nils-herrmann/clean_scirepeval huggingface dataset:
Analysing Co-evolution Among Artificial 3D Creatures

We present results from our work on the coevolution of artificial creatures similar to those introduced by . In the present article we are mostly concerned with coevolutionary analysis. Coevolution is prone to complex dynamics which are often difficult to analyse. We introduce an improved analysis method based on Master Tournament matrices , which we argue is both less costly to compute and more informative than the original method. Based on visible features of the resulting graphs, we can identify particular trends and incidents in the dynamics of coevolution and look for their causes. Finally, considering that coevolutionary progress is not necessarily identical to global overall progress, we extend this analysis by cross-validating individuals from different evolutionary runs, which we argue is more appropriate than single-record analysis method for evaluating the global performance
Infliximab administration prior to surgery does not increase surgical site infections in patients with ulcerative colitis

The high incidence of infectious complications in ulcerative colitis (UC) is generally recognized to be due to several factors related to a compromised host. In our previous study, a high dose of corticosteroid was shown to be a risk factor for surgical site infection (SSI). Recently, infliximab (IFX) has been used for refractory UC. In this study, the effect of IFX on the occurrence of infectious postoperative complications for UC was evaluated, because it remains controversial. A total of 196 UC patients who underwent laparotomy between January 2010 and September 2012 were included. Possible factors related to complications were analyzed to identify significant predictors. Twenty-two patients had IFX before surgery. The overall incidence of SSI was 47/196 (24.0 %). The incidence of infections, including SSI and other infections, was 69/196 (35.2 %). On multivariate analysis, national nosocomial infection surveillance (NNIS) risk index ≥2 (p<0.01) and preoperative prednisolone dose ≥0.2 mg/kg/day (p = 0.01) were identified as independent risk factors for overall SSI; NNIS risk index ≥2 (p <0.01) and duration from onset of UC ≥6.3 years (p = 0.045) were identified as independent risk factors for incisional SSI; contaminated wound class (p <0.01), preoperative hospital stay ≥6 days (p = 0.048), severe/fulminant disease activity (p = 0.04), and pancolitis (p = 0.02) were identified as independent risk factors for organ/space SSI; and contaminated wound (p < 0.01), severe/fulminant disease activity (p = 0.02), and age at surgery ≥43 years (p = 0.047) were identified as independent risk factors for total infectious complications. IFX administration was not associated with infectious complications for UC surgery.
Extracorporeal shock wave therapy in early osteonecrosis of the femoral head: prospective clinical study with long-term follow-up

Extracorporeal shock wave therapy (ESWT) may exert beneficial effects in avascular necrosis of femoral head (AVNFH). The current study evaluated the effectiveness of ESWT in reducing pain and in slowing down the progression of bone damage in 36 patients with unilateral AVNFH of stage Association Research Circulation Osseous (ARCO) I, II and III. At the beginning of the study, 10 hips were classified as stage I, 11 as stage II and 15 as stage III. Each treatment cycle included four sessions, with 2,400 impulses each administered at 0.50 mJ/mm2, at 48–72 h intervals. Follow-up examinations were scheduled at 3, 6, 12 and then 24 months. Clinical assessments included assessment of pain scores, Harris Hip Scores and Roles and Maudsley score. Plain radiographs and magnetic resonances of the hip were used to evaluate the size of the lesion, the extent of collapse of subchondral bone, and degenerative changes of the hip joint. Patients from ARCO stage I group and stage II group achieved significantly better results than patients from ARCO stage III group at all follow-up time points (p < 0.005). During the follow-up period, 10 of the 15 stage III ARCO patients received an arthroplasty. ARCO stages I and II lesions were unchanged on radiographs and on magnetic resonance images. ESWT in ARCO stages I and II may help to prevent progression of the area of avascular necrosis and manage pain.
Usefulness of the Immunological Rapid Urease Test for Detection of Helicobacter pylori in Patients Who are Reluctant to Undergo Endoscopic Biopsies

Cardiovascular diseases and liver cirrhosis are in the list of Helicobacter pylori-related extragastric diseases. Patients with cirrhosis and cardiovascular diseases under the control of aspirin have increased risk of gastrointestinal bleeding. The immunological rapid urease test (IRUT) provides a rapid and safe diagnostic test for H. pylori using gastric mucus collected at endoscopy. We investigated its usefulness in 93 patients with these extragastric diseases including 46 with H. pylori infection assessed by urea breath test and serology. Twenty H. pylori-infected patients received eradication therapy and the IRUT was assessed to evaluate the efficacy of bacterial eradication. The sensitivity, specificity, and positive and negative predictive values for IRUT were 96%, 90%, 90%, and 96%, respectively. The results of IRUT completely agreed with those of urea breath test following anti-H. pylori therapy. The IRUT has acceptable diagnostic performance in such cohorts reluctant to undergo endoscopic biopsies due to the risk of bleeding.
Matrix metalloproteinase-9 pretreatment level predicts intracranial hemorrhagic complications after thrombolysis in human stroke.

