nils-herrmann/clean_scirepeval huggingface dataset:
ISO: numeric representation of nucleic acid form

We report a representation, ISO, that unambiguously and compactly describes patterns in nucleic acid secondary structure. ISO is equally as expressive as other methodologies including dot-parenthesis notation, and various structure graph variations, for representation of well-formed structure patterns. ISO naturally expresses pseudoknot structures as well, without a change or extension in notation, an advantage not possible with commonly used representations. The numerical basis of ISO is readily amenable to development of mathematical evaluation rules, distance metrics, and further abstraction for either design or analysis purposes. For structure analysis, we show how to write feature filters that determine the presence of bulges, internal loops, hairpins, stem-loops, multibranches, and pseudoknots, along with their precise sizes. We additionally show use of ISO for high-throughput in silico screening of sequence variants used to architect new synthetic systems. ISO provides an easy mechanism to further understanding of structure-function relationships in natural systems, and to automate design tasks in synthetic systems.
Can dialysis modality influence quality of life in chronic hemodialysis patients? Low-flux hemodialysis versus high-flux hemodiafiltration: a cross-over study.

Hemodiafiltration with online preparation of the substitution [online high-flux hemodiafiltration (OHDF)] and hemodiafiltration with prepared bags of substitution (HDF) are important, recently widely used renal replacement therapies in patients with end-stage renal disease. However, there is little information on the comparative impacts of these modalities versus conventional low-flux hemodialysis (HD) on the quality of life (QoL) of HD patients. This study investigates the effect of dialysis modality on QoL in chronic HD patients.



In this prospective, randomized, cross-over, open label study, 24 patients were enrolled. Their age were 62 ± 13.34 years (mean ± SD), with the duration of dialysis of 31 ± 23.28 months (mean ± SD). Five of the patients were women. QoL was measured by the Short-Form Health Survey with 36 questions (SF-36) and subscale scores were calculated. Each patient received HD, OHDF, and HDF for 3 months, with the dialysis modality subsequently being altered. They completed the questionnaire of QoL at the end of each period.



There were statistical significant differences in QoL for the total SF-36 [36.1 (26.7-45.7) and 40.7 (30.2-62.8)], for classic low-flux HD and high-flux hemodiafiltration, for bodily pain [45 (26.9-66.9) and 55 (35.6-87.5)], and for role limitations due to emotional functioning [0 (0-33.3) and 33.3 (0-100)], respectively. The scores did not differ significantly between the two types of hemodiafiltration.



Our study indicates that QoL differs significantly among patients receiving low-flux HD and high-flux hemodiafiltration, on total SF-36, bodily pain, and role limitations due to emotional functioning. Convective modalities may offer better QoL than diffusive HD.
High-nitrate vegetable diet increases plasma nitrate and nitrite concentrations and reduces blood pressure in healthy women.

Epidemiological studies suggest that green leafy vegetables, which are high in dietary nitrate, are protective against CVD such as stroke. High blood pressure (BP) is a major risk factor for stroke and inorganic nitrate has been shown to reduce BP. The objective of the present study was to test the hypothesis that diets containing high-nitrate (HN) vegetables would increase plasma nitrate and nitrite concentrations and reduce BP in healthy women.



A randomized, crossover trial, where participants received HN vegetables (HN diet) or avoided HN vegetables (Control diet) for 1 week. Before and after each intervention, resting BP and plasma nitrate and nitrite concentrations were measured.



University of Exeter, UK.



Nineteen healthy women (mean age 20 (sd 2) years; mean BMI 22·5 (sd 3·8) kg/m2).



The HN diet significantly increased plasma nitrate concentration (before HN diet: mean 24·4 (sd 5·6) µmol/l; after HN diet: mean 61·0 (sd 44·1) µmol/l, P<0·05) and plasma nitrite concentration (before HN diet: mean 98 (sd 91) nmol/l; after HN diet: mean 185 (sd 34) nmol/l, P<0·05). No significant change in plasma nitrate or nitrite concentration was observed after the Control diet. The HN diet significantly reduced resting systolic BP (before HN diet: mean 107 (sd 9) mmHg; after HN diet: mean 103 (sd 6) mmHg, P<0·05). No significant change in systolic BP was observed after the Control diet (before Control diet: mean 106 (sd 8) mmHg; after Control diet: mean 106 (sd 8) mmHg).



Consumption of HN vegetables significantly increased plasma nitrate and nitrite concentrations and reduced BP in normotensive women.
Improved detection of hypervascular liver lesions with CAIPIRINHA-Dixon-TWIST-volume-interpolated breath-hold examination.

