nils-herrmann/clean_scirepeval huggingface dataset:
Procalcitonin testing for diagnosis and short-term prognosis in bacterial infection complicated by congestive heart failure: a multicenter analysis of 4,698 cases

Procalcitonin (PCT) is a biomarker for the clinical diagnosis of bacterial infection that is more specific and earlier than fever, changes in white blood cell count, and blood cultures. Congestive heart failure is an important cause of endotoxin resorption from the intestine, which significantly increases PCT expression in noninfected patients with heart failure. The diagnostic performance and cut-off value of PCT in patients with bacterial infection complicated by congestive heart failure needs to be confirmed.



A total of 4,698 cases from different cities in China, including those with different classes of congestive heart failure, bacterial infection, bacterial infection complicated by heart failure and healthy individuals, were chosen for the diagnostic value analysis of PCT and screening candidate predictors of mortality in subjects with bacterial infection complicated by congestive heart failure.



Patients with simple heart failure had significantly higher PCT levels than normal controls (P < 0.01), whereas patients with bacterial infection complicated by congestive heart failure had significantly higher PCT levels than those with simple infection (P < 0.01). Although it was useful for the diagnosis of infection (area under the receiver operating characteristic curve >80%), the positive predictive value of PCT decreased significantly with increasing severity of heart failure (P < 0.05), and the cut-off value of PCT concentrations for infection complicated by classes II, III and IV heart failure were 0.086, 0.192 and 0.657 μg/L, respectively. Heart failure degree, PCT level, and age were the candidate predictors of mortality in patients with bacterial infection complicated by congestive heart failure.



These data suggest that complicated heart failure elevates the PCT level in patients with bacterial infection. Thus, the results of the PCT test must be analyzed correctly in consideration of the severity of heart failure. Close attention should be paid to cardiac function and PCT expression in aged patients with infection complicated by congestive heart failure.
Accuracy of Billing Codes Used in the Therapeutic Care of Diabetic Retinopathy.

Insurance billing claim databases represent a growing field of scientific inquiry within ophthalmology. Validating the accuracy of billing claim codes used during the care of diabetic retinopathy is a necessary precursor to fully understanding the underlying data and subsequent results of these types of studies.



To determine the accuracy of diagnostic, procedural, and therapeutic billing codes used in the treatment of diabetic retinopathy.



This retrospective medical record review was conducted at 3 clinical practices (1 academic and 2 private). Insured patients with diabetic retinopathy were seen by the practices between 2011 and 2013. Each patient then had every visit for 2 years reviewed twice, once for billing data and the second for data from the medical record. Data were collected and analyzed from October 2015 to July 2016.



The positive predictive value (PPV) and negative predictive value (NPV) for each code of interest. Sensitivity and specificity were secondary outcomes.



A total of 146 patients (mean [SD] age, 60.3 [12.5] years) from 11 physicians had 1072 encounters reviewed over 2 calendar years. Among the included patients, 49.3% were female (n = 72), 48.6% were white (n = 71), 37.0% were black (n = 54), and 18.5% had type 1 diabetes and a mean (SD) hemoglobin A1C level of 7.7% (1.8) (n = 27). Nearly all codes of interest that were used frequently also had a high PPV (range, 89.5%-100%) and NPV (88.6%-100%) including billing codes for intravitreal injection, focal laser, panretinal photocoagulation, laterality of procedure, ranibizumab, bevacizumab, fundus photographs, fluorescein angiography, and optical coherence tomography. Codes that were used infrequently (<20 instances) but still had a high PPV (all 100%) and NPV (99.7%-100%) were codes for aflibercept, triamcinolone, and the dexamethasone implant. Only the codes for infrequently used B-scan ultrasonography (PPV, 69.6%) and subtenon injection (PPV, 100%; NPV, 99.7%, but sensitivity of only 40%) were found to be of questionable accuracy. Other than subtenon injection (40%), all codes were also found to have a high sensitivity (range, 87.6%-100%) and a high specificity (range, 97.2%-100%).



