nils-herrmann/clean_scirepeval huggingface dataset:
Three biomarkers identified from serum proteomic analysis for the detection of early stage ovarian cancer.

Early detection remains the most promising approach to improve long-term survival of patients with ovarian cancer. In a five-center case-control study, serum proteomic expressions were analyzed on 153 patients with invasive epithelial ovarian cancer, 42 with other ovarian cancers, 166 with benign pelvic masses, and 142 healthy women. Data from patients with early stage ovarian cancer and healthy women at two centers were analyzed independently and the results cross-validated to discover potential biomarkers. The results were validated using the samples from two of the remaining centers. After protein identification, biomarkers for which an immunoassay was available were tested on samples from the fifth center, which included 41 healthy women, 41 patients with ovarian cancer, and 20 each with breast, colon, and prostate cancers. Three biomarkers were identified as follows: (a) apolipoprotein A1 (down-regulated in cancer); (b) a truncated form of transthyretin (down-regulated); and (c) a cleavage fragment of inter-alpha-trypsin inhibitor heavy chain H4 (up-regulated). In independent validation to detect early stage invasive epithelial ovarian cancer from healthy controls, the sensitivity of a multivariate model combining the three biomarkers and CA125 [74% (95% CI, 52-90%)] was higher than that of CA125 alone [65% (95% CI, 43-84%)] at a matched specificity of 97% (95% CI, 89-100%). When compared at a fixed sensitivity of 83% (95% CI, 61-95%), the specificity of the model [94% (95% CI, 85-98%)] was significantly better than that of CA125 alone [52% (95% CI, 39-65%)]. These biomarkers demonstrated the potential to improve the detection of early stage ovarian cancer.
Biological Activities of Tetrodotoxin-Producing Enterococcus faecium AD1 Isolated from Puffer Fishes

Puffer fishes were collected from the central sea in Vietnam from spring to summer season. The eggs were incubated in MRS broth that was used to test the toxicity in mice and isolate the lactic acid bacteria community that could produce tetrodotoxin (TTX). Thin layer chromatography (TLC) and high performance lipid chromatography (HPLC) were used to detect and quantify TTX. As a result, Enterococcus faecium AD1 which was identified by biochemical test and 16S rRNA analysis could produce TTX 0.3 mg/mL when cultured in MRS broth. The bacterium was optimized for TTX production and gave 0.18 mg/mL, 0.07 mg/mL, and 0.15 mg/mL in media prepared from the meat-washing water of freshwater fishes (Pangasius bocourti, Oreochromis sp.) and sea fish (Auxis thazard), respectively, that are also hopeful to answer some poisoning cases related to eating fishes. Enterococcus faecium also showed the wide antimicrobial activities on yeast, Gram-negative and -positive bacteria. Extracted exopolysaccharide (EPS) that reacted with 2,2-diphenyl-1-picrylhydrazyl to give IC50 at 5 mg/mL equaled 11 mg/mL ascorbic acid which could show effects on Hela-6 and Hep G2 using sulforhodamine B test. Enterococcus faecium can be claimed as a promising source in tetrodotoxin and biological compounds.
PipeCloud: using causality to overcome speed-of-light delays in cloud-based disaster recovery

Recovery (DR) is a desirable feature for all enterprises, and a crucial one for many. However, adoption of DR remains limited due to the stark tradeoffs it imposes. To recover an application to the point of crash, one is limited by financial considerations, substantial application overhead, or minimal geographical separation between the primary and recovery sites. In this paper, we argue for cloud-based DR and pipelined synchronous replication as an antidote to these problems. Cloud hosting promises economies of scale and on-demand provisioning that are a perfect fit for the infrequent yet urgent needs of DR. Pipelined synchrony addresses the impact of WAN replication latency on performance, by efficiently overlapping replication with application processing for multi-tier servers. By tracking the consequences of the disk modifications that are persisted to a recovery site all the way to client-directed messages, applications realize forward progress while retaining full consistency guarantees for client-visible state in the event of a disaster. PipeCloud, our prototype, is able to sustain these guarantees for multi-node servers composed of black-box VMs, with no need of application modification, resulting in a perfect fit for the arbitrary nature of VM-based cloud hosting. We demonstrate disaster failover to the Amazon EC2 platform, and show that PipeCloud can increase throughput by an order of magnitude and reduce response times by more than half compared to synchronous replication, all while providing the same zero data loss consistency guarantees.
Phase II trial of cetuximab in patients with metastatic or locally advanced soft tissue or bone sarcoma.