Matrix metalloproteinase (MMP) expression is related to blood brain barrier disruption after cerebral ischemia. Moreover, MMP inhibitors reduce hemorrhagic transformation (HT) after embolic ischemia in tissue plasminogen activator (t-PA)-treated animals. We aimed to correlate plasmatic MMP levels with the appearance of intracranial bleeding complications in stroke patients treated with t-PA.



Serial MMP-2 and MMP-9 determinations were performed (ELISA, ng/mL) in 41 strokes involving the middle cerebral artery territory in patients who received t-PA within 3 hours of stroke onset. Blood samples were obtained at baseline (pretreatment) and at 12 and 24 hours after symptom onset. Hemorrhagic events were classified according to CT criteria (petechial hemorrhagic infarctions [HI, 1 to 2] and large parenchymal hemorrhages [PH, 1 to 2]). Brain CT scan was obtained at 48 hours or when a neurological worsening occurred. HT was present in 36.5% of the patients (24.4% HI and 12.1% PH). MMP-2 values were unrelated to any subtype of HT. The highest baseline MMP-9 level (normal range <97 ng/mL) corresponded to patients who later developed a PH (PH: 270.2+/-87.8, non-HT: 126.3+/-127.5, HI: 94.6+/-88.7; P=0.047). A graded response was found between mean baseline MMP-9 levels and the degree of bleeding (HI-1=37.4; HI-2=111.0; PH-1=202.5; PH-2=337.8). Baseline MMP-9 was the most powerful predictor of PH appearance in the multiple logistic regression model (OR= 9.62; CI 1.31 to 70.26; P=0.025).



Baseline MMP-9 level predicts PH appearance after t-PA treatment. Therefore, we suggest that MMP determination may increase the safety profile for thrombolysis and, in the future, anti-MMP drugs might be combined with t-PA to prevent hemorrhagic complications.
Intermittent pneumatic compression acts synergistically with manual lymphatic drainage in complex decongestive physiotherapy for breast cancer treatment-related lymphedema.

The application of intermittent pneumatic compression (IPC) as a part of complex decongestive physiotherapy (CDP) remains controversial. The aim of this study was to investigate whether the combination of IPC with manual lymph drainage (MLD) could improve CDP treatment outcomes in women with secondary lymphedema after breast cancer treatment. A randomized study was undertaken with 13 subjects receiving MLD (60 min) and 14 receiving MLD (30 min) plus IPC (30 min) followed by standardized components of CDP including multilayered compression bandaging, physical exercise, and skin care 10 times in a 2-week-period. Efficacy of treatment was evaluated by limb volume reduction and a subjective symptom questionnaire at end of the treatment, and one and two months after beginning treatment. The two groups had similar demographic and clinical characteristics. Mean reductions in limb volumes for each group at the end of therapy, and at one and two months were 7.93% and 3.06%, 9.02% and 2.9%, and 9.62% and 3.6%, respectively (p < 0.05 from baseline for each group and also between groups at each measurement). Although a significant decrease in the subjective symptom survey was found for both groups compared to baseline, no significant difference between the groups was found at any time point. The application of IPC with MLD provides a synergistic enhancement of the effect of CDP in arm volume reduction.
Directional Field Synthesis, Design, and Processing

Direction fields and vector fields play an increasingly important role in computer graphics and geometry processing. The synthesis of directional fields on surfaces, or other spatial domains, is a fundamental step in numerous applications, such as mesh generation, deformation, texture mapping, and many more. The wide range of applications resulted in definitions for many types of directional fields: from vector and tensor fields, over line and cross fields, to frame and vector-set fields. Depending on the application at hand, researchers have used various notions of objectives and constraints to synthesize such fields. These notions are defined in terms of fairness, feature alignment, symmetry, or field topology, to mention just a few. To facilitate these objectives, various representations, discretizations, and optimization strategies have been developed. These choices come with varying strengths and weaknesses. This report provides a systematic overview of directional field synthesis for graphics applications, the challenges it poses, and the methods developed in recent years to address these challenges.
FIND-CKD: a randomized trial of intravenous ferric carboxymaltose versus oral iron in patients with chronic kidney disease and iron deficiency anaemia

The optimal iron therapy regimen in patients with non-dialysis-dependent chronic kidney disease (CKD) is unknown.



Ferinject® assessment in patients with Iron deficiency anaemia and Non-Dialysis-dependent Chronic Kidney Disease (FIND-CKD) was a 56-week, open-label, multicentre, prospective and randomized study of 626 patients with non-dialysis-dependent CKD, anaemia and iron deficiency not receiving erythropoiesis-stimulating agents (ESAs). Patients were randomized (1:1:2) to intravenous (IV) ferric carboxymaltose (FCM), targeting a higher (400-600 µg/L) or lower (100-200 µg/L) ferritin or oral iron therapy. The primary end point was time to initiation of other anaemia management (ESA, other iron therapy or blood transfusion) or haemoglobin (Hb) trigger of two consecutive values <10 g/dL during Weeks 8-52.