These data suggest diagnostic, procedure, and therapeutic codes derived from insurance billing claims accurately reflect the medical record for patients with diabetic retinopathy.
A Discrete Wavelet Based Feature Extraction and Hybrid Classification Technique for Microarray Data Analysis

Cancer classification by doctors and radiologists was based on morphological and clinical features and had limited diagnostic ability in olden days. The recent arrival of DNA microarray technology has led to the concurrent monitoring of thousands of gene expressions in a single chip which stimulates the progress in cancer classification. In this paper, we have proposed a hybrid approach for microarray data classification based on nearest neighbor (KNN), naive Bayes, and support vector machine (SVM). Feature selection prior to classification plays a vital role and a feature selection technique which combines discrete wavelet transform (DWT) and moving window technique (MWT) is used. The performance of the proposed method is compared with the conventional classifiers like support vector machine, nearest neighbor, and naive Bayes. Experiments have been conducted on both real and benchmark datasets and the results indicate that the ensemble approach produces higher classification accuracy than conventional classifiers. This paper serves as an automated system for the classification of cancer and can be applied by doctors in real cases which serve as a boon to the medical community. This work further reduces the misclassification of cancers which is highly not allowed in cancer detection.
Krill Oil Improves Mild Knee Joint Pain: A Randomized Control Trial

Krill oil is an edible oil extracted from krill, a small red-colored crustacean found in the Antarctic Ocean. The administration of krill oil is reported to mitigate inflammation in patients with cardiac disease, rheumatoid arthritis, or osteoarthritis. However, the effect of krill oil on mild knee pain has not yet been determined.



To assess the effect of krill oil on mild knee pain.



A randomized, double-blind, parallel-group, placebo-controlled trial of fifty adults (38-85 years old) with mild knee pain attending the Fukushima Orthopedic Clinic (Tochigi, Japan) between September 2014 and March 2015.



Participants were randomized to receive 2 g per day of either krill oil or an identical placebo for 30 days.



The primary outcome was improvement in subjective symptoms of knee pain as assessed by the Japanese Knee Osteoarthritis Measure (JKOM) and Japanese Orthopaedic Association score (JOA). Secondary outcomes included blood and urine biochemical parameters.



Both the placebo and krill oil groups showed significant improvements in the questions in the JKOM and JOA questionnaires after administration. After the intervention, krill oil group showed more improvements than placebo group in two questions regarding the pain and stiffness in knees in JKOM. Controlling for age, sex, weight, and smoking and drinking habits, krill oil significantly mitigated knee pain in sleeping (P < 0.001), standing (P < 0.001) and the range of motion of both right and left knees (both P = 0.011) compared to placebo. Krill oil administration raised plasma EPA (P = 0.048) and EPA/AA ratio (P = 0.003).



This study indicates that krill oil administration (2 g/day, 30 days) improved the subjective symptoms of knee pain in adults with mild knee pain.
The impact of hospital mergers on treatment intensity and health outcomes.

To analyze the impact of hospital mergers on treatment intensity and health outcomes.



Hospital inpatient data from California for 1990 through 2006, encompassing 40 mergers.



I used a geographic-based IV approach to determine the effect of a zip code's exposure to a merger. The merged facility's market share represents exposure, instrumented with combined premerge shares. Additional specifications include Herfindahl Index (HHI), instrumented with predicted change in HHI.



The primary specification results indicate that merger completion is associated with a 3.7 percent increase in the utilization of bypass surgery and angioplasty and a 1.7 percent increase in inpatient mortality above averages in 2000 for the average zip code. Isolating the competition mechanism mutes the treatment intensity result slightly, but it more than doubles the merger exposure effect on inpatient mortality to a 3.9 percent increase. The competition mechanism is associated with a sizeable increase in number of procedures.