The aim of this study was to assess the diagnostic performance of a dynamic, multiphasic contrast-enhanced volume-interpolated sequence with advanced parallel imaging techniques, Dixon fat saturation, and view sharing with 5 hepatic arterial subphases for the detection of focal liver lesions.



Twenty-four consecutive patients (13 females, 11 males; mean [SD] age, 58  years) with focal liver lesions were included in this prospective study. The examination was performed at a 3-T magnetic resonance imaging system (MAGNETOM Skyra; Siemens Healthcare, Erlangen, Germany). Five dynamic arterial subphases with a temporal resolution of 2.6 seconds, starting 17 seconds after injection of the hepatobiliary contrast agent gadolinium ethoxybenzyl diethylenetriaminepentaacetic acid (Eovist; Bayer HealthCare, Leverkusen, Germany), were acquired using an accelerated parallel imaging volume-interpolated sequence with view sharing (multiarterial controlled aliasing in parallel imaging results in higher acceleration-Dixon-time-resolved angiography with interleaved stochastic trajectories-volumetric interpolated breath-hold examination [MA-CDT-VIBE]). The fourth of the 5 arterial acquisition phases (ie, at 24.8 seconds after the start of contrast agent injection) was considered the equivalent of a standard hepatic arterial phase (equivalent standard arterial phase [ESAP]). The diagnostic value of all 5 dynamic arterial phases for the detection of focal liver lesions, as compared with the single ESAP, was judged in 2 independent consensus readings. The 2 consensus reading groups were blinded to each others' results. The complete, comprehensive multisequence magnetic resonance imaging examination, including T1-weighted, T2-weighted, and multiphasic contrast-enhanced sequences, served as the standard of reference for lesion detection.



Forty-six percent of the patients (11/24) had hypervascular lesions. In 79 % of all patients (19/24), the best arterial parenchymal contrast of one of the MA-CDT-VIBE acquisition phases was considered better than that of the ESAP. In one third of all cases (8/24 for the first and 6/24 for the second consensus reading), MA-CDT-VIBE showed an improved lesion detection rate compared with ESAP, especially in hypervascular lesions (4/11, representing 36% of all patients with hypervascular lesions). There was a high degree of interrater agreement between the 2 consensus reading groups (the Cohen κ, 0.71-1.00; P < 0.001).



Compared with a standard hepatic arterial phase, MA-CDT-VIBE with 5 hepatic arterial subphases demonstrated greater diagnostic accuracy for the detection of hypervascular focal liver lesions and provided a robust and optimized hepatic arterial acquisition phase.
DIRAE study: seasonal allergic rhinitis distribution in Spain.

National epidemiological study to observe if among patients with pollinic seasonal allergic rhinitis (SAR), there are differences between those visited by primary care physicians (GPs) or allergists (ALs).



758 and 739 adults were recruited respectively by GPs and ALs. The physicians filled in a questionnaire: ARIA classification, prescribed treatment, and asthma incidence. The patient completed a visual analogical scale (VAS) to evaluate the severity of the rhinitis. Rhinitis control (controlled, partially controlled, and not controlled) was assessed by physician and patient.



No significant differences were found among patients visited by GPs or ALs concerning the ARIA classification and rhinitis severity. Treatment with oral antihistamines was 92.3% and 89.3% for GPs and ALs, respectively. The use of nasal corticosteroids was 76.7% and 60.4% for GP and AL patients, respectively. 31.9% of the patients visited by the ALs were treated with immunotherapy. The use of alternative medicine was 10.9% and 7.6% in GP and AL patients, respectively. The perception of "controlled" rhinitis was similar among patients (40.0%) and doctors (40.1%), although patients referred differences depending if they were visited by GP (44.8%) or AL (34.9%). Asthma prevalence was higher in those who suffered persistent as compared to intermittent rhinitis (OR=1.81, 95% CI: 1.39-2.36, p<0.001), and moderate/severe vs. mild rhinitis (OR=1.68, 95% CI: 1.05-2.68, p=0.029).



