nils-herrmann/clean_scirepeval huggingface dataset:
Source localization of ictal epileptic activity investigated by high resolution EEG and validated by SEEG

High resolution electroencephalography (HR-EEG) combined with source localization methods has mainly been used to study interictal spikes and there have been few studies comparing source localization of scalp ictal patterns with depth EEG. To address this issue, 10 patients with four different scalp ictal patterns (ictal spikes, rhythmic activity, paroxysmal fast activity, obscured) were investigated by both HR-EEG and stereoelectroencephalography (SEEG). Sixty-four scalp-EEG sensors and a sampling rate of 1kHz were used to record scalp ictal patterns. Five different source models (moving dipole, rotating dipole, MUSIC, LORETA, and sLORETA) were used in order to perform source localization. Seven to 10 intracerebral electrodes were implanted during SEEG investigations. For each source model, the concordance between ictal source localization and epileptogenic zone defined by SEEG was assessed. Results were considered to agree if they localized in the same sublobar area as defined by a trained epileptologist. Across the study population, the best concordance between source localization methods and SEEG (9/10) was obtained with equivalent current dipole modeling. MUSIC and LORETA had a concordance of 7/10 whereas sLORETA had a concordance of only 5/10. Four of our patients classified into different groups (ictal spikes, paroxysmal fast activity, obscured) had complete concordance between source localization methods and SEEG. A high signal to noise ratio, a short time window of analysis (<1s) and bandpass filtering around the frequency of rhythmic activity allowed improvement of the source localization results. A high level of agreement between source localization methods and SEEG can be obtained for ictal spike patterns and for scalp-EEG paroxysmal fact activities whereas scalp rhythmic discharges can be accurately localized but originated from seizure propagation network.
Risk of Recurrent Pancreatitis and Progression to Chronic Pancreatitis After a First Episode of Acute Pancreatitis.

Patients with a first episode of acute pancreatitis can develop recurrent or chronic pancreatitis (CP). However, little is known about the incidence or risk factors for these events.



We performed a cross-sectional study of 669 patients with a first episode of acute pancreatitis admitted to 15 Dutch hospitals from December 2003 through March 2007. We collected information on disease course, outpatient visits, and hospital readmissions, as well as results from imaging, laboratory, and histology studies. Standardized follow-up questionnaires were sent to all available patients to collect information on hospitalizations and interventions for pancreatic disease, abdominal pain, steatorrhea, diabetes mellitus, medications, and alcohol and tobacco use. Patients were followed up for a median time period of 57 months. Primary end points were recurrent pancreatitis and CP. Risk factors were evaluated using regression analysis. The cumulative risk was assessed using Kaplan-Meier analysis.



Recurrent pancreatitis developed in 117 patients (17%), and CP occurred in 51 patients (7.6%). Recurrent pancreatitis developed in 12% of patients with biliary disease, 24% of patients with alcoholic etiology, and 25% of patients with disease of idiopathic or other etiologies; CP occurred in 3%, 16%, and 10% of these patients, respectively. Etiology, smoking, and necrotizing pancreatitis were independent risk factors for recurrent pancreatitis and CP. Acute Physiology and Chronic Health Evaluation II scores at admission also were associated independently with recurrent pancreatitis. The cumulative risk for recurrent pancreatitis over 5 years was highest among smokers at 40% (compared with 13% for nonsmokers). For alcohol abusers and current smokers, the cumulative risks for CP were similar-approximately 18%. In contrast, the cumulative risk of CP increased to 30% in patients who smoked and abused alcohol.



Based on a retrospective analysis of patients admitted to Dutch hospitals, a first episode of acute pancreatitis leads to recurrent pancreatitis in 17% of patients, and almost 8% of patients progress to CP within 5 years. Progression was associated independently with alcoholic etiology, smoking, and a history of pancreatic necrosis. Smoking is the predominant risk factor for recurrent disease, whereas the combination of alcohol abuse and smoking produces the highest cumulative risk for chronic pancreatitis.
Improving care for depression in obstetrics and gynecology: a randomized controlled trial.

To evaluate an evidence-based collaborative depression care intervention adapted to obstetrics and gynecology clinics compared with usual care.



A two-site, randomized controlled trial included screen-positive women (Patient Health Questionnaire-9 score of at least 10) who met criteria for major depression, dysthymia, or both (Mini-International Neuropsychiatric Interview). Women were randomized to 12 months of collaborative depression management or usual care; 6-month, 12-month, and 18-month outcomes were compared. The primary outcomes were change from baseline to 12 months in depression symptoms and functional status. Secondary outcomes included at least 50% decrease and remission in depressive symptoms, global improvement, treatment satisfaction, and quality of care.