Unlike previous studies, this analysis finds that hospital mergers are associated with increased treatment intensity and higher inpatient mortality rates among heart disease patients. Access to additional outcome measures such as 30-day mortality and readmission rates might shed additional light on whether the relationship between these outcomes is causal.
Recognition of depression and anxiety and their association with quality of life, hospitalization and mortality in primary care patients with heart failure – study protocol of a longitudinal observation study

International disease management guidelines recommend the regular assessment of depression and anxiety in heart failure patients. Currently there is little data on the effect of screening for depression and anxiety on the quality of life and the prognosis of heart failure (HF). We will investigate the association between the recognition of current depression/anxiety by the general practitioner (GP) and the quality of life and the patients' prognosis.



In this multicenter, prospective, observational study 3,950 patients with HF are recruited by general practices in Germany. The patients fill out questionnaires at baseline and 12-month follow-up. At baseline the GPs are interviewed regarding the somatic and psychological comorbidities of their patients. During the follow-up assessment, data on hospitalization and mortality are provided by the general practice. Based on baseline data, the patients are allocated into three observation groups: HF patients with depression and/or anxiety recognized by their GP (P+/+), those with depression and/or anxiety not recognized (P+/-) and patients without depression and/or anxiety (P-/-). We will perform multivariate regression models to investigate the influence of the recognition of depression and/or anxiety on quality of life at 12 month follow-up, as well as its influences on the prognosis (hospital admission, mortality).



We will display the frequency of GP-acknowledged depression and anxiety and the frequency of installed therapeutic strategies. We will also describe the frequency of depression and anxiety missed by the GP and the resulting treatment gap. Effects of correctly acknowledged and missed depression/anxiety on outcome, also in comparison to the outcome of subjects without depression/anxiety will be addressed. In case results suggest a treatment gap of depression/anxiety in patients with HF, the results of this study will provide methodological advice for the efficient planning of further interventional research.
Patient specific instrumentation.

Patient specific instrumentation (PSI) has recently been developed as a replacement for traditional instrumentation in total knee arthroplasty (TKA). The study aim was to assess efficiency via the mean total OR time using the PSI versus computer-assisted (CAS) TKAs with accuracy as a secondary endpoint. Sixty patients were randomized to CAS or PSI. A formula was developed to derive a profit ratio (PR) that incorporated costs, revenue, and total OR time. The PSI cases were 1.45 times more profitable than CAS allowing for approximately 3 PSI cases versus 2 CAS cases in one 8 hour OR day. Results from this series show that PSI improves OR efficiency, but does not improve accuracy.
A cluster randomised trial to assess the impact of clinical pathways on AMI management in rural Australian emergency departments

People living in rural Australia are more likely to die in hospital following an acute myocardial infarction than those living in major cities. While several factors, including time taken to access hospital care, contribute to this risk, it is also partially attributable to the lower uptake of evidence-based guidelines for the administration of thrombolytic drugs in rural emergency departments where up to one-third of eligible patients do not receive this life-saving intervention. Clinical pathways have the potential to link evidence to practice by integrating guidelines into local systems, but their impact has been hampered by variable implementation strategies and sub-optimal research designs. The purpose of this study is to determine the impact of a five-step clinical pathways implementation process on the timely and efficient administration of thrombolytic drugs for acute myocardial infarctions managed in rural Australian emergency departments.



The design is a two-arm, cluster-randomised trial with rural hospital emergency departments that treat and do not routinely transfer acute myocardial infarction patients. Six rural hospitals in the state of Victoria will participate, with three in the intervention group and three in the control group. Intervention hospitals will participate in a five-step clinical pathway implementation process: engagement of clinicians, pathway development according to local resources and systems, reminders, education, and audit and feedback. Hospitals in the control group will each receive a hard copy of Australian national guidelines for chest pain and acute myocardial infarction management. Each group will include 90 cases to give a power of 80% at 5% significance level for the two primary outcome measures: proportion of those eligible for thrombolysis receiving the drug and time to delivery of thrombolytic drug.