The patients with pollinic SAR visited by GPs or ALs show no differences in severity. Less than half of the patients can be considered as "controlled".
Changes in Serum Concentrations of Fibroblast Growth Factor 23 and Soluble Klotho in Hemodialysis Patients after Total Parathyroidectomy

We examined the changes in circulating fibroblast growth factor 23 (FGF23) and Klotho concentrations in hemodialysis patients after parathyroidectomy (PTX).  We enrolled a cohort of hemodialysis patients who received PTX. Postoperatively, patients received calcium supplements and/or vitamin D analogue (calcitriol) to maintain serum calcium within 7.0-8.0 mg/dL. Information on clinical parameters including bone-mineral metabolic variables was collected pre-PTX and on days 5 and 90 after PTX. Concomitantly, serum full-length FGF23 and α-Klotho levels were measured. The relationship between FGF23 and clinical parameters was analyzed by single linear regression.  Forty-six participants (33 women; 13 men) were enrolled in the study. Their mean age was 56.49 years. Serum FGF23 and α-Klotho concentrations were elevated on days 5 and 90 after PTX compared to baseline (p > 0.05). Serum FGF23 concentrations negatively correlated with serum calcium concentrations pre-PTX (Beta -0.31; R2 0.0949; p = 0.040), day 5 post-PTX (Beta -0.31; R2 0.0982; p = 0.036), and day 90 post-PTX (Beta -0.39; R2 0.1528; p = 0.008).  There was no change in circulating FGF23 and Klotho concentrations after PTX in hemodialysis patients given postoperative calcium supplements and/or vitamin D analogue. Serum FGF23 concentrations pre-PTX and at days 5 and 90 after PTX were inversely related to serum calcium concentrations.
Two year follow-up of clinical and inflammation parameters in children monosensitized to mites undergoing subcutaneous and sublingual immunotherapy.

Both SCIT (subcutaneous immunotherapy) and SLIT (sublingual immunotherapy) have clinical and immunologic efficacy in children with rhinitis and asthma but comparative studies are scarce.



To investigate the clinical and immunological efficacy of mite-specific SLIT and SCIT in children with rhinitis and asthma.



Thirty children monosensitized to house dust mite were randomized to receive either active SCIT or SLIT or placebo for 1 yr in a double-blind double-dummy placebo controlled design (Yukselen A et al., ). Thereafter, the placebo group was randomized to receive SCIT or SLIT, and for 1 yr all patients received active treatment with SCIT or SLIT. Symptom scores, drug usage, titrated skin prick tests, nasal and bronchial allergen provocation doses, serum house dust mite-specific immunglobulin E, sIgG4, IL-10 and IFN- g levels were evaluated.



The reduction of clinical scores with SLIT was more evident after 2 years of treatment in comparison to both the baseline and DBPC phase of the study. The change in titrated skin prick tests and nasal provocative doses was more prominent with both SCIT and SLIT at the end of the open phase. Although the increase inbronchial provocative doses was not significant at the end of the first year of treatment with SLIT, it reached a statistically significant difference after two years of treatment.



The clinical efficacy of SLIT is more prominent at the end of the second year, although this improvement is observed from the first year of treatment with SCIT in mite-sensitive children.
Combined IL-21–primed polyclonal CTL plus CTLA4 blockade controls refractory metastatic melanoma in a patient

Adoptive transfer of peripheral blood-derived, melanoma-reactive CD8(+) cytotoxic T lymphocytes (CTLs) alone is generally insufficient to eliminate bulky tumors. Similarly, monotherapy with anti-CTLA4 infrequently yields sustained remissions in patients with metastatic melanoma. We postulated that a bolus of enhanced IL-21-primed polyclonal antigen-specific CTL combined with CTLA4 blockade might boost antitumor efficacy. In this first-in-human case study, the combination successfully led to a durable complete remission (CR) in a patient whose disease was refractory to both monoclonal CTL and anti-CTLA4. Long-term persistence and sustained anti-tumor activity of transferred CTL, as well as responses to nontargeted antigens, confirmed mutually beneficial effects of the combined treatment. In this first-in-human study, Chapuis et al. demonstrate that the combination of adoptive cellular therapy with CTLA4 blockade induces long-term remission in a melanoma patient resistant to both modalities administered serially and individually.
Vitamin D, d-dimer, Interferon γ, and sCD14 Levels are Independently Associated with Immune Reconstitution Inflammatory Syndrome: A Prospective, International Study☆

