nils-herrmann/clean_scirepeval huggingface dataset:
Mechanisms of gene-environment interactions in depression: evidence that genes potentiate multiple sources of adversity.

Previous work suggests that daily life stress-sensitivity may be an intermediary phenotype associated with both genetic risk for depression and developmental stress exposures. In the current analysis we hypothesized that genetic risk for depression and three environmental exposures over the course of development [prenatal stress, childhood adversity and adult negative life events (NLEs)] combine synergistically to produce the phenotype of stress-sensitivity.



Twin pairs (n=279) participated in a momentary assessment study using the Experience Sampling Method (ESM), collecting appraisals of stress and negative affect (NA) in the flow of daily life. Prospective data on birthweight and gestational age, questionnaire data on childhood adversity and recent NLEs, and interview data on depression were used in the analyses. Daily life stress-sensitivity was modelled as the effect of ESM daily life stress appraisals on ESM NA.



All three developmental stress exposures were moderated by genetic vulnerability, modelled as dizygotic (DZ) or monozygotic (MZ) co-twin depression status, in their effect on daily life stress-sensitivity. Effects were much stronger in participants with MZ co-twin depression and a little stronger in participants with DZ co-twin depression status, compared to those without co-twin depression. NLE main effects and NLE genetic moderation were reducible to birthweight and childhood adversity.



The findings are consistent with the hypothesis that adult daily life stress-sensitivity is the result of sensitization processes initiated by developmental stress exposures. Genes associated with depression may act by accelerating the process of stress-induced sensitization.
Left ventricular diastolic dysfunction in congenital chronic anaemias during childhood as determined by comprehensive echocardiographic imaging including acoustic quantification.

To evaluate prospectively the left ventricular performance in thalassaemia major and sickle cell disease using comprehensive echocardiographic imaging including acoustic quantification during early childhood.



Twenty-three patients with thalassaemia and 26 patients with sickle cell disease underwent echocardiographic examination including M-mode, 2-D, Doppler and acoustic quantification. All patients were matched for age, sex, weight and height with 20 normal controls. All patients were below 13 years of age. Thalassaemia and sickle cell disease patients were significantly anaemic when compared with normals (P<0.0001). All patients had normal left ventricular systolic parameters. Acoustic quantification-derived left ventricular volumes, filling rates, and emptying rates were not different in thalassaemia patients from controls. Left ventricular volumes, however, were larger in sickle cell disease patients than in controls. In contrast, by Doppler technique, left ventricular filling occurs mainly in early diastole (E wave) in thalassaemia patients and mainly in late diastole (A wave) in sickle cell disease patients, (P=0.03 and 0.01 respectively). E/A ratio was lower and diastolic filling period was shorter than normal in sickle cell disease but not in thalassaemia patients. Patients in both groups had left ventricular mass (determined by M-mode) significantly higher than normal (P<0.0001).



The left ventricular systolic performance is well preserved in patients with chronic anaemia due to thalassaemia major and sickle cell disease during early childhood. In both diseases, however, there is left ventricular hypertrophy and measurable abnormalities in the diastolic filling detected by Doppler. Such changes do not fit a specific cardiomyopathic pattern due to diastolic dysfunction i.e. restrictive physiology vs delayed relaxation. Acoustic quantification of left ventricular diastolic parameters (filling rates) was less sensitive than Doppler in detecting these early diastolic abnormalities in both diseases.
Regulation of cilium length and intraflagellar transport by the MAP kinases MAK, MRK, and MOK

Cilia are assembled and maintained by intraflagellar transport (IFT), which moves cargo bi-directionally along the axoneme of the cilium. Regulation of IFT allows modulation of cilia length and influences signaling pathways that initiate in the cilium. We characterized C. elegans’ DYF-5, a MAP kinase that regulates cilia length and IFT. DYF-5 has three mammalian homologues: MAK (male germ cellassociated kinase), MRK (MAK-related kinase) and MOK (MAPK/MAK/MRK overlapping kinase). Here we analyzed the functions of MAK, MRK and MOK. GFP fusions of MAK, MRK and MOK showed that all three proteins localize along the length of the cilia of IMCD3 and RPE cells, and accumulate at the distal tip. Knockdown of MRK or MOK resulted in longer cilia, while overexpression of MAK or MRK resulted in short and stumpy cilia. Interestingly, overexpression of MOK did not affect cilia length. These effects on cilia length are in line with our data on DYF-5 function in C. elegans (Burghoorn et al., 2007) and published data on MAK (Omori et al., 2010). To visualize IFT and measure its speed we have generated IMCD3 cell lines that stably express GFP-fusion constructs of different components of the IFT complex: Kinesin-II, Kif17, complex A, complex B, and the BBSome. All these GFP fusion proteins showed an average anterograde speed of ~0.4 μm/s and a similar average retrograde speed. Knock down of MOK using shRNAs resulted in increased anterograde speeds of all constructs to ~0.6 μm/s, while knock down of MRK had no effect. Retrograde speeds were not affected.
KGCAK: a K-mer based database for genome-wide phylogeny and complexity evaluation