The epidermal growth factor receptor (EGFR) tyrosine kinase is overexpressed in many sarcoma subtypes. In vitro studies suggest a role of the EGFR pathway in growth and differentiation in some sarcomas. We conducted a phase II trial of cetuximab, a monoclonal antibody to EGFR, in patients with advanced sarcomas.



Cetuximab was administered intravenously as a loading dose on 400 mg/m on day 1, cycle 1 and subsequently 250 mg/m on days 1, 8, 15, and 21 of a 28 day cycle. Using a Simon 2-stage design, 21 EGFR patients were to be accrued in the first stage, with an additional 11 patients if >3 patients met the primary endpoint of 4-month progression-free survival (PFS). An exploratory subgroup of EGFR patients was also included.



Twenty-one and 15 evaluable patients enrolled in the EGFR and EGFR subgroup, respectively. One of 21 EGFR patients (4.8%) achieved 4-month PFS. Median PFS and overall survival were 1.7 months [95% confidence interval (CI), 1.6-1.8] and 7.7 months (95% CI, 4.2-10.7), respectively. Three of 15 EGFR patients (20%) achieved 4-month PFS. Median PFS and overall survival were 1.8 months (95% CI, 0.8-2.5) and 15.7 months (95% CI, 7.7-25.3), respectively. No responses were seen in either group. There was no correlation between clinical outcomes and expression of MAP-K, PTEN, and phospho-EGFR.



Cetuximab is not an active as a single agent in advanced sarcoma. Further study of anti-EGFR therapy in sarcoma should only be considered after identification of molecular abnormalities predictive of benefit.
Usefulness of noise adaptive non-linear gaussian filter in FDG-PET study.

In positron emission tomography (PET) studies, shortening transmission (TR) scan time can improve patient comfort and increase scanner throughput. However, PET images from short TR scans may be degraded due to the statistical noise included in the TR image. The purpose of this study was to apply non-linear Gaussian (NLG) and noise adaptive NLG (ANLG) filters to TR images, and to evaluate the extent of noise reduction by the ANLG filter in comparison with that by the NLG filter using phantom and clinical studies.



In phantom studies, pool phantoms of various diameters and injected doses of 2-deoxy-2-[18F]fluoro-D-glucose (FDG) were used and the coefficients of variation (CVs) of the counts in the TR images processed with the NLG and ANLG filters were compared. In clinical studies, two normal volunteers and 13 patients with tumors were studied. In volunteer studies, the CV values in the liver were compared. In patient studies, the standardized uptake values (SUVs) of tumors in the emission images were obtained after processing the TR images using the NLG and ANLG filters.



In phantom studies, the CV values in the TR images processed with the ANLG filter were smaller than those in the images processed with the NLG filter. When using the ANLG filter, their dependency on the phantom size, injected dose of FDG and TR scan time was smaller than when using the NLG filter. In volunteer studies, the CV values in the images processed with the ANLG filter were smaller than those in the images processed with the NLG filter, and were almost constant regardless of the TR scan time. In patient studies, there was an excellent correlation between the SUVs obtained from the images with a TR scan time of 7 min processed with the NLG filter (x) and those obtained from the images with a TR scan time of 4 min processed with the ANLG filter (y) (r = 0.995, y = 1.034x - 0.075).



Our results suggest that the ANLG filter is effective and useful for noise reduction in TR images and shortening TR scan time while maintaining the quantitative accuracy of FDG-PET studies.
Comparison of systemic and mucosal delivery of 2 canarypox virus vaccines expressing either HIV-1 genes or the gene for rabies virus G protein.

Since the primary routes of human immunodeficiency type 1 (HIV-1) infection are across mucosal barriers, a randomized trial of canarypox virus-based vectors was conducted in 84 individuals, with delivery of vaccine by mucosal routes, and was accompanied by a detailed analysis of humoral, cellular, and mucosal immune responses.



Over the course of 6 months, HIV-1-specific (vCP 205) and rabies (vCP 65) canarypox virus vectors were delivered systemically and/or mucosally into the nose, mouth, vagina, or rectum in a 4-dose schedule, followed by 2 doses of HIV-1 MN recombinant glycoprotein (rgp) 120 or subunit rabies vaccine administered by the intramuscular route.



