nils-herrmann/clean_scirepeval huggingface dataset:
Quantitative lung ventilation using Fourier decomposition MRI; comparison and initial study

The Fourier decomposition (FD) method is a noninvasive method for assessing ventilation and perfusion-related information in the lungs, but the lack of quantifiable values is a drawback. We demonstrate a novel technique for quantification of the FD ventilation maps, compare it to two published methods, and show results from both healthy volunteers and patients diagnosed with lung cancer. We quantified the standard FD ventilation images by utilizing additional information, i.e., the zero-frequency component image, which is also obtained from the Fourier analysis. This image acts as a baseline for the changes recorded in the FD ventilation image and can therefore be used to calculate the ventilation. Using this technique, we compared the ventilation values from ten healthy volunteers and ten patients to two previously published methods for quantitative ventilation assessment. All methods showed good overall agreement (mean difference between the methods was 14–38 ml/min). The mean minute ventilation for the FD method was calculated to be 693 ml/min for a 2D slice, which is in the expected range. The zero-frequency component image can be used as a baseline to quantify the FD ventilation maps. Our initial study showed good agreement with published methods in healthy volunteers, but less so in patients with lung cancer.
Effects of Brief Behavioural Activation on Approach and Avoidance Tendencies in Acute Depression: Preliminary Findings.

It has been suggested that the behavioural activation (BA) treatments for depression unfold their effects, at least partly, through changes in approach and avoidance tendencies. However, as yet, little research has examined the cognitive effects of these interventions.



This study investigated the impact of a single session of BA on depressive symptomatology, self-reported avoidance, and behavioural approach and avoidance tendencies.



Forty-six patients with a diagnosis of Major Depression were recruited from primary care psychological therapies services and block randomized to either a single session of behavioural activation (n = 22) or waiting list control (n = 24) delivered by an unblinded therapist. Self-reports of symptoms and cognitive factors were assessed before and after the one-week intervention phase. Approach and avoidance behavioural tendencies were assessed using the Approach-Avoidance Task (AAT).



Data from 40 participants (n = 20 in each group) was available for analyses. Depressive symptoms significantly decreased, and activation significantly increased from before to after treatment in the treatment group, but not in the control group. Performance on the AAT showed a trend indicating increased approach to positive valence stimuli in the treatment group, but not in the control group. Mediational analyses indicated small indirect effects of self-reported change in activation as mediators of the effect of condition on symptoms.



The findings suggest that a single session of BA can have significant effects on symptoms in clinically depressed patients. Results hint at the possibility that increased behavioural approach might mediate the effect of BA.
Comparison of hemodynamic performance of the balloon-expandable SAPIEN 3 versus SAPIEN XT transcatheter valve.

The SAPIEN 3 valve (S3V) is a new-generation transcatheter valve with enhanced anti-paravalvular leak properties, but no data comparing with earlier transcatheter valve systems are available. We aimed to compare the hemodynamic performance of the S3V and the SAPIEN XT valve (SXTV) in a case-matched study with echo core laboratory analysis. A total of 27 patients who underwent transcatheter aortic valve replacement (TAVR) with the S3V were matched for prosthesis size (26 mm), aortic annulus area, and mean diameter measured by computed tomography, left ventricular ejection fraction, body surface area, and body mass index with 50 patients treated with the SXTV. The prosthesis size was determined by oversizing of 1% to 15% of annulus area. Doppler echocardiographic images collected at baseline and 1-month follow-up were analyzed in a central echocardiography core laboratory. The need for postdilation was higher in the SXTV group (20% vs 4%, p=0.047), and mean residual gradient and effective orifice area were similar in both groups (p>0.05). The incidence of paravalvular aortic regurgitation was greater with the SXTV (≥mild: 42%, moderate: 8%) than with the S3V (≥mild: 7%, moderate: 0%; p=0.002 for ≥mild vs SXTV). The implantation of an S3V was the only factor associated with trace or no paravalvular leak after TAVR (p=0.007). In conclusion, TAVR with the S3V was associated with a very low rate of paravalvular leaks and need for balloon postdilation, much lower than that observed with the earlier generation of balloon-expandable valve (SXTV). The confirmation of these results in a larger cohort of patients will represent a major step forward in using transcatheter valves for the treatment of aortic stenosis.
Efficacy of melphalan and prednisone plus thalidomide in patients older than 75 years with newly diagnosed multiple myeloma: IFM 01/01 trial.

