nils-herrmann/clean_scirepeval huggingface dataset:
Automatic Segmentation of Liver Region through Blood Vessels on Multi-Phase CT

Recently four phases CT has been widely used for diagnosing liver diseases, especially cancer. This paper describes an automatic method for segmenting the liver region from third phase abdominal CT. First, blood vessels in the liver are extracted with a threshold. Then morphological dilation enables us to define an approximate liver region, which is found to be very useful for removing abutting organs. The final liver region is extracted with a threshold. Experiments were conducted for eight CT data. The extracted regions agree well with those detected manually.
Monitoring mobile and spatially distributed cyber-physical systems

Cyber-Physical Systems (CPS) consist of collaborative, networked and tightly intertwined computational (logical) and physical components, each operating at different spatial and temporal scales. Hence, the spatial and temporal requirements play an essential role for their correct and safe execution. Furthermore, the local interactions among the system components result in global spatio-temporal emergent behaviors often impossible to predict at the design time. In this work, we pursue a complementary approach by introducing STREL a novel spatio-temporal logic that enables the specification of spatio-temporal requirements and their monitoring over the execution of mobile and spatially distributed CPS. Our logic extends the Signal Temporal Logic [15]with two novel spatial operators reach and escape from which is possible to derive other spatial modalities such as everywhere, somewhere and surround. These operators enable a monitoring procedure where the satisfaction of the property at each location depends only on the satisfaction of its neighbours, opening the way to future distributed online monitoring algorithms. We propose both a qualitative and quantitative semantics based on constraint semirings, an algebraic structure suitable for constraint satisfaction and optimisation. We prove that, for a subclass of models, all the spatial properties expressed with reach and escape, using euclidean distance, satisfy all the model transformations using rotation, reflection and translation. Finally, we provide an offline monitoring algorithm for STREL and, to demonstrate the feasibility of our approach, we show its application using the monitoring of a simulated mobile ad-hoc sensor network as running example.
Inhaled hypertonic saline in infants and toddlers with cystic fibrosis: short-term tolerability, adherence, and safety.

Inhaled hypertonic saline (HS) is an attractive agent for chronic maintenance therapy in infants and toddlers with cystic fibrosis (CF) because it improves defective mucociliary clearance. Prior to undertaking a clinical trial of HS efficacy in young children with CF, tolerability, adherence, and safety must be established.



Three-center, open label evaluation of the short-term tolerability, adherence, and safety of 7% HS administered twice daily for 14 days in children with CF 12-30 months of age. The primary objective was to evaluate the proportion of participants unable to tolerate single and repeated doses of 7% HS according to protocol-defined criteria. Participants inhaled a test dose of HS at the enrollment visit; test dose intolerance was defined as fulfillment of at least one of 4 criteria. Participants who tolerated the test dose inhaled 7% HS twice daily for 14±2 days.



Twenty children were enrolled. One was withdrawn due to maternal concern over fussiness with application of the facemask for the test dose. Of the 19 participants administered the test dose, 1 was withdrawn due to test dose intolerance (5%, 95% confidence interval 0, 26%). Eighteen participants completed the study; 1 was intolerant (95% CI 0, 27%) at the final visit due to new wheezes on exam in association with an upper respiratory infection and otitis media. Home symptom diaries demonstrated cough as the main symptom in the hour following inhalation, which decreased in frequency over the study period. Adherence as assessed by daily home diary and returned study drug ampoules was high. Participants reported receiving both treatments on a median of 100% of days; a median of 25 ampoules were used during a median of 13 days.



7% HS appears well tolerated for up to 14 days in infants and toddlers with CF, with high adherence. These results provide encouraging short-term tolerability and adherence data for future trials assessing the safety and efficacy of 7% HS in young children with CF.
Comparison of the clinical characteristics and outcomes of Klebsiella pneumoniae and Streptococcus pneumoniae meningitis.