The K-mer approach, treating genomic sequences as simple characters and counting the relative abundance of each string upon a fixed K, has been extensively applied to phylogeny inference for genome assembly, annotation, and comparison. To meet increasing demands for comparing large genome sequences and to promote the use of the K-mer approach, we develop a versatile database, KGCAK ( http://kgcak.big.ac.cn/KGCAK/ ), containing ~8,000 genomes that include genome sequences of diverse life forms (viruses, prokaryotes, protists, animals, and plants) and cellular organelles of eukaryotic lineages. It builds phylogeny based on genomic elements in an alignment-free fashion and provides in-depth data processing enabling users to compare the complexity of genome sequences based on K-mer distribution. We hope that KGCAK becomes a powerful tool for exploring relationship within and among groups of species in a tree of life based on genomic data. This article was reviewed by Prof Mark Ragan and Dr Yuri Wolf.
Second-line antiretroviral therapy in resource-limited settings: the experience of Médecins Sans Frontières.

To describe the use of second-line protease-inhibitor regimens in Médecins Sans Frontières HIV programmes, and determine switch rates, clinical outcomes, and factors associated with survival.



We used patient data from 62 Médecins Sans Frontières programmes and included all antiretroviral therapy-naive adults (> 15 years) at the start of antiretroviral therapy and switched to a protease inhibitor-containing regimen with at least one nucleoside reverse transcriptase inhibitor change after more than 6 months of nonnucleoside reverse transcriptase inhibitor first-line use. Cumulative switch rates and survival curves were estimated using Kaplan-Meier methods, and mortality predictors were investigated using Poisson regression.



Of 48,338 adults followed on antiretroviral therapy, 370 switched to a second-line regimen after a median of 20 months (switch rate 4.8/1000 person-years). Median CD4 cell count at switch was 99 cells/microl (interquartile ratio 39-200; n = 244). A lopinavir/ritonavir-based regimen was given to 51% of patients and nelfinavir-based regimen to 43%; 29% changed one nucleoside reverse transcriptase inhibitor and 71% changed two nucleoside reverse transcriptase inhibitors. Median follow-up on second-line antiretroviral therapy was 8 months, and probability of remaining in care at 12 months was 0.86. Median CD4 gains were 90 at 6 months and 135 at 12 months. Death rates were higher in patients in World Health Organization stage 4 at antiretroviral therapy initiation and in those with CD4 nadir count less than 50 cells/microl.



The rate of switch to second-line treatment in antiretroviral therapy-naive adults on non-nucleoside reverse transcriptase inhibitor-based first-line antiretroviral therapy was relatively low, with good early outcomes observed in protease inhibitor-based second-line regimens. Severe immunosuppression was associated with increased mortality on second-line treatment.
How to avoid discontinuation of antihypertensive treatment. The experience in São Paulo, Brazil

To evaluate the importance of providing guidelines to patients via active telephone calls for blood pressure control and for preventing the discontinuation of treatment among hypertensive patients.



Many reasons exist for non-adherence to medical regimens, and one of the strategies employed to improve treatment compliance is the use of active telephone calls.



Hypertensive patients (n=354) who could receive telephone calls to remind them of their medical appointments and receive instruction about hypertension were distributed into two groups: a) "uncomplicated" - hypertensive patients with no other concurrent diseases and b) "complicated" - severe hypertensive patients (mean diastolic ≥ 110 mmHg with or without medication) or patients with comorbidities. All patients, except those excluded (n=44), were open-block randomized to follow two treatment regimens ("traditional" or "current") and to receive or not receive telephone calls ("phone calls" and "no phone calls" groups, respectively).



Significantly fewer patients in the "phone calls" group discontinued treatment compared to those in the "no phone calls" group (4 vs. 30; p<0.0094). There was no difference in the percentage of patients with controlled blood pressure in the "phone calls" group and "no phone calls" group or in the "traditional" and "current" groups. The percentage of patients with controlled blood pressure (<140/90 mmHg) was increased at the end of the treatment (74%), reaching 80% in the "uncomplicated" group and 67% in the "complicated" group (p<0.000001).



Guidance to patients via active telephone calls is an efficient strategy for preventing the discontinuation of antihypertensive treatment.
Impact of androgen-deprivation therapy on physical function and quality of life in men with nonmetastatic prostate cancer.

This prospective longitudinal study evaluated the effect of androgen deprivation therapy (ADT) on objective and self-reported physical function.