Until recently, melphalan and prednisone were the standards of care in elderly patients with multiple myeloma. The addition of thalidomide to this combination demonstrated a survival benefit for patients age 65 to 75 years. This randomized, placebo-controlled, phase III trial investigated the efficacy of melphalan and prednisone plus thalidomide in patients older than 75 years with newly diagnosed myeloma.



Between April 2002 and December 2006, 232 previously untreated patients with myeloma, age 75 years or older, were enrolled and 229 were randomly assigned to treatment. All patients received melphalan (0.2 mg/kg/d) plus prednisone (2 mg/kg/d) for 12 courses (day 1 to 4) every 6 weeks. Patients were randomly assigned to receive 100 mg/d of oral thalidomide (n = 113) or placebo (n = 116), continuously for 72 weeks. The primary end point was overall survival.



After a median follow-up of 47.5 months, overall survival was significantly longer in patients who received melphalan and prednisone plus thalidomide compared with those who received melphalan and prednisone plus placebo (median, 44.0 v 29.1 months; P = .028). Progression-free survival was significantly prolonged in the melphalan and prednisone plus thalidomide group (median, 24.1 v 18.5 months; P = .001). Two adverse events were significantly increased in the melphalan and prednisone plus thalidomide group: grade 2 to 4 peripheral neuropathy (20% v 5% in the melphalan and prednisone plus placebo group; P < .001) and grade 3 to 4 neutropenia (23% v 9%; P = .003).



This trial confirms the superiority of the combination melphalan and prednisone plus thalidomide over melphalan and prednisone alone for prolonging survival in very elderly patients with newly diagnosed myeloma. Toxicity was acceptable.
Five-year data and prognostic factor analysis of oxaliplatin and irinotecan combinations for advanced colorectal cancer: N9741.

In this report, we update survival (OS) and time-to-progression (TTP) data for the Intergroup trial N9741 after a median 5 years of follow-up by using risk-stratified and prognostic factor analyses to determine if treatment outcomes differ in specific patient subgroups.



A total of 1,691 patients were randomly assigned to one of seven fluorouracil-, oxaliplatin-, and irinotecan-containing regimens. OS and TTP were calculated by treatment arm and baseline risk group (on the basis of WBC, performance status, number of sites of disease, and alkaline phosphatase). Multivariate prognostic factor analysis was used to assess clinical factors for their relationships to OS, TTP, response, and toxicity by using Cox and logistic regression models.



The observed 5-year survival with infusional fluorouracil, leucovorin, and oxaliplatin (FOLFOX) of 9.8% was better than with irinotecan plus bolus fluorouracil and leucovorin (IFL; 3.7%; P = .04) or with bolus irinotecan/oxaliplatin (IROX; 5.1%; P = .128). OS and TTP were significantly longer for FOLFOX (20.2 months and 8.9 months, respectively) than for IFL (14.6 months and 6.1 months, respectively; P < .001 for both) or for IROX (17.3 months and 6.7 months, respectively; P < .001 for both). OS differed by risk group: 20.7 months for low risk, 17.4 months for intermediate risk, and 9.4 months for high risk (P < .001). FOLFOX treatment was superior in all risk groups and was the most powerful prognostic factor for OS, TTP, response rate, and toxicity.



The 9.8% 5-year OS in patients with metastatic colorectal cancer who were treated with first-line FOLFOX sets a new benchmark. Neither baseline risk group nor any prognostic factor examined was predictive of treatment-specific outcome. However, treatment efficacy and patient longevity varied as a function of risk group.
A Venue-Based Approach to Reaching MSM, IDUs and the General Population with VCT: A Three Study Site in Kenya