Administration of vaccine and collection of samples were well tolerated. Serum IgG HIV-1-specific antibodies to rgp120 were rarely seen after either systemic or mucosal delivery of canarypox virus vaccine. In contrast, serum IgG rabies and canarypox antibodies were detected in all individuals after systemic, but rarely after mucosal, delivery of vaccine. Suggestions of mucosal recognition of HIV-1 antigen included a cytotoxic T lymphocyte response in 4 of 8 individuals after administration of vaccine by the intrarectal route and a limited immunoglobulin A response at the same site.



Each of the routes of vaccine administration was feasible in the context of a phase 1 study with motivated individuals. However, with the doses and routes of administration used, canarypox virus was not an effective mucosal immunogen.
Reduction of ischemic sequelae following spontaneous subarachnoid hemorrhage: a double-blind, randomized comparison of enoxaparin versus placebo

Cerebral vasospasm, including its ischemic sequelae, remains a leading cause of death and disability following subarachnoid hemorrhage (SAH). This study was designed to evaluate whether the low-molecular-weight heparin (LMWH) enoxaparin reduces the occurrence of cerebral vasospasm and ischemia following spontaneous SAH.



A prospective, double-blind, randomized study was conducted in 120 consecutive patients with SAH (Hunt Hess Scale (HHS) I-III). Patients received one subcutaneous injection per day of either 20mg enoxaparin or placebo for 3 weeks following SAH. Efficacy endpoints were the occurrence of cerebral vasospasm, delayed ischemic deficit (DID), cerebral infarction, and overall outcome at 1 year following SAH.



At 1-year follow-up, enoxaparin significantly reduced DID and cerebral infarction. Delayed ischemic deficit occurred in 8.8% of the enoxaparin group versus 66.7% of the placebo group (P<0.001), while 3.5% of vasospasm-related cerebral infarctions occurred in enoxaparin-treated patients and 28.3% in placebo-treated patients (P<0.001). Severe shunt-dependent hydrocephalus was significantly lower in the enoxaparin group (1.8% versus 16.7%; P=0.019). Compared with the placebo group, the enoxaparin group had fewer intracranial bleeding events and better overall outcomes at 1-year follow-up. Although there was potential bias as a result of patients in the placebo group being more severely affected (in terms of HHS), treatment with enoxaparin for 3 weeks improved long-term outcome following SAH.



Enoxaparin is safe and effective in reducing cerebral vasospasm and ischemia following SAH (Hunt Hess grades I-III), resulting in a better long-term outcome for the patient.
Impact of extracorporeal blood flow rate on blood pressure, pulse rate and cardiac output during haemodialysis.

If blood pressure (BP) falls during haemodialysis (HD) [intradialytic hypotension (IDH)] a common clinical practice is to reduce the extracorporeal blood flow rate (EBFR). Consequently the efficacy of the HD (Kt/V) is reduced. However, only very limited knowledge on the effect of reducing EBFR on BP exists and data are conflicting. The aim of this study was to evaluate the effect and the potential mechanism(s) involved by investigating the impact of changes in EBFR on BP, pulse rate (PR) and cardiac output (CO) in HD patients with arteriovenous-fistulas (AV-fistulas).



We performed a randomized, crossover trial in 22 haemodynamically stable HD patients with AV-fistula. After a conventional HD session each patient was examined during EBFR of 200, 300 and 400 mL/min in random order. After 15 min when steady state was achieved CO, BP and PR were measured at each EFBR, respectively.



Mean (SD) age was 71 (11) years. Systolic BP was significantly higher at an EBFR of 200 mL/min as compared with 300 mL/min [133 (23) versus 128 (24) mmHg; P < 0.05], but not as compared with 400 mL/min [133 (23) versus 130 (19) mmHg; P = 0.20]. At EBFR of 200, 300 and 400 mL/min diastolic BP, mean arterial pressure, PR and CO remained unchanged.



Our study does not show any consistent trend in BP changes by a reduction in EBFR. Reduction in EBFR if BP falls during IDH is thus not supported. However, none of the patients experienced IDH. Further studies are required to evaluate the impact of changes in EBFR on BP during IDH.
Self-rated health predicts acute exacerbations and hospitalizations in patients with COPD.

Self-rated health predicts outcome in chronic disease, but such information is scarce in COPD. We aimed to assess self-rated health as an outcome predictor in carefully characterized patients with this condition.