Men with nonmetastatic prostate cancer (PC) starting continuous ADT were enrolled in this matched cohort study. Physical function was assessed with the 6-minute walk test (6MWT), grip strength, and the timed-up-and-go (TUG) test, representing endurance and upper and lower extremity strength, respectively. Quality of life (QOL) was measured with the Medical Outcomes Study Short-Form 36 (SF-36) questionnaire. Subjects were assessed at baseline, 3, 6, and 12 months. Two control groups (PC without ADT; no PC), matched on age, education, and baseline function were enrolled. Mixed effects regression models were fitted, adjusting for baseline covariates.



We enrolled 87 patients on ADT, 86 PC controls, and 86 healthy controls; groups were similar in age (mean, 69.1 years; range, 50 to 87) and physical function. The 6MWT distance remained stable in the ADT group (P = .96) but improved in both control groups (P < .05). Grip strength declined in the ADT group (P = .04), remained stable in PC controls (P = .31), and improved in healthy controls (P = .008). TUG scores remained stable over time and across groups (P > .10). The SF-36 physical function summary score declined in the ADT group (P < .001), but increased in both control groups (P < .001). Negative effects on outcomes were observed within 3 months of starting ADT and were generally independent of age.



Endurance, upper extremity strength, and physical components of QOL are affected within 3 months of starting ADT. Up-front exercise interventions to counteract these losses are warranted.
Evaluating the Lions-Quest "Skills for Adolescence" drug education program: first-year behavior outcomes.

Thirty-four schools (n=7426 consented sixth graders, 71% of the eligible population) were randomized to conditions to test the hypothesis that "Skills for Adolescence" (SFA) is more effective than standard care in deterring and delaying substance use through middle school. One-year posttest data were collected from 6239 seventh graders (84% of those eligible). Initiation of "ever" and "recent" use of five substances for baseline nonusers and changes in recent use for baseline users by experimental condition were compared using mixed model regression to control for school clustering. For pretest nonusers, recent cigarette smoking was lower for SFA than controls (P<.05), as was lifetime marijuana use (P<.06). There were also three Treatment x Ethnicity interactions around drinking behaviors. Hispanics in SFA were less likely to ever and recently drink, and to recently binge drink than Hispanic controls; there were no treatment differences among non-Hispanics. For baseline users, there were three significant SFA delays in transition to experimental or recent use of more "advanced" substances: drinking to smoking, drinking to marijuana use, and binge drinking to marijuana.
Scaled Log Likelihood Ratios for the Detection of Abbreviations in Text Corpora

We describe a language-independent, flexible, and accurate method for the detection of abbreviations in text corpora. It is based on the idea that an abbreviation can be viewed as a collocation, and can be identified by using methods for collocation detection such as the log likelihood ratio. Although the log likelihood ratio is known to show a good recall, its precision is poor. We employ scaling factors which lead to a strong improvement of precision. Experiments with English and German corpora show that abbreviations can be detected with high accuracy.
A Similarity-Based Method Retrieval Technique to Improve Effectiveness in Code Search

The effectiveness of a code search engine is reduced if semantically similar code fragments are not indexed under common and proper terms. In this paper, a technique named Feature-Wise Similar Method Finder (FWSMF) is proposed which checks functional similarity among codes by executing and matching outputs against the same set of inputs. It then determines appropriate index terms by finding keywords that are found in most of the code snippets. As a result, code fragments that contain different keywords but implement the same feature, can be retrieved all together. Experimental analysis shows that on an average, FWSMF produces 61% and 29% more precision than two existing techniques named Keyword Based Code Search (KBCS) and Interface Driven Code Search (IDCS) respectively. It also shows 34% and 55% more recall than KBCS and IDCS correspondingly. It retrieves self executable code snippets which can be easily pluggable in the intended development context and thus reduces time and effort while reusing code.
Decrease in oxidative stress through supplementation of vitamins C and E is associated with a reduction in blood pressure in patients with essential hypertension.

Oxidative stress has been associated with mechanisms of EH (essential hypertension). The aim of the present study was to test the hypothesis that the antioxidant properties of vitamins C and E are associated with a decrease in BP (blood pressure) in patients with EH. A randomized double-blind placebo-controlled clinical trial was conducted in 110 men with grade 1 EH (35-60 years of age without obesity, dyslipidaemia and diabetes mellitus, non-smokers, not undergoing vigorous physical exercise, without the use of any medication and/or high consumption of fruit and vegetables). Participants were randomly assigned to receive either vitamins C+E [vitamin C (1 g/day) plus vitamin E (400 international units/day)] or placebo for 8 weeks. Measurements included 24 h ambulatory BP and blood analysis of oxidative-stress-related parameters in erythrocytes (GSH/GSSH ratio, antioxidant enzymes and malondialdehyde) and plasma [FRAP (ferric reducing ability of plasma)], and levels of 8-isoprostane, vitamins C and E were measured at baseline and after treatment. Following administration of vitamins C+E, patients with EH had significantly lower systolic BP, diastolic BP and mean arterial BP and higher erythrocyte and serum antioxidant capacity compared with either placebo-treated patients with EH or the patients with EH at baseline prior to treatment. BP correlated positively with plasma 8-isoprostane levels and negatively with plasma FRAP levels in the vitamins C+E- and placebo-treated groups. In conclusion, the present study supports the view that oxidative stress is involved in the pathogenesis of EH, and that enhancement of antioxidant status by supplementation with vitamins C and E in patients with EH is associated with lower BP. This suggests intervention with antioxidants as an adjunct therapy for hypertension.
Limited Durability of Viral Control following Treated Acute HIV Infection