Participants were, on average, 39 years old, 44% were nonwhite, and 56% had posttraumatic stress disorder. Intervention (n=102) compared with usual care (n=103) patients had greater improvement in depressive symptoms at 12 months (P<.001) and 18 months (P=.004). The intervention group compared with usual care group had improved functioning over the course of 18 months (P<.05), were more likely to have at least 50% decrease in depressive symptoms at 12 months (relative risk [RR] 1.74, 95% confidence interval [CI] 1.11-2.73), greater likelihood of at least four specialty mental health visits (6-month RR 2.70, 95% CI 1.73-4.20; 12-month RR 2.53, 95% CI 1.63-3.94), adequate dose of antidepressant (6-month RR 1.64, 95% CI 1.03-2.60; 12-month RR 1.71, 95% CI 1.08-2.73), and greater satisfaction with care (6-month RR 1.70, 95% CI 1.19-2.44; 12-month RR 2.26, 95% CI 1.52-3.36).



Collaborative depression care adapted to women's health settings improved depressive and functional outcomes and quality of depression care.
The use of weekly text messaging over 6 months was a feasible method for monitoring the clinical course of low back pain in patients seeking chiropractic care.

This study critically evaluates a new method of collecting frequent data using mobile phones and text messages. Fluctuating conditions such as low back pain (LBP) need frequent monitoring to describe the clinical course in detail and to account for individual and subgroup variations.



In this multicentre prospective observational study, 262 subjects with nonspecific LBP were followed with weekly text messages for 6 months, with the question "How many days this previous week has your low back pain been bothersome?" The text replies were instantly recorded in a data file to be merged with baseline and follow up data (age, gender, pain intensity, duration, and self- rated health) collected through ordinary questionnaires. The response rate, user-friendliness, and compliance of this method were evaluated.



The mean response rate for the text messages throughout the study was 82.5% and was unaffected by season. The method was found to be user friendly. Dropout was not affected by age and gender, but compliance was possibly somewhat affected by outcome.



Weekly text messages are a useful method of data collection to examine the clinical course of LBP in the primary care sector.
Heart rate responses to standardized trauma-related pictures in acute posttraumatic stress disorder

Physiological responses to trauma reminders are one of the core symptoms of posttraumatic stress disorder (PTSD). Nevertheless, screening measures for PTSD largely rely on symptom self-reports. It has been suggested that psychophysiological assessments may be useful in identifying trauma survivors with PTSD (Orr and Roth, 2000). This study investigated whether heart rate (HR) responses to standardized trauma-related pictures distinguish between trauma survivors with and without acute PTSD. Survivors of motor vehicle accidents or physical assaults (N=162) watched standardized trauma-related, generally threatening and neutral pictures at 1 month post-trauma while their ECG was recorded. At 1 and 6 months, structured clinical interviews assessed PTSD diagnoses. Participants completed self-report measures of PTSD severity and depression, peritraumatic responses, coping behaviors and appraisals. Trauma survivors with acute PTSD showed greater HR responses to trauma-related pictures than those without PTSD, as indicated by a less pronounced mean deceleration, greater peak responses, and a greater proportion showing HR acceleration of greater than 1 beat per minute. There were no group differences in HR responses to generally threatening or neutral pictures. HR responses to trauma-related pictures contributed to the prediction of PTSD diagnosis over and above what could be predicted from self-reports of PTSD and depression. HR responses to trauma-related pictures were related to fear and data-driven processing during the trauma, safety behaviors, suppression of trauma memories, and overgeneralized appraisals of danger. The results suggest that HR responses to standardized trauma-related pictures may help identify a subgroup of patients with acute PTSD who show generalized fear responses to trauma reminders. The early generalization of triggers of reexperiencing symptoms observed in this study is consistent with associative learning and cognitive models of PTSD.
Tissue-Specific MicroRNA Expression Patterns in Four Types of Kidney Disease.

MicroRNAs contribute to the development of kidney disease. Previous analyses of microRNA expression in human kidneys, however, were limited by tissue heterogeneity or the inclusion of only one pathologic type. In this study, we used laser-capture microdissection to obtain glomeruli and proximal tubules from 98 human needle kidney biopsy specimens for microRNA expression analysis using deep sequencing. We analyzed specimens from patients with diabetic nephropathy (DN), FSGS, IgA nephropathy (IgAN), membranoproliferative GN (MPGN) (n=19-23 for each disease), and a control group (n=14). Compared with control glomeruli, DN, FSGS, IgAN, and MPGN glomeruli exhibited differential expression of 18, 12, two, and 17 known microRNAs, respectively. The expression of several microRNAs also differed between disease conditions. Specifically, compared with control or FSGS glomeruli, IgAN glomeruli exhibited downregulated expression of hsa-miR-3182. Furthermore, in combination, the expression levels of hsa-miR-146a-5p and hsa-miR-30a-5p distinguished DN from all other conditions except IgAN. Compared with control proximal tubules, DN, FSGS, IgAN, and MPGN proximal tubules had differential expression of 13, 14, eight, and eight microRNAs, respectively, but expression of microRNAs did not differ significantly between the disease conditions. The abundance of several microRNAs correlated with indexes of renal function. Finally, we validated the differential glomerular expression of select microRNAs in a second cohort of patients with DN (n=19) and FSGS (n=21). In conclusion, we identified tissue-specific microRNA expression patterns associated with several kidney pathologies. The identified microRNAs could be developed as biomarkers of kidney diseases and might be involved in disease mechanisms.
Pregnancy in HIV Clinical Trials in Sub Saharan Africa: Failure of Consent or Contraception?