This multicenter, retrospective cohort study compared the clinical characteristics and outcomes of community-acquired Klebsiella pneumoniae meningitis (CA-KPM) with those of community-acquired Streptococcus pneumoniae meningitis (CA-SPM). Eighty-three adult patients, 27 with CA-KPM and 56 with CA-SPM, were included. Diabetes mellitus (48.1% versus 21.4%; P=0.01) and liver cirrhosis (22.2% versus 5.4%; P=0.05) were more commonly associated with CA-KPM.  mental status (40.7% versus 12.5%; P=0.01), septic shock (44.4% versus 8.9%; P<0.001), and concomitant extrameningeal infections (40.7% versus 7.1%; P=0.001) were also more common in the CA-KPM group. The 28-day mortality (44.4% versus 10.7%; P<0.001) and inhospital mortality (51.9% versus 14.3%; P<0.001) were higher in the CA-KPM group. In conclusion, diabetes mellitus and liver cirrhosis are more common in the CA-KPM patients who were also more likely to present with severe manifestations and poor outcomes.
Methylphenidate and memory: Dissociated effects in hyperactive children

Fourteen children with Attention Deficit Disorder with Hyperactivity (ADD + H) were administered the psychostimulant methylphenidate in a double-blind, placebo-controlled, crossover study. Subjects were evaluated on a well-validated measure of verbal memory and learning with an experimental design comprised of four conditions: placebo and active drug at three doses. Positive memory effects were found in the drug conditions. Significant dose-response relationships were found, indicating enhanced learning from placebo to low to medium to high dose. However, there was a differential drug effect on the memory task; methylphenidate selectively enhanced storage and retrieval mechanisms without affecting immediate acquisition.
Geriatric Assessment of Older Adults With Cancer During Unplanned Hospitalizations: An Opportunity in Disguise.

Geriatric assessment (GA) is an important tool for management of older cancer patients; however, GA research has been performed primarily in the outpatient setting. The primary objective of this study was to determine feasibility of GA during an unplanned hospital stay. Secondary objectives were to describe deficits found with GA, to assess whether clinicians recognized and addressed deficits, and to determine 30-day readmission rates.



The study was designed as an extension of an existing registry, "Carolina Senior: Registry for Older Patients." Inclusion criteria were age 70 and older and biopsy-proven solid tumor, myeloma, or lymphoma. Patients had to complete the GA within 7 days of nonelective admission to University of North Carolina Hospital.



A total of 142 patients were approached, and 90 (63%) consented to participation. All sections of GA had at least an 83% completion rate. Overall, 53% of patients reported problems with physical function, 63% had deficits in instrumental activities of daily living, 34% reported falls, 12% reported depression, 31% had ≥10% weight loss, and 12% had abnormalities in cognition. Physician documentation of each deficit ranged from 20% to 46%. Rates of referrals to allied health professionals were not significantly different between patients with and without deficits. The 30-day readmission rate was 29%.



GA was feasible in this population. Hospitalized older cancer patients have high levels of functional and psychosocial deficits; however, clinician recognition and management of deficits were poor. The use of GA instruments to guide referrals to appropriate services is a way to potentially improve outcomes in this vulnerable population.



Geriatric assessment (GA) is an important tool in the management of older cancer patients; however, its primary clinical use has been in the outpatient setting. During an unplanned hospitalization, patients are extremely frail and are most likely to benefit from GA. This study demonstrates that hospitalized older adults with cancer have high levels of functional deficits on GA. These deficits are under-recognized and poorly managed by hospital-based clinicians in a tertiary care setting. Incorporation of GA measures during a hospital stay is a way to improve outcomes in this population.
Which factors influence spontaneous state transitions during resuscitation?

The clinical state (i.e. ventricular fibrillation/tachycardia: VF/VT, asystole: ASY, pulseless electrical activity: PEA, or return of spontaneous circulation, ROSC) during cardiopulmonary resuscitation determines patient management. We investigate how spontaneous transitions (i.e. not forced by DC shock) between these states are influenced by factors like age, gender, bystander CPR, CPR quality, proportion of time spent in a state, or the number of state transitions.



Detailed recordings from CPR attempts in 304 out-of-hospital cardiac arrests in Akershus (Norway), Stockholm (Sweden), and London (UK) were obtained from modified Heartstart 4000 defibrillators. Spontaneous state transitions were studied using a non-parametric intensity regression method that can handle dynamic factors like the state history properly.