Improved compliance with thrombolytic guidelines via clinical pathways will increase acute myocardial infarction survival rates in rural hospitals and thereby help to reduce rural-urban mortality inequalities. Such knowledge translation has the potential to be adapted for a range of clinical problems in a wide array of settings.
Open versus laparoscopic partial nephrectomy for clinical T1a renal masses: a matched-pair comparison of 280 patients with TRIFECTA outcomes (RECORd Project)

To report a matched-pair comparative analysis between open (OPN) and laparoscopic partial nephrectomy (LPN) for clinical (c) T1a renal masses from a large prospective multicenter dataset. The RECORd Project includes all patients who underwent OPN and LPN for kidney cancer between January 2009 and January 2011 at 19 Italian centers. Open and laparoscopic groups were compared regarding clinical, surgical, pathologic, functional results and TRIFECTA outcome. Multivariable logistic regression models were used to analyze predictors of WIT >25 min, surgical complications (SC) and the achievement of the TRIFECTA outcome. Overall, 301 patients had OPN and 149 LPN. Groups were matched 1:1 (140 matched pairs) for clinical diameter, tumor location and type of indication. Laparoscopic partial nephrectomy was associated with a significantly mean longer WIT (19.9 vs. 15.1 min; p < 0.001), and it was an independent predictor of a WIT >25 min (RR 6.29, p < 0.0001). The TRIFECTA was achieved in 78.6 and 74.3 % after OPN and LPN (p = ns), respectively, and the surgical approach was not a predictor of a negative TRIFECTA and SC at multivariable analysis. At 6-month follow-up, no significant differences were observed between the OPN and LPN group both in estimated glomerular filtration rate (eGFR) (∆GFR 1.1 vs. 4.1 mL/min) and in new-onset stage III–V chronic kidney disease (CKD) rate (0 vs. 0.7 %). No significant difference in achieving the TRIFECTA outcome was reported after OPN and LPN. LPN was associated with a significantly longer WIT. However, eGFR at 6-month follow-up did not differ significantly between the two surgical approaches.
Co-administration of intravesical bacillus Calmette-Guérin and interferon α-2B as first line in treating superficial transitional cell carcinoma of the urinary bladder.

• To evaluate the efficacy and toxicity of the combination of bacillus Calmette-Guérin (BCG) and interferon α-2B (IFNα-2B) in treating superficial bladder cancer (SBC). The mentioned combination has shown synergism in pre-clinical studies.



• The present study is a single-arm, open-label, single-institution prospective trial. Patients with Ta, T1 or in situ carcinoma and no previous intravesical therapy were included between July 2002 and June 2009.  Patients were treated with weekly intravesical instillation of 27 mg of BCG mixed with 10 million units (MU) of IFNα-2B for six consecutive weeks followed by 3-weekly booster instillations at 3 months if there was no recurrence. • The primary endpoint was disease recurrence. Secondary endpoints were disease progression and toxicity. • Patients were followed-up with cystoscopy and urine cytology every 3 months.



• In all, 50 patients were included. • At a median follow-up of 55.8 months, 31 (62%) patients were recurrence-free. • Progression to muscle invasion occurred in two (4%) and metastasis occurred in two (4%) patients. • Treatment was well tolerated, with grade III dysuria and frequency occurring in 18 and 14% of patients, respectively, and with 74% of patients being able to complete the maintenance dosage.



• The combination of BCG and IFNα-2B in the patient population with SBC has similar efficacy and toxicity to BCG monotherapy.
Cost and burden of gastroesophageal reflux disease among patients with persistent symptoms despite proton pump inhibitor therapy: an observational study in France

Gastrointestinal reflux disease (GERD) is a common disorder that negatively impacts health-related quality of life (HRQL) and work productivity. Many patients have only a partial response to proton pump inhibitor (PPI) therapy and continue to experience GERD symptoms despite optimized treatment. This observational study aimed to provide information on symptoms, HRQL, resource usage, costs and treatment pathways associated with partial response to PPI therapy in French patients with GERD.



Patients with partial response to PPI therapy, defined as persistent GERD symptoms ≥3 days/week despite optimized treatment with a PPI, were recruited for this 12-month observational study. GERD symptoms, HRQL, work productivity and resource use were assessed by patient surveys. Costs were calculated based on lost work productivity and resource use.