To determine the immunological profile most important for IRIS prediction, we evaluated 20 baseline plasma biomarkers in Acquired Immunodeficiency Syndrome (AIDS) patients initiating antiretroviral therapy (ART). Patients were enrolled in a randomized, placebo-controlled ART initiation trial in South Africa and Mexico to test whether maraviroc could prevent IRIS. Participants were classified prospectively as having IRIS within 6 months of ART initiation. Twenty plasma biomarkers were measured at study enrollment for 267 participants. Biomarkers were tested for predicting IRIS with adjustment for covariates chosen through forward stepwise selection. Sixty-two participants developed IRIS and of these 19 were tuberculosis (TB)-IRIS. Baseline levels of vitamin D and higher d-dimer, interferon gamma (IFNγ), and sCD14 were independently associated with risk of IRIS in multivariate analyses. TB-IRIS cases exhibited a distinct biosignature from IRIS related to other pathogens, with increased levels of C-reactive protein (CRP), sCD14, IFNγ, and lower levels of Hb that could be captured by a composite risk score. Elevated markers of Type 1 T helper (Th1) response, monocyte activation, coagulation and low vitamin D were independently associated with IRIS risk. Interventions that decrease immune activation and increase vitamin D levels warrant further study.
A phase I study of indole-3-carbinol in women: tolerability and effects.

We completed a phase I trial of indole-3-carbinol (I3C) in 17 women (1 postmenopausal and 16 premenopausal) from a high-risk breast cancer cohort. After a 4-week placebo run-in period, subjects ingested 400 mg I3C daily for 4 weeks followed by a 4-week period of 800 mg I3C daily. These chronic doses were tolerated well by all subjects. Hormonal variables were measured near the end of the placebo and dosing periods, including determination of the urinary 2-hydroxyestrone/16alpha-hydroxyestrone ratio. Measurements were made during the follicular phase for premenopausal women. Serum estradiol, progesterone, luteinizing hormone, follicle-stimulating hormone, and sex hormone binding globulin showed no significant changes in response to I3C. Caffeine was used to probe for cytochrome P450 1A2 (CYP1A2), N-acetyltransferase-2 (NAT-2), and xanthine oxidase. Comparing the results from the placebo and the 800 mg daily dose period, CYP1A2 was elevated by I3C in 94% of the subjects, with a mean increase of 4.1-fold. In subjects with high NAT-2 activities, these were decreased to 11% by I3C administration but not altered if NAT-2 activity was initially low. Xanthine oxidase was not affected. Lymphocyte glutathione S-transferase activity was increased by 69% in response to I3C. The apparent induction of CYP1A2 was mirrored by a 66% increase in the urinary 2-hydroxyestrone/16alpha-hydroxyestrone ratio in response to I3C. The maximal increase was observed with the 400 mg daily dose of I3C, with no further increase found at 800 mg daily. If the ratio of hydroxylated estrone metabolites is a biomarker for chemoprevention, as suggested, then 400 mg I3C daily will elicit a maximal protective effect.
Inspiratory muscle training improves breathing pattern during exercise in COPD patients.

Dyspnoea is typically the main symptom limiting exercise capacity in patients with chronic obstructive pulmonary disease (COPD) [1–3]. Exertional dyspnoea has been linked to dynamic hyperinflation (DH), when lung expansion critically encroaches upon the inspiratory reserve volume (IRV) . Consequently, patients develop a rapid and shallow breathing pattern, which is energetically opposite to the pattern required to minimise the work of breathing [5]. Furthermore, the restriction of tidal volume (VT) expansion has recently been linked to daily physical activity limitation [6].
Advantage of Pulsatility in Left Ventricular Reverse Remodeling and Aortic Insufficiency Prevention During Left Ventricular Assist Device Treatment.

A continuous flow (CF) left ventricular assist device (LVAD) has various advantages over a pulsatile flow (PF) LVAD, but the extent of preventing aortic insufficiency (AI) by each type of LVAD remains controversial.



Of 86 patients with non-ischemic cardiomyopathy who underwent LVAD implantation between 2006 and 2015, 20 propensity score-matched patients with PF LVADs and 20 with CF LVADs were enrolled in this study. There were no significant differences in the baseline variables of both groups. During the 6-month LVAD treatment, the LV ejection fraction of the PF group was significantly higher than that of the CF group; the PF group also had a wider pulse pressure and less enlargement of the aortic root (P<0.05 for all). Patients in the PF group experienced more frequent opening of the native aortic valve and less AI than those in the CF group (P<0.05 for both). The PF LVAD was explanted in 5 patients (25%), and a CF LVAD was explanted in 1 patient (5%).