The initial state tended to preserve itself, as did cumulative time in any state. Recent DC shock, bystander CPR, location, response time, gender, compression depth, and ventilation rate were important for some transitions. More ventilation during PEA might possibly avert development to ASY and favour ROSC; otherwise observed variations in CPR quality had little impact.



Using a novel intensity regression approach we studied the influence of various factors on spontaneous (i.e. non-shock) state transitions during CPR. State development was largely determined by the initial state, the proportion of time spent in a state, and the transition frequency; all probably reflecting the underlying aetiology.
Geoadditive models to assess spatial variation of HIV infections among women in Local communities of Durban, South Africa

The severity of the HIV/AIDS epidemic in South Africa varies between and within provinces, with differences noted even at the suburban scale. We investigated the geographical variability of HIV infection in rural areas of the eThekwini Metropolitan Municipality in KwaZulu-Natal province, South Africa.



We used geoadditive models to assess nonlinear geographical variation in HIV prevalence while simultaneously controlling for important demographic and sexual risk factors. A total of 3,469 women who were screened for a Phase-III randomized trial were included in the current analysis.



We found significant spatial patterns that could not be explained by demographic and sexual risk behaviors. In particular, the epidemic was determined to be much worse 44 km south of Durban after controlling for all demographic and sexual risk behaviors.



The study revealed significant geographic variability in HIV infection in the eThekwini Metropolitan Municipality in KwaZulu-Natal, South Africa.
Early and long-term outlook of percutaneous coronary intervention for bifurcation lesions in young patients.

Coronary artery disease is most common in older patients, but may occur in younger subjects. The outlook of young patients after percutaneous coronary intervention (PCI) of challenging lesion subsets such as coronary bifurcations, is not established. We thus aimed to appraise the early and long-term results of PCI for bifurcations in young patients.



A multicenter, retrospective study was conducted enrolling consecutive patients undergoing bifurcation PCI between 2002 and 2006 in 22 Italian centers. Patients were divided in 2 groups: age ≤ 45 years, and age > 45 years. The primary end-point was long-term rate of major adverse cardiac events (MACE).



4,314 patients were included: 195 (4.5%) in the younger group, and 4119 (95.5%) in the older group. 30-day outcomes did not show significant differences in MACE rates, with 1.0% in the ≤ 45 years group and 2.1% in the >45 years group (p=0.439), with death in 0.5% and 1.2% (p=0.388). At long-term follow-up (24.4 ± 15.1 months), younger patients showed similar rates of MACE, (12.8% vs. 16.6%, p=0.161), myocardial infarction (3.1% vs. 3.7%, p=0.633), target lesion revascularization (11.3% vs. 12.5%, p=0.627), or stent thrombosis (1.5% vs. 2.8%, p=0.294), despite an increased risk of death in older patients (1.0% vs. 5.0%, p=0.012). Even at extensive multivariable analysis, younger patients still faced a similar risk of MACE (HR=0.78 [0.48-1.27], p=0.318).



Despite their low age, young patients undergoing PCI for bifurcation face a significant risk of early and late non-fatal adverse events. Thus, they should not be denied careful medical management and follow-up.
Association of tattooing and hepatitis C virus infection: a multicenter case-control study.

Although injection drug use (IDU) and blood transfusions prior to 1992 are well-accepted risk factors for hepatitis C virus (HCV) infection, many studies that evaluated tattooing as a risk factor for HCV infection did not control for a history of IDU or transfusion prior to 1992. In this large, multicenter, case-control study, we analyzed demographic and HCV risk factor exposure history data from 3,871 patients, including 1,930 with chronic HCV infection (HCV RNA-positive) and 1,941 HCV-negative (HCV antibody-negative) controls. Crude and fully adjusted odds ratios (ORs) of tattoo exposure by multivariate logistic regression in HCV-infected versus controls were determined. As expected, IDU (65.9% versus 17.8%; P < 0.001), blood transfusion prior to 1992 (22.3% versus 11.1%; P < 0.001), and history of having one or more tattoos (OR, 3.81; 95% CI, 3.23-4.49; P < 0.001) were more common in HCV-infected patients than in control subjects. After excluding all patients with a history of ever injecting drugs and those who had a blood transfusion prior to 1992, a total of 1,886 subjects remained for analysis (465 HCV-positive patients and 1,421 controls). Among these individuals without traditional risk factors, HCV-positive patients remained significantly more likely to have a history of one or more tattoos after adjustment for age, sex, and race/ethnicity (OR, 5.17; 95% CI, 3.75-7.11; P < 0.001).