This was a prospective study in 127 clinically stable patients with COPD (64 +/- 8 years, 79% men, 82% Global Initiative for Chronic Obstructive Lung Disease stage II or III). Self-rated health was assessed using a 5-grade Likert scale ranging from very poor to very good.



During 26.0 +/- 4.9 months of follow-up, 78 patients experienced acute exacerbation, 39 were hospitalized, and 10 died. Poor or very poor self-rated health was reported by 19 patients (15%) and was more common in patients experiencing acute exacerbations (20% vs 6%, P = .027) and hospitalizations (19% vs 5%, P = .039). Kaplan-Meier curves demonstrated more acute exacerbations (P = .003) and hospitalizations (P = .008) in patients with poor or very poor self-rated health. In a fully adjusted Cox model of proportional hazard, poor or very poor self-rated health remained predictive of acute exacerbations (hazard ratio [HR], 1.80; 95% CI, 1.03-3.11) and hospitalizations (HR, 1.93; 95% CI, 1.12-3.68) but not of death.



This study suggests that self-rated health is predictive of acute exacerbations and hospitalizations. Although prediction of mortality was limited, the study is supportive of self-rated health testing in COPD.
Mental health self-assessment in patients with moderate to severe psoriasis: an observational, multicenter study of 1164 patients in Spain (the VACAP Study).

Poor self-assessed mental health appears to be related to the severity of psoriasis.



To evaluate the impact of psoriasis severity on mood and anxiety disorders.



A prospective, observational, multicenter study was conducted by 123 dermatologists in Spain. Patients (n=164; mean [SD] age, 45.11 [13.92] years; 60.8% males) with moderate to severe psoriasis were evaluated at baseline and 4 months later. Psoriasis severity was measured using the Psoriasis Area and Severity Index (PASI), with a score range of 0 (mild) to 72 (severe); body surface area involvement (BSA); and physician global assessment (PGA) scores, with a range of 1 (mild) to 7 (severe). Mental health was assessed using the Hospital Anxiety and Depression Scale (HADS), with a total possible score of 0-42 (higher scores representing worse mental health). Mean first and second visit scores were compared.



Mean (SD) scores improved between the first and second visit as follows: 13.24 (9.50) to 5.07 (6.03) for PASI, 12.52 (7.92) to 10.78 (7.32) for overall HADS, 7.83 (4.55) to 6.85 (4.21) for the HADS anxiety subscale, and 4.72 (4.12) to 3.95 (3.76) for the HADS depression subscale (P<.001 in all cases). Multivariate analyses showed that the main factors related to anxiety were psoriasis severity, sex, and completion of graduate studies. The independent variables included in the model for depression were psoriasis severity, sex, and psoriasis located on the head.



Reductions in disease severity improve self-assessed mood and anxiety disorders in patients with moderate to severe psoriasis.
Automatic and Objective Assessment of Alternating Tapping Performance in Parkinson's Disease

This paper presents the development and evaluation of a method for enabling quantitative and automatic scoring of alternating tapping performance of patients with Parkinson's disease (PD). Ten healthy elderly subjects and 95 patients in different clinical stages of PD have utilized a touch-pad handheld computer to perform alternate tapping tests in their home environments. First, a neurologist used a web-based system to visually assess impairments in four tapping dimensions ('speed', 'accuracy', 'fatigue' and 'arrhythmia') and a global tapping severity (GTS). Second, tapping signals were processed with time series analysis and statistical methods to derive 24 quantitative parameters. Third, principal component analysis was used to reduce the dimensions of these parameters and to obtain scores for the four dimensions. Finally, a logistic regression classifier was trained using a 10-fold stratified cross-validation to map the reduced parameters to the corresponding visually assessed GTS scores. Results showed that the computed scores correlated well to visually assessed scores and were significantly different across Unified Parkinson's Disease Rating Scale scores of upper limb motor performance. In addition, they had good internal consistency, had good ability to discriminate between healthy elderly and patients in different disease stages, had good sensitivity to treatment interventions and could reflect the natural disease progression over time. In conclusion, the automatic method can be useful to objectively assess the tapping performance of PD patients and can be included in telemedicine tools for remote monitoring of tapping.
Thyroxine in acute myocardial infarction (ThyrAMI) - levothyroxine in subclinical hypothyroidism post-acute myocardial infarction: study protocol for a randomised controlled trial

Cardiac disease is the most common cause of morbidity and mortality in the United Kingdom. Even minor changes in thyroid hormone concentration may impact adversely on the cardiovascular system. Subclinical hypothyroidism (SCH) after admission for an acute cardiac problem has been associated with an increase in cardiac mortality and overall death. We have designed protocols for a prospective observational study to assess the association of thyroid function at the time of acute myocardial infarction (AMI) with cardiovascular outcomes, and a double-blinded randomised placebo-controlled trial of levothyroxine to evaluate its effect on LV function and vascular health.