A venue-based HIV prevention study which included Voluntary Counseling and Testing (VCT) was conducted in three diverse areas of Kenya—Malindi, Nanyuki and Rachounyo. Aims of the study were to: (1) assess the acceptability of VCT for the general population, men who have sex with men (MSM), and injecting drug users (IDUs) within the context of a venue-based approach; (2) determine if there were differences between those agreeing and not agreeing to testing; and (3) study factors associated with being HIV positive. Approximately 98% of IDUs and 97% of MSM agreed to VCT, providing evidence that populations with little access to services and whose behaviors are stigmatized and often considered illegal in their countries can be reached with needed HIV prevention services. Acceptability of VCT in the general population ranged from 60% in Malindi to 48% in Nanyuki. There were a few significant differences between those accepting and declining testing. Notably in Rachuonyo and Malindi those reporting multiple partners were more likely to accept testing. There was also evidence that riskier sexual behavior was associated with being HIV positive for both men in Rachounyo and women in Malindi. Overall HIV prevalence was higher among the individuals in this study compared to individuals sampled in the 2008–2009 Kenya Demographic and Health Survey, indicating the method is an appropriate means to reach the highest risk individuals including stigmatized populations.
Oesophageal sensation in response to high PCO(2) and acidic solutions in nonerosive reflux disease.

Heartburn is commonly associated with the presence of acid in the oesophageal lumen. However, in patients with nonerosive reflux disease (NERD), the mechanism by which acid traverses the mucosa is not clear. We hypothesized that the luminal acid signal traverses the oesophageal epithelium in the form of the highly permeant gas CO(2) , which then is reconverted to H(+) in the submucosa.


Ten patients with heartburn, normal upper endoscopy and increased oesophageal acid exposure (NERD patients) and 10 healthy subjects were enrolled. Perceptual responses to intraoesophageal acid (0·1 N HCl solution) and a high PCO(2) solution were determined using a randomized cross over design. Stimulus-response functions to perfusions were quantified by three parameters: lag time to symptom perception, intensity rating and perfusion sensitivity score.


In NERD patients, the difference in lag time to typical symptom perception, intensity rating and perfusion sensitivity score between high PCO(2) and acid perfusions was statistically significant (P = 0·02, 0·01 and 0·02, respectively). However, the difference in the same perfusion parameters between acid and high PCO(2) perfusions was nonsignificant in healthy controls. When NERD and controls were compared, the difference between the different perfusion variables was nonsignificant (adjusted to age).



In NERD subjects, acid perfusion reliably evoked heartburn symptoms of greater intensity than in healthy controls. Nevertheless, a high PCO(2) perfusion failed to produce symptoms in either group.
Linkage/association study of a locus modulating total serum IgE on chromosome 14q13-24 in families with asthma.

A study was undertaken to validate a locus modulating total serum IgE levels on 14q13-24.



A linkage and association study was performed between total serum IgE and a panel of seven microsatellites which map to the 14q13-24 region in 69 families with asthma recruited from Leeds, UK.



Non-parametric, multipoint, sib pair analysis showed no evidence of genetic linkage between the quantitative trait "log IgE" and any of the tested markers. However, a significant association was observed between locus D14S63 (14q23) and total serum IgE (p = 0.017). Allelic analysis showed an association between low total IgE and allele 157 of D14S63 (p = 0.01, OR = 0.63, 95% CI 0.44 to 0.90). Modelling of allele 157 genotypes as a continuous covariate indicated evidence of a significant inverse linear trend across the three genotypes where 157 homozygotes had the lowest mean log IgE (p = 0.045). Association of D14S63 with log IgE was confirmed in the analysis of a combined dataset of 53 families from Southampton, UK and the 69 families from Leeds (total 122 families). An association was observed at the locus level (p = 0.022) and the allelic level where allele 165 showed an association with high total IgE (p = 0.001, OR = 3.79, 95% CI 1.54 to 9.7) and allele 157 showed an association with low total IgE (p = 0.041, OR = 0.77, 95% CI 0.6 to 0.99). The transmission disequilibrium test was positive for allele 165 (p<0.05) and negative for allele 157 (p>0.05).



Despite the lack of linkage, the findings of this study support the previous observation of a gene(s) at 14q23 that modulates total serum IgE.
A diet rich in high-glucoraphanin broccoli interacts with genotype to reduce discordance in plasma metabolite profiles by modulating mitochondrial function123

Observational and experimental studies suggest that diets rich in cruciferous vegetables and glucosinolates may reduce the risk of cancer and cardiovascular disease (CVD).