Early treatment of acute HIV infection with highly active antiretroviral therapy, followed by supervised treatment interruption (STI), has been associated with at least transient control of viremia. However, the durability of such control remains unclear. Here we present longitudinal follow-up of a single-arm, open-label study assessing the impact of STI in the setting of acute HIV-1 infection.



Fourteen patients were treated during acute HIV-1 infection and subsequently subjected to an STI protocol that required retreatment if viral load exceeded 50,000 RNA copies/ml plasma or remained above 5,000 copies/ml for more than three consecutive weeks. Eleven of 14 (79%) patients were able to achieve viral loads of less than 5,000 RNA copies/ml for at least 90 d following one, two, or three interruptions of treatment. However, a gradual increase in viremia and decline in CD4+ T cell counts was observed in most individuals. By an intention-to-treat analysis, eight (57%), six (43%), and three (21%) of 14 patients achieved a maximal period of control of 180, 360, and 720 d, respectively, despite augmentation of HIV-specific CD4+ and CD8+ T cell responses. The magnitude of HIV-1-specific cellular immune responses before treatment interruption did not predict duration of viremia control. The small sample size and lack of concurrent untreated controls preclude assessment of possible clinical benefit despite failure to control viremia by study criteria.



These data indicate that despite initial control of viremia, durable viral control to less than 5,000 RNA copies/ml plasma in patients following treated acute HIV-1 infection occurs infrequently. Determination of whether early treatment leads to overall clinical benefit will require a larger and randomized clinical trial. These data may be relevant to current efforts to develop an HIV-1 vaccine designed to retard disease progression rather than prevent infection since they indicate that durable maintenance of low-level viremia may be difficult to achieve.
Genetic Algorithm in spatial clustering

Clustering has been utilized a great deal in statistical data mining as well as machine learning in case of unsupervised learning. Clustering is a centeral task in knowledge discovery and data mining. One of the limitations that clustering methods usually encounter is prede ned number of clusters. The method that is going to be presented in this paper is not constrained by such a limitation. Genetic algorithm with variable length chromosomes allows the system to pick up a needed number of clusters to successfully partition an heterogeneous data set into groups of non exclusive, more homogeneous charactersistics. The genetic algorithm utilizes the Finite Mixture Density as its objective function. Tournament selection is used to select the best tness. 2-point crossover and mutation help exploit and explore the search space.
Increased bacterial infections after transfusion of leukoreduced non-irradiated blood products in recipients of allogeneic stem cell transplants after reduced-intensity conditioning.

Blood components transfused to hematopoietic stem cell transplant (HSCT) recipients are irradiated to prevent transfusion-associated graft-versus-host disease (TA-GVHD). The effect of transfusing non-irradiated blood products in HSCT outcome, including incidence of transplant complications, bacterial infections, acute and chronic GVHD presentation, and characteristics, has not been documented. Clinical records as well as blood bank and electronic databases of HSCT patients grafted after reduced-intensity conditioning who received irradiated versus non-irradiated blood products, after blood irradiation became unavailable at our center, were scrutinized for transplant outcome, clinical evolution, engraftment characteristics including days to neutrophil and platelet recovery, acute and chronic GVHD, rate and type of infections, and additional transplant-related comorbidities. All transfused blood products were leukoreduced. A total of 156 HSCT recipients was studied, 73 received irradiated and 83 non-irradiated blood components. Bacterial infections were significantly more frequent in patients transfused with non-irradiated blood products, P = .04. Clinically relevant increased rates of fever and neutropenia and mucositis were also documented in these patients. No cases of TA-GVHD occurred. Classical GVHD developed in 37 patients (50.7%) who received irradiated blood products and 36 (43.9%) who received non-irradiated blood products, P = .42. Acute GVHD developed in 28 patients (38.4%) in the blood-irradiated and 33 patients (39.8%) in the non-irradiation group, P = .87. The 2-year GVHD-free survival rate was 40% in the irradiated versus 40.6% in the non-irradiation group, P = .071. Increased bacterial infections were found in HSCT recipients transfused with non-irradiated blood products, which ideally must always be irradiated.