Higher than expected pregnancy rates have been observed in HIV related clinical trials in Sub-Saharan Africa. We designed a qualitative study to explore the factors contributing to high pregnancy rates among participants in two HIV clinical trials in Sub-Saharan Africa.



Female and male participants enrolled in one of two clinical HIV trials in south-west Uganda were approached. The trials were a phase III microbicide efficacy trial among HIV negative women using vaginal gel (MDP); and a trial of primary prevention prophylaxis for invasive cryptococcal disease using fluconazole among HIV infected men and women in Uganda (CRYPTOPRO). 14 focus group discussions and 8 in-depth interviews were conducted with HIV positive and negative women and their male partners over a six month period. Areas explored were their experiences about why and when one should get pregnant, factors affecting use of contraceptives, HIV status disclosure and trial product use.



All respondents acknowledged being advised of the importance of avoiding pregnancy during the trial. Factors reported to contribute to pregnancy included; trust that the investigational product (oral capsules/vaginal gel) would not harm the baby, need for children, side effects that led to inconsistent contraceptive use, low acceptance of condom use among male partners. Attitudes towards getting pregnant are fluid within couples over time and the trials often last for more than a year. Researchers need to account for high pregnancy rates in their sample size calculations, and consider lesser used female initiated contraceptive options e.g. diaphragm or female condoms. In long clinical trials where there is a high fetal or maternal risk due to investigational product, researchers and ethics committees should consider a review of participants contraceptive needs/pregnancy desire review after a fixed period, as need for children, partners and health status of participants may alter over time.
Survey of Recent Operating Systems Research, Designs and Implementations

This paper surveys the recent theoretical and experimental advancements in the operating systems area. On the theoretical side much effort is being expended in rigorously defining the specifications and the logical structure (the hierarchical levels approach, the kernel approach with user defined subsystems, and so on) of an operating system, deriving proofs about the satisfaction of many properties (deadlock-free, synchronization constraints, protection requirements, and so on) and in proposing new theories, models and constructs. Researchers make extensive use of the results in the areas of graph theory, automata theory, operations research, computer architecture and software engineering. On the experimental side new operating systems with novel features are being designed and implemented. With the increased use of computers for solving many complex tasks on dedicated and general purpose systems, operating systems are required to provide many new facilities. Existing systems are being used for various experimental investigations testing different hypotheses (about new memory management policies, scheduling disciplines, interprocess communication facilities, performance monitoring, process structures, and so on). Operating systems are being modified to enhance their capabilities (like providing virtual machines, support for new devices and multilevel storage hierarchies, parallel processing capabilities, and so on). The developments in the areas of firmware, data base management and distributed processing are also having a great impact on the operating systems area. As one reads through this paper the interplay of these various factors will become apparent. This paper is the result of an attempt to collect together much information and provide pointers to the relevant literature.
Comparing integrated training of the hand and arm with isolated training of the same effectors in persons with stroke using haptically rendered virtual environments, a randomized clinical trial

Robotically facilitated therapeutic activities, performed in virtual environments have emerged as one approach to upper extremity rehabilitation after stroke. Body function level improvements have been demonstrated for robotically facilitated training of the arm. A smaller group of studies have demonstrated modest activity level improvements by training the hand or by integrated training of the hand and arm. The purpose of this study was to compare a training program of complex hand and finger tasks without arm movement paired with a separate set of reaching activities performed without hand movement, to training the entire upper extremity simultaneously, utilizing integrated activities. Forty individuals with chronic stroke recruited in the community, participated in a randomized, blinded, controlled trial of two interventions. Subjects were required to have residual hand function for inclusion. The first, hand and arm separate (HAS) training (n = 21), included activities controlled by finger movement only, and activities controlled by arm movement only, the second, hand and arm together (HAT) training (n = 20) used simulations controlled by a simultaneous use of arm and fingers. No adverse reactions occurred. The entire sample demonstrated mean improvements in Wolf Motor Function Test scores (21%) and Jebsen Test of Hand Function scores (15%), with large effect sizes (partial r2 = .81 and r2 = .67, respectively). There were no differences in improvement between HAS and HAT training immediately after the study. Subjects in the HAT group retained Wolf Motor Function Test gains better than in the HAS group measured three months after the therapy but the size of this interaction effect was small (partial r2 = .17). Short term changes in upper extremity motor function were comparable when training the upper extremity with integrated activities or a balanced program of isolated activities. Further study of the retention period is indicated. NCT01072461 .
Method of Detection of Well-Differentiated Thyroid Cancers in Obese and Non-Obese Patients