ThyrAMI 1: This will be a prospective longitudinal observational study of patients with AMI that will be followed for 24 months to study the association between thyroid status at the time of AMI (within 24 hours of diagnosis) with vascular outcomes. ThyrAMI 2: This will be a prospective double-blinded randomised placebo-controlled trial of levothyroxine of 12 months duration in patients with AMI and SCH.



Patients will be recruited from five hospitals in the North East of England.



One hundred patients with thyroid function tests within the subclinical hypothyroid range upon admission with an AMI and no previous history of thyroid disease.



Levothyroxine will be administered at a starting dose of 25 mcg once daily, which will be increased at intervals if needed to maintain a TSH level between 0.4 to 2.5 mU/L, versus a placebo.



Participants will be randomized with a computerised randomisation algorithm, stratified by type of MI (NSTEMI versus STEMI), in a 1:1 ratio to levothyroxine therapy or placebo (as container or bottle numbers), starting within 21 (+/- 7) days of AMI.


BLINDING
Assignment to either the LT4 or placebo arm will be double-blinded.



The outcome will be the effect of levothyroxine on ventricular function, endothelial function and blood coagulability and rheology.



There is evidence to suggest that treatment of SCH can improve cardiovascular parameters. Therefore, ThyrAMI 1 and ThyrAMI 2 will be the first trials investigating SCH in AMI to give a better insight into whether thyroid hormone levels are a key target for improving cardiovascular outcomes.
Atypical Antipsychotic Quetiapine in the Management of Severe Refractory Functional Gastrointestinal Disorders

Management of severe refractory functional gastrointestinal disorders (FGIDs) is difficult. Quetiapine, an atypical antipsychotic, may benefit patients by mitigating associated anxiety and sleep disturbances, augmenting the effect of antidepressants, and providing an independent analgesic effect. Outpatient records from a university-based FGID clinic were reviewed, and 21 patients with refractory symptoms who received quetiapine were identified and interviewed. Outcomes included global relief of symptoms, treatment efficacy questionnaire, and change in gastrointestinal (GI) and psychological symptoms. Eleven of 21 patients continued therapy at the time of interview. Six of 11 demonstrated global relief of symptoms, and 9 were satisfied with treatment. The remaining 10 of 21 discontinued therapy because of somnolence and lack of GI benefits. Quetiapine in low doses appeared beneficial in more than half of the adults with severe FGIDs who stayed on treatment. This response in otherwise refractory patients suggests quetiapine might augment the effectiveness of antidepressants in severe FGIDs.
Complications Following D3 Gastrectomy: Post Hoc Analysis of a Randomized Trial

A single institutional surgical trial for gastric cancer had demonstrated increased morbidity but not mortality. This report analyzes risk factors affecting morbidity. Risk factors for morbidity in 221 patients treated with curative intent were evaluated in a prospective randomized trial comparing D1 and D3 surgery for curable gastric cancer. The surgeon’s experience after 25 nodal dissections had no influence on surgical or overall complications, nor did the patients’ co-morbidity (e.g., respiratory system disease, cardiac disease, diabetes mellitus). Distal pancreatectomy negatively affected surgical morbidity [relative risk (RR) 6.21, 95% confidence interval (CI) 1.869–20.626] and overall morbidity (RR 5.50, 95% CI 1.671–18.082). All of the patients with a distal pancreatectomy underwent concomitant splenectomy. Multivariate analysis found splenectomy and nodal dissection to be the only two independent risk factors adversely affecting operative morbidity. The RR of splenectomy for surgical complications was 4.19 (95% CI 1.327–13.208), and for overall complications it was 3.88 (95% CI 1.259–11.973). The RR of nodal dissection for surgical complications was 2.51 (95% CI 1.336–4.730), and for overall complications it was 1.93 (95% CI 1.149–3.255). Splenectomy (with or without pancreatectomy) and nodal dissection are risk factors for operative morbidity but not mortality.