We tested the hypothesis that a 12-wk dietary intervention with high-glucoraphanin (HG) broccoli would modify biomarkers of CVD risk and plasma metabolite profiles to a greater extent than interventions with standard broccoli or peas.



Subjects were randomly assigned to consume 400 g standard broccoli, 400 g HG broccoli, or 400 g peas each week for 12 wk, with no other dietary restrictions. Biomarkers of CVD risk and 347 plasma metabolites were quantified before and after the intervention.



No significant differences in the effects of the diets on biomarkers of CVD risk were found. Multivariate analyses of plasma metabolites identified 2 discrete phenotypic responses to diet in individuals within the HG broccoli arm, differentiated by single nucleotide polymorphisms associated with the PAPOLG gene. Univariate analysis showed effects of sex (P < 0.001), PAPOLG genotype (P < 0.001), and PAPOLG genotype × diet (P < 0.001) on the plasma metabolic profile. In the HG broccoli arm, the consequence of the intervention was to reduce variation in lipid and amino acid metabolites, tricarboxylic acid (TCA) cycle intermediates, and acylcarnitines between the 2 PAPOLG genotypes.



The metabolic changes observed with the HG broccoli diet are consistent with a rebalancing of anaplerotic and cataplerotic reactions and enhanced integration of fatty acid β-oxidation with TCA cycle activity. These modifications may contribute to the reduction in cancer risk associated with diets that are rich in cruciferous vegetables.
Knowing its gender without knowing its name: differential access to lexical information in a jargonaphasic patient.

According to recent models of word production, when we name a picture, we first retrieve the meaning of the object, and then we independently retrieve the written or sound form of the word corresponding to the picture. In languages like French, in which words have a gender, theoretical models disagree with respect to the moment at which this information is retrieved. The lemma model (Levelt et al., 1999) posits that we access this information before the sound or written form of the word is retrieved. In contrast, the"Independent network"(IN) model (Caramazza, 1997) model posits that we access gender after retrieval of either the sound or written form of the word. This paper reports a single-case study of an aphasic patient, BA, who showed deficits affecting spoken and written production in the presence of largely preserved comprehension abilities. Experimental testing indicated that she presented with a deficit functionally localized in the access to lexical representations. Results in picture naming and in gender identification also revealed that BA identified the gender above chance level, whether she produced a correct response, a phonemic error, or a neologism. In contrast, when she was unable to produce a spoken or written response, she could not identify the gender. This pattern of performance is consistent with the lemma model in which access to lexical syntax is required before access to phonological form can take place.
Japanese study of tofogliflozin with type 2 diabetes mellitus patients in an observational study of the elderly (J‐STEP/EL): A 12‐week interim analysis

Sodium-glucose co-transporter 2 inhibitors are a promising treatment for type 2 diabetes mellitus, but are associated with concerns about specific adverse drug reactions. We carried out a 1-year post-marketing surveillance of tofogliflozin, a novel agent in this class, in Japanese elderly patients with type 2 diabetes mellitus and here report the results of a 12-week interim analysis, focusing on adverse drug reactions of special interest.



The present prospective observational study included all type 2 diabetes mellitus patients aged ≥65 years who started tofogliflozin during the first 3 months after its launch. Data on demographic and baseline characteristics, clinical course and adverse events were collected.



Of 1,535 patients registered, 1,506 patients whose electronic case report forms were collected and who had at least one follow-up visit were included in the safety analysis at 12 weeks. A total of 178 of 1,506 patients (11.82%) had at least one adverse drug reaction to tofogliflozin. The incidence of adverse drug reactions of special interest (polyuria/pollakiuria, volume depletion-related events, urinary tract infection, genital infection, skin disorders and hypoglycemia) was 2.19, 2.32, 1.33, 1.13, 1.46 and 0.73%, respectively. No new safety concerns were identified. Among those evaluable for clinical effectiveness, the mean (standard deviation) glycated hemoglobin decreased from 7.65% (1.35%) at baseline to 7.25% (1.16%) at 12 weeks by 0.39% (0.94%; P < 0.0001).



This interim analysis characterized the safety profile of tofogliflozin in Japanese elderly patients with type 2 diabetes mellitus during the early post-marketing period.
In vivo detection of basal cell carcinoma using imaging spectroscopy.

