation in soybean

The relative abundance of five dominant fatty acids (FAs) (palmitic, stearic, oleic, linoleic and linolenic acids) is a major factor determining seed quality in soybean. To clarify the currently poorly understood genetic architecture of FAs in soybean, targeted association analysis was conducted in 421 diverse accessions phenotyped in three environments and genotyped using 1536 pre-selected SNPs. The population of 421 soybean accessions displayed significant genetic variation for each FA. Analysis of the molecular data revealed three subpopulations, which reflected a trend depending on latitude of cultivation. A total of 37 significant (p < 0.01) associations with FAs were identified by association mapping analysis. These associations were represented by 33 SNPs (occurring in 32 annotated genes); another four SNPs had a significant association with two different FAs due to pleiotropic interactions. The most significant associations were cross-verified by known genes/QTL or consistency across cultivation year and subpopulations. The detected marker-trait associations represent a first important step towards the implementation of molecular-marker-based selection of FA composition with the potential to substantially improve the seed quality of soybean with benefits for human health and for food processing.
Hemodynamic effects of orally administered isosorbide dinitrate in patients with congestive heart failure.

The efficacy of orally administered isosorbide dinitrate (IS) has been questioned. Recently vasodilators have been shown to lower left ventricular filling pressure (LVFP) and raise cardiac output in heart failure. In the present study oral IS was evaluated in 12 patients with high LVFP due to heart failure. After right heart catheterization, patients with LVFP > 14 mm Hg were randomized double-blind to receive either 20 mg IS
Concordance of sustained virological response 4, 12, and 24 weeks post-treatment with sofosbuvir-containing regimens for hepatitis C virus.

Historically, clinical trials of regimens to treat chronic infection with hepatitis C virus (HCV) have used, as their primary efficacy endpoint, a sustained virological response (SVR)—defined as HCV RNA levels below a designated threshold of quantification—24 weeks after the end of treatment (SVR24). More recently, regulatory authorities have begun to accept SVR at 12 weeks post-treatment (SVR12) as a valid efficacy endpoint because of its high rate of concordance with SVR24. However, the concordance between SVR12 and SVR24 has not been systematically assessed with new regimens of recently approved direct-acting antiviral agents. The aim of this study was to assess the concordance between SVR at various post-treatment time points in phase III clinical trials of sofosbuvir (SOF)-containing regimens. We conducted a retrospective analysis of five trials enrolling 863 patients infected with HCV genotypes 1-6. The concordance between SVR at 4 weeks post-treatment (SVR4) and SVR12, and between SVR12 and SVR24, were determined, as well as positive predictive values (PPVs) and negative predictive values (NPVs). Overall, 779 of 796 patients (98.0%) with an SVR4 also achieved an SVR12, making the PPV of SVR4 for SVR12 98% and the NPV 100%. Of the 779 patients with an SVR12, 777 (99.7%) also achieved an SVR24, making the PPV of SVR12 for SVR24 >99% and the NPV 100%. Of patients who relapsed post-therapy, 77.6% did so within 4 weeks of completing therapy.



Data from phase III studies demonstrate that with SOF-based regimens, with or without interferon, SVR12 and SVR24 correlate closely. Thus, SVR12 can be used effectively to determine "cure" rates in trials and in clinical practice.
Factors Associated with Early Attrition from Psychosocial Rehabilitation Programs

This study aimed to identify characteristics associated with early dropout from a vocationally oriented psychosocial rehabilitation (PSR) program for clients with severe mental illness. The sample consisted of 194 individuals who participated in a study comparing a supported employment program to a stepwise vocational program. Study participants who dropped out of the PSR program within 6 months of study entry were compared to those who continued for at least 6 months. Dropouts had poorer competitive employment outcomes than those who continued. Participants with at least a high school diploma, never married, with a schizophrenia-spectrum diagnosis, and those assigned to a stepwise model of vocational rehabilitation were more likely to dropout. The implications of these findings are discussed.
Virologic, immunologic and clinical response of infants to antiretroviral therapy in Kampala, Uganda

Antiretroviral therapy (ART) is known to save lives. Among HIV-infected infants living in resource constrained settings, the short and long term benefits of ART are only partially known. This study was designed to determine the virologic, immunologic and clinical outcomes of antiretroviral therapy in a cohort of HIV-infected infants receiving care from an outpatient clinic in Kampala, Uganda.



A prospective cohort of HIV-infected infants receiving treatment at the Baylor-Uganda clinic was analyzed. Patients were diagnosed, enrolled and followed up at the clinic. HIV viral load, CD4 cell counts and clinical progress were assessed during follow-up. Descriptive statistical analysis and logistic regression modeling to determine predictors of treatment success were conducted.



Of 91 HIV-infected infants enrolled into the cohort, 53 (58.2%) infants were female; 43 (47.3%) were 6 months of age or younger, and 50 (55.6%) had advanced HIV/AIDS disease (Clinical stage 3 or 4). Eighty four infants started ART and 78 (92.9%) completed 6 months of treatments. Fifty six (71.8%) infants attained virologic suppression by month-6 of ART, and at month-12 of ART, the cumulative probability of attaining viral suppression was 83.1%. None of the baseline infant factors (age, sex, WHO stage, CD4 cell percent, weight for age, or height for age z-score) predicted treatment success. There was an increase in CD4 cells from a baseline mean of 23% to 30% at month-6 of treatment (p<0.001) and by month-24 of ART, the mean CD4 percent was 36%. A total of 7 patients died while on ART and another 7 experienced adverse events that were related to treatment.



Our results show that, even among very young patients from resource constrained settings, ART dramatically suppresses HIV replication, allows immune recovery and clinical improvement, and is safe. However, baseline characteristics do not predict recovery in this age group.