The patient population (n=262; mean age, 54 years; 40% men) carried a significant symptom burden, with 98% of patients having moderate-to-severe GERD symptoms and 65% of patients experiencing daily symptoms at baseline. HRQL and work productivity were significantly impaired, with a greater degree of impairment in patients with higher symptom burden. The mean total cost per patient over the 12-month follow-up period was €5237, of which €4674 (89%) was due to lost work productivity.



Partial response to PPI therapy for GERD is associated with a high symptom burden, significant impairment of HRQL and work productivity, and substantial GERD-related costs.
Adolescent Cancer Education (ACE) to increase adolescent and parent cancer awareness and communication: study protocol for a cluster randomised controlled trial

Raising cancer awareness among adolescents has potential to increase their knowledge and confidence in identifying cancer symptoms and seeking timely medical help in adolescence and adulthood. Detecting cancer at an early stage is important because it reduces the risk of dying of some cancers and thereby contributes to improved cancer survival. Adolescents may also play an important role in increasing cancer communication within families. However, there are no randomised controlled trials (RCT) of the effectiveness of school-based educational interventions to increase adolescents' cancer awareness, and little is known about the role of adolescents in the upward diffusion of cancer knowledge to parents/carers. The aim of this study is to determine the effectiveness of a school-based educational intervention to raise adolescent and parent cancer awareness and adolescent-parent cancer communication.



The Adolescent Cancer Education (ACE) study is a school-based, cluster RCT. Twenty secondary schools in the area covered by Glasgow City Council will be recruited. Special schools for adolescents whose additional needs cannot be met in mainstream education are excluded. Schools are randomised to receive a presentation delivered by a Teenage Cancer Trust educator in Autumn 2013 (intervention group) or Spring 2014 following completion of six-month follow-up measures (control group). Participants will be students recruited at the end of their first year of secondary education (S1) (age 12 to 13 years) and one parent/carer for each student, of the student's choice. The primary outcome is recognition of cancer symptoms two weeks post-intervention. Secondary outcomes are parents' cancer awareness and adolescent-parent cancer communication. Outcomes will be assessed at baseline (when adolescents are in the final term of S1), two-week, and six-month follow-up (when adolescents are in S2, age 13 to 14 years). Differences in outcomes between trial arms will be tested using multiple regression methods, adjusted for clustering by school. An audit of cancer-related and health-promotion activity within the school curriculum and environment during the RCT will be conducted at six-month follow-up to contextualise the intervention effect.



Results from the ACE study will provide evidence about the public health effectiveness of a school-based intervention designed to increase adolescent and parent cancer awareness and adolescent-parent cancer communication.
Biological feature validation of estimated gene interaction networks from microarray data: a case study on MYC in lymphomas

Gene expression is a dynamic process where thousands of components interact dynamically in a complex way. A major goal in systems biology/medicine is to reconstruct the network of components from microarray data. Here, we address two key aspects of network reconstruction: (i) ergodicity supports the interpretation of the measured data as time averages and (ii) confounding is an important aspect of network reconstruction. To elucidate these aspects, we explore a data set of 214 lymphoma patients with translocated or normal MYC gene. MYC (c-Myc) translocations to immunoglobulin heavy-chain (IGH@) or light-chain (IGK@, IGL@) loci lead to c-Myc overexpression and are widely believed to be the crucial initiating oncogenic events. There is a rich body of knowledge on the biological implications of the different translocations. In the context of these data, the article reflects the relationship between the biological knowledge and the results of formal statistical estimates of gene interaction networks. The article identifies key steps to provide a trustworthy biological feature validation: (i) analysing a medium-sized network as a subnet of a more extensive environment to avoid bias by confounding, (ii) the use of external data to demonstrate the stability and reproducibility of the derived structures, (iii) a systematic literature review on the relevant issue, (iv) use of structured knowledge from databases to support the derived findings and (v) a strategy for biological experiments derived from the findings in steps (i-iv).