The incidence of well-differentiated thyroid cancer (WDTC) is increasing rapidly. Many authors feel that this increase is due to over-diagnosis and that one of the contributing factors is the increasing use of various imaging studies. The rate of obesity has also been increasing in the United States. It has been suggested that patients with an increased body mass index (BMI kg/m2) have a higher incidence of WDTC than patients with normal BMI. One might hypothesize that thyroid nodules are more difficult to palpate in obese patients and that as more cancers are detected by imaging the apparent rate of increase in WDTC in obese patients would appear to be greater than in non-obese patients. This study was undertaken to evaluate this hypothesis by determining if there is any difference in the way thyroid cancers are initially detected in obese and non-obese patients.



The medical records of all 519 patients with a postoperative diagnosis of WDTC who underwent thyroidectomy at NYU Langone Medical Center from January 1, 2007 through August 31, 2010 by the three members of NYU Endocrine Surgery Associates were reviewed. Patients were divided into Non-obese (BMI<30 kg/m2) and Obese (BMI≥30 kg/m2) groups. Patients were also divided by the initial method of detection of their tumor into Palpation, Imaging, and Incidental groups.



The final study group contained 270 patients, 181(67%) of whom were in the Non-obese Group and 89(33%) were in the Obese Group. In the Non-obese group, 81(45%) of tumors were found by palpation, 72(40%) were found by imaging, and 28(16%) were found incidentally. In the Obese group, 40(45%) were found by palpation, 38(43%) were found by imaging, and 11(12%) were found incidentally. These differences were not statistically significant (p-value 0.769).



We show that BMI does not play a role in the method of initial detection in patients with WDTC. This suggests that the prevalence of WDTC detected by imaging is not an artifact caused by an increasingly obese population and that any association of WDTC and obesity is not related to the way in which these tumors are detected.
Reachset Conformance Testing of Hybrid Automata

Industrial-sized hybrid systems are typically not amenable to formal verification techniques. For this reason, a common approach is to formally verify abstractions of (parts of) the original system. However, we need to show that this abstraction conforms to the actual system implementation including its physical dynamics. In particular, verified properties of the abstract system need to transfer to the implementation. To this end, we introduce a formal conformance relation, called reachset conformance, which guarantees transference of safety properties, while being a weaker relation than the existing trace inclusion conformance. Based on this formal relation, we present a conformance testing method which allows us to tune the trade-off between accuracy and computational load. Additionally, we present a test selection algorithm that uses a coverage measure to reduce the number of test cases for conformance testing. We experimentally show the benefits of our novel techniques based on an example from autonomous driving.
Therapeutic angiogenesis in patients with severe limb ischemia by transplantation of a combination stem cell product.

Angiogenesis involves the interplay of endothelial progenitor cells, pericytes, growth factors, and cellular matrix components. The use of mesenchymal stem cells, which are closely related to pericytes and produce diverse angiogenic growth factors and matrix molecules, seems to be a promising therapeutic modality. We postulate that the use of a combination cell product (mesenchymal stem cells in conjunction with a source of endothelial progenitor cells) is safe and efficient and may optimize the clinical results obtained with the use of endothelial progenitor cells alone. This study assessed whether the intramuscular infusion of a combination cell product represents a viable, effective, and lasting therapeutic modality to improve perfusion in severely ischemic limbs.



Patients with limb ischemia (n=26) received an intramuscular (gastrocnemius) infusion of the combination cell product in the most ischemic leg and a placebo product in the (less ischemic) contralateral leg. Clinical follow-up (months 0.5, 1, 2, and 4 postinfusion) included evaluation of pain-free walking time, ankle-brachial index, perfusion scintigraphy, and quality of life survey.



No adverse events occurred after infusion. Efficacy assessment indicated that after cell infusion there was a significant improvement in walking time and ankle-brachial index. In addition, technetium-99m-tetrofosmin scintigraphy demonstrated a significant increase of perfusion in the treated limbs compared with the respective control legs.



This phase II clinical trial shows that the use of a combination cell therapy is safe and effective in increasing blood flow in the ischemic legs of patients with limb ischemia.