Photodynamic therapy has become an interesting alternative to conventional therapy for basal cell carcinomas. Delta-aminolevulinic acid is a precursor in the biosynthesis of protoporphyrin IX that accumulates to a large extent in tumour tissue. We have compared in vivo protoporphyrin IX fluorescence with the extent of basal cell carcinomas on the face, trunk and thigh determined by histological mapping in 30 lesions in 22 patients. A new non-laser based set-up was used to record the fluorescence images. Delta-aminolevulinic acid was applied for 4 h inducing high concentrations of protoporphyrin IX. Routine vertical histological sections and Mohs micrographic surgery were used to map the extent of the tumours. In 50% of lesions we found a good correlation between the fluorescence imaging and histological mapping. In 23% the correlation was partial. In the other lesions we found no correlation at all. This method may be used to delineate basal cell carcinomas more accurately than current methods.
Human papilloma virus infection and cervical dysplasia.

Pap testing is considered to be the best screening tool for cervical cancer but there is currently great interest in the possible application of human papilloma virus (HPV) testing to supplement Pap screening for cervical cancer.



To determine the prevalence of high-risk HPV types in the studied population and to explore the association between high-risk HPV types and cervical dysplasia.



Cross-sectional study conducted at the Iasi Cuza Voda Obstetrics-Gynecology Hospital and Suceava County Hospital. 332 women who underwent colposcopy for cervical lesions between 2006 and 2011 were included in this study.



The overall prevalence of HPV was 57.23%. HPV prevalence differs significantly in the three age groups up to 50 years. It was highest in patients below the age of 40 and progressively lower with advancing age. The overall prevalence of cervical dysplasia was 56.62%. The prevalence of cervical dysplasia was highest in the age groups up to 40 years. The most important determinant of HPV infection is age.



Persistence of HPV appears to be associated with progression to squamous intraepithelial lesion. Dysplasia is often missed in a cervical sample either because of human error in screening and interpretation, or because of suboptimal quality of Pap smear. Incorporation of HPV testing into the present Pap screening program has the potential of making screening for cervical cancer more effective, and a necessary prelude to assessing this is by determining the prevalence of the high-risk types.
Pharmacokinetics, Pharmacodynamics, and Safety of MEDI4212, an Anti-IgE Monoclonal Antibody, in Subjects with Atopy: A Phase I Study.

The anti-IgE therapy omalizumab is currently licensed for the treatment of moderate to severe allergic asthma and chronic idiopathic urticaria. Owing to limitations in the use of omalizumab, a need exists for optimized anti-IgE therapies to broaden clinical indications and patient populations, and to improve dosing schedules. The objective of this phase I, randomized, placebo/omalizumab-controlled, first-in-human, dose-escalation study was to evaluate the pharmacokinetics, pharmacodynamics, and safety of the high-affinity, anti-IgE therapy MEDI4212 in non-Japanese and Japanese subjects with atopy and/or diagnostic IgE ≥ 30 IU/mL.



Subjects with atopy and/or baseline IgE ≥ 30 IU/mL were randomized to a single dose of subcutaneous (5, 15, 60, 150, or 300 mg) or intravenous (300 mg) MEDI4212, subcutaneous omalizumab, or placebo. Following administration, pharmacokinetic, pharmacodynamic [IgE (free and total), and cellular FcεRI expression], and safety assessments were made.



MEDI4212 rapidly suppressed free serum IgE to a greater extent than omalizumab; however, recovery of free IgE to baseline in MEDI4212-dosed subjects was rapid when compared with the slow and gradual recovery seen in omalizumab-dosed individuals. The loss of IgE suppression corresponded with a rapid decrease of serum MEDI4212. FcεRI expression on dendritic cells and basophils was reduced following MEDI4212 dosing. MEDI4212 was well tolerated by subjects; adverse events were generally of low severity and no subjects discontinued due to adverse events.



The increased potency of MEDI4212 may be of clinical interest for individuals with high-diagnostic IgE levels where more extensive IgE suppression is required for clinical response. However, the modest duration of free IgE suppression below the target concentration noted with MEDI4212 in this study suggests limited potential for dosing schedule advantages over omalizumab.



MedImmune.