Compared with CF LVADs, PF LVADs seem to have an advantage in improving LV reverse remodeling and preventing AI. It may be best to incorporate pulsatility into current CF LVADs while retaining their existing benefits.
The impact of two multiple-choice question formats on the problem-solving strategies used by novices and experts

Pencil-and-paper examination formats, and specifically the standard, five-option multiple-choice question, have often been questioned as a means for assessing higher-order clinical reasoning or problem solving. This study firstly investigated whether two paper formats with differing number of alternatives (standard five-option and extended-matching questions) can test problem-solving abilities. Secondly, the impact of the alternatives number on psychometrics and problem-solving strategies was examined.



Think-aloud protocols were collected to determine the problem-solving strategy used by experts and non-experts in answering Gastroenterology questions, across the two pencil-and-paper formats.



The two formats demonstrated equal ability in testing problem-solving abilities, while the number of alternatives did not significantly impact psychometrics or problem-solving strategies utilized.



These results support the notion that well-constructed multiple-choice questions can in fact test higher order clinical reasoning. Furthermore, it can be concluded that in testing clinical reasoning, the question stem, or content, remains more important than the number of alternatives.
Imatinib mesylate as a preoperative therapy in dermatofibrosarcoma: results of a multicenter phase II study on 25 patients.

The treatment of dermatofibrosarcoma protuberans (DFSP) involves wide local excision with frequent need for reconstructive surgery. A t(17;22) translocation resulting in COL1A1-PDGFB fusion is present in >95% of cases. Certain patient observations and a report on nine patients suggest that imatinib mesylate, targeting platelet-derived growth factor receptor beta, has clinical potential in DFSP. The primary aim of this phase II multicenter study was to define the percentage of clinical responders (Response Evaluation Criteria in Solid Tumors) to a 2-month preoperative daily administration of 600 mg of imatinib mesylate before wide local excision. The secondary aims were to determine tolerance, objective response from imaging results (ultrasound and magnetic resonance imaging), and pathologic responses observed in sequential tissue specimens.



A two-stage flexible design was used with interim analysis after the recruitment of six patients. Twenty-five adults suffering from primary or recurrent DFSP were included from July 2004 to May 2006.



The COL1A1-PDGFB fusion gene was detected in 21 out of 25 patients following fluorescence in situ hybridization analysis (two cases were noninformative). A clinical response was achieved in nine (36%) patients (95% confidence interval, 18.9-57.5). The median relative tumoral decrease was 20.0% (range, -12.5 to 100). Apart from expected grade 1 or 2 side effects, we observed one grade 3 neutropenia, one grade 3 maculopapular rash, and one grade 4 transient transaminitis.



Our results support the use of imatinib in a neoadjuvant setting in nonresectable DFSP, or when surgery is difficult or mutilating. These results will be useful for setting hypotheses in the evaluation of new drugs to treat primary or secondary resistance to imatinib.
Psychometric Validation of a General Health Quality of Life Tool for Cats Used to Compare Healthy Cats and Cats with Chronic Kidney Disease

Numerous validated psychometric tools are available to assess impact of disease on a human's quality of life (QoL). To date, no psychometrically validated general health-related QoL tool exists for cats.



To develop and validate a tool for assessment of owner-perceived QoL in cats (CatQoL) and to use this tool to compare QoL between healthy cats and those with chronic kidney disease (CKD).



Total of 204 owners of young healthy cats (YH, n = 99; <9 years), older healthy cats (OH, n = 35), and cats diagnosed with CKD (CKD, n = 70) completed the CatQoL.



Discussions with a focus group and 2 pilot surveys informed design of 16 QoL questions grouped into 4 domains. Each item scored according to frequency and importance, and item-weighted-impact-scores were calculated. The validity of the tool was assessed using principal components analysis and Cronbach's α. The average item-weighted-impact-score (AWIS) was compared among groups and domains.



Sixteen-item CatQoL showed good internal consistency reliability (Cronbach's α, 0.77) and unidimensionality with significant loadings (0.2-0.7) and communalities (>0.3). Young healthy cats had significantly higher AWIS (median [IQR], 1.25 [0.63, 1.88]) than OH (0.56 [-0.06, 1.00]) and CKD cats (-0.06 [-0.81, 0.88]), P < .001). CKD cats had significantly lower AWIS for eating domain (YH: 2.00 [1.00, 3.00]; OH: 2.00 [0.67, 3.00]; CKD : 1.00 [0.00, 2.67]) when compared with the YH group and OH group, and all groups differed significantly in their management domain (YH: -0.50 [-1.00, 0.00]; OH: -1.00 [-1.88, -0.50]; CKD : -1.50 [-2.50, -1.00], P < .001).



The CatQoL was validated for use in cats, and can be used as additional assessment parameter in clinical and research settings.