Tattooing is associated with HCV infection, even among those without traditional HCV risk factors such as IDU and blood transfusion prior to 1992.
Successful Treatment with Peginterferon alfa-2b of HBeAg-positive HBV Non-Responders to Standard Interferon or Lamivudine

Antiviral therapy leads to HBeAg seroconversion in 10–40% of the patients with HBeAg-positive chronic hepatitis B. Nonresponse may result in progression of liver disease and increased risk of hepatocellular carcinoma. As part of a global randomized controlled trial we investigated the efficacy (i.e., loss of HBeAg at the end of follow-up) of peginterferon alfa-2b (Peg-IFN α2b) in patients who failed to respond to previous courses of standard interferon (IFN) or lamivudine.We analyzed a total of 76 previous nonresponders: 37 were nonresponders to standard IFN, 17 were nonresponders to lamivudine, and 22 were nonresponders to both therapies. All patients received a 52-wks course of 100 μg Peg-IFN α2b weekly combined with either 100 mg lamivudine daily or a placebo. After therapy patients were followed for 26 wks.Thirteen (35%) nonresponders to previous IFN, five (29%) nonresponders to previous lamivudine, and four (22%) nonresponders to both IFN and lamivudine responded to treatment with Peg-IFN α2b. No difference in response was found for those treated with Peg-IFN α2b alone or in combination with lamivudine. Nonresponders to prior IFN therapy with baseline ALT (alanine aminotransferase) > 4 × ULN (upper limit of normal) responded better to Peg-IFN α2b than those with ALT levels ≤ 4 × ULN (53% vs 20%, respectively, p = 0.036).CONCLUSIONS:Peg-IFN α2b is effective in approximately one-third of patients who failed to respond to previous treatment with standard IFN or lamivudine. High serum ALT level at baseline of Peg-IFN α2b therapy was the best predictor for response in these patients.
Construct validity of an attention rating scale for traumatic brain injury.

Attention deficits are nearly ubiquitous after traumatic brain injury (TBI). In the subacute phase of moderate to severe TBI, these deficits may be difficult to measure with the precision needed to predict outcomes, assess degree of recovery, and monitor treatment response. This article reports the findings of four studies, three observational and one a randomized, controlled treatment trial of methylphenidate (MP), designed to provide construct validation of the Moss Attention Rating Scale (MARS), an observational measure of attention dysfunction following TBI. One hundred seven participants with moderate to severe TBI were enrolled during treatment on an inpatient rehabilitation unit. MARS scores were provided independently by four rehabilitation disciplines (Physical, Occupational and Speech Therapies and Nursing). Results indicated that the MARS: (1) is more strongly related to concurrent measures of cognitive versus physical disability, supporting its validity as a measure of cognition, (2) is more strongly related to concurrent psychometric measures of attention versus measures thought to rely less on attention, supporting its validity as a measure of attention; and (3) predicts 1-year outcomes of TBI better than psychometric measures of attention. However, the MARS (4) was not differentially affected by MP versus placebo treatment. Results support the construct validity and utility of the MARS, with further research needed to clarify its role in treatment outcome assessment.
Delays and adverse clinical outcomes associated with unrecognized pacing indications.

A recent UK audit showed that a significant proportion of patients who received pacemakers had pacing indications previously overlooked, leading to significant delays to pacemaker implantation.



To investigate the reasons for, and morbidity associated with, overlooked pacing indications.



Prospective observational study in a UK regional pacing centre and its referring district hospitals.



Hospital records from referring and implanting centres were reviewed for 95 consecutive patients undergoing first pacemaker implant to determine symptoms, investigations and hospitalisations occurring after documentation of a pacing indication.



Thirty-three of ninety-five patients (35%) had a pacing indication overlooked, which was Class I in 14 patients and Class IIa in 19. Reasons for not making a pacing referral in these patients included: failure to recognize the indication in 14, making adjustments to potentially culprit medication in 15 and requesting additional 'confirmatory' tests in 4. Twenty-six patients (79%) with missed indications experienced adverse events after documentation of an indication, and before receiving a pacemaker: 23 had ongoing symptoms (including one cardiac arrest), three received temporary pacing wires and 18 were hospitalized with symptoms related to cardiac rhythm. Twenty-seven patients (82%) had a total of 38 additional specialist investigations after documentation of a pacing indication.



Documentation of an indication for pacing failed to trigger referral for permanent pacing in 35% of patients. This failure led to significant delays, morbidity and use of health service resource, which may have been avoided if timely recognition of the pacing indication had prompted referral. Failure to recognize pacing indications and reassessing symptoms and repeating investigation after changes to medication, often required for the management of associated tachyarrhythmias or other medical conditions, contribute to these delays, perhaps unnecessarily.
Clinical features and outcomes of Hodgkin’s lymphoma in Korea: Consortium for Improving Survival of Lymphoma (CISL)

Ethnic and regional differences in the epidemiology and pathological aspects of Hodgkin’s lymphoma (HL) between Western and Asian patients may be associated with differences in clinical features and prognosis. We retrospectively analyzed the clinical and histopathological characteristics, therapeutic outcomes, and prognostic factors of 539 HL patients treated at 16 centers in Korea. We found that the incidence of histological subtypes of HL in Korea was similar to that in Western and other Asian countries. However, the incidence peaked between 16 and 30 years of age, unlike the bimodal age distribution seen in Western countries. In patients with stage I–IIA non-bulky disease, the complete response (CR) rate was similar between combined modality therapy and chemotherapy alone (93% vs. 84%, P = 0.44), and there was no difference in relapse-free survival (RFS) and overall survival (OS). Patients with stage I–II disease plus unfavorable factors and those with advanced-stage disease treated with combination chemotherapy regimens had an overall CR rate of 77%, with no difference between doxorubicin, bleomycin, vinblastine, and dacarbazine (ABVD) and non-ABVD regimens (77.2% vs. 76.8%, P = 0.95). Among those patients who achieved final CR, there was no significant difference in RFS or OS between those who achieved interim CR and PR. Only the presence of B symptoms was independently predictive of a shorter RFS. Age > 45 years, Eastern Cooperative Oncology Group 2–4, and B symptoms were independent risk factors for death. Although the incidence of HL was lower in Korea than in Western countries, the distribution of morphological subtypes, treatment outcomes, and patient prognosis were similar.
Randomised double blind crossover study comparing ondansetron, granisetron and tropisetron. A cost–benefit analysis

The goals of this work were to compare the relative efficacy of ondansetron, granisetron and tropisetron in a randomised double blind crossover trial, evaluating objective, subjective and pharmacoeconomic parameters. To this end, 136 patients were enrolled, 120 of whom were eligible and evaluable. Each patient received three identical chemotherapy cycles with an antiemetic protocol which consisted in dexamethasone 20 mg i.v. and a tapering dose schedule for 4 days, and a single i.v. dose of an antiserotoninergic drug in each cycle. Arm A patients received tropisetron 5 mg; arm B patients, granisetron 3 mg; and arm C patients, ondansetron 24 mg. Numbers of patients and days with emetic episodes, grade of nausea, patient preference, headaches, need for metoclopramide, nursing or medical consultation, or admission to emergency room or ward were evaluated. There was no difference in the percentage incidence of acute or delayed nausea and vomiting. Twenty-five per cent of patients preferred tropisetron, 30% preferred granisetron, and 45% preferred ondansetron (P<0.01). Toxicity was mild in less than 10% of patients. Direct and indirect costs of treatment varied from 19.74 to 28.53 euros for tropisetron, 31.07–46.51 euros for granisetron and 22.76–62.61 euros for ondansetron. There was no difference in objective activity. In the schedules studied, patients preferred ondansetron. Indirect costs amount to less than 10% of the total antiemetic cost. Direct costs varied widely and should be considered whenever an antiemetic drug is selected.