The primary end point occurred in 36 patients (23.5%), 49 patients (32.2%) and 98 patients (31.8%) in the high-ferritin FCM, low-ferritin FCM and oral iron groups, respectively [hazard ratio (HR): 0.65; 95% confidence interval (CI): 0.44-0.95; P = 0.026 for high-ferritin FCM versus oral iron]. The increase in Hb was greater with high-ferritin FCM versus oral iron (P = 0.014) and a greater proportion of patients achieved an Hb increase ≥1 g/dL with high-ferritin FCM versus oral iron (HR: 2.04; 95% CI: 1.52-2.72; P < 0.001). Rates of adverse events and serious adverse events were similar in all groups.



Compared with oral iron, IV FCM targeting a ferritin of 400-600 µg/L quickly reached and maintained Hb level, and delayed and/or reduced the need for other anaemia management including ESAs. Within the limitations of this trial, no renal toxicity was observed, with no difference in cardiovascular or infectious events.
Neonatal ECMO Study of Temperature (NEST) - a randomised controlled trial

Existing evidence indicates that once mature neonates with severe cardio-respiratory failure become eligible for Extra Corporeal Membrane Oxygenation (ECMO) their chances of intact survival are doubled if they actually receive ECMO. However, significant numbers survive with disability. NEST is a multi-centre randomised controlled trial designed to test whether, in neonates requiring ECMO, cooling to 34 degrees C for the first 48 to 72 hours of their ECMO course leads to improved later health status. Infants allocated to the control group will receive ECMO at 37 degrees C throughout their course, which is currently standard practice around the world. Health status of both groups will be assessed formally at 2 years corrected age.



All infants recruited to the study will be cared for in one of the four United Kingdom (UK) ECMO centres. Babies who are thought to be eligible will be assessed by the treating clinician who will confirm eligibility, ensure that consent has been obtained and then randomise the baby using a web based system, based at the National Perinatal Epidemiology Unit (NPEU) Clinical Trials Unit. 
For the primary analysis, children will be analysed in the groups to which they are assigned, comparing the outcome of all babies allocated to "ECMO with cooling" with all those allocated to "ECMO" alone, regardless of deviation from the protocol or treatment received. For the primary outcome the analysis will compare the mean scores for each group of surviving babies. The rationale for this choice of primary analysis is to give a fair representation of the average ability of assessable children, accepting the limitation that excluding deaths might impose.The consistency of the effect of cooling on the group of babies recruited to the trial will be explored to see whether cooling is of particular help, or not, to specific subgroups of infants, using the statistical test of interaction. Therefore pre-specified subgroup analyses include: (i) whether the ECMO is veno-arterial or veno-venous; (ii) whether the child's oxygenation index at the time of recruitment is <60 or > or = 60; (iii) initial aEEG pattern shown on the cerebral function monitor, and (iv) primary diagnostic group.
Helicobacter Pylori Infection and Serum Pepsinogen I Concentration in Peptic Ulcer Patients: Effect of Bacterial Eradication

In order to test the hypothesis that H. pylori infections in the gastric antrum increase pepsinogen I release, fasting serum pepsinogen I concentrations were compared in peptic ulcer patients with and without H. pylori infection. A randomized prospective study was performed to determine whether the increased serum pepsinogen I concentrations associated with H. pylori infection respond to treatment that eradicates H. pylori.



Fasting serum pepsinogen I concentrations were measured by RIA in 736 patients with endoscopically and histologically confirmed benign peptic ulcer with and without H. pylori infection. Out of 511 patients with H. pylori infection, 110 patients (group 1) were randomly selected and were treated with metronidazole and tripotassium dicitrato bismuthate combined with ranitidine and antacid, and 97 patients (group 2) were treated only with ranitidine and antacid. The third group, 54 patients free of H. pylori infection, was designed to evaluate the influence of H2-receptor antagonist and antacid on the change of pepsinogen I. Fasting pepsinogen I concentration and H. pylori status were compared before and after the treatment.



Patients infected by H. pylori (gastric ulcer 208, duodenal ulcer 303; total 511) had significantly higher fasting serum pepsinogen I concentrations than H. pylori negative patients (gastric ulcer 110, duodenal ulcer 115; total 225). Mean pepsinogen I level of the former was 124.3 +/- 46.9 and that of the latter was 77.9 +/- 25.8 ng/ml. (p < 0.0001). The difference in serum pepsinogen I concentrations according to the location of ulcer crater was significant only in non-infected subjects e.g., mean pepsinogen I level H. pylori-negative gastric ulcer was significantly lower than that of H. pylori-negative duodenal ulcer patients. H. pylori was eradicated in all the patients who had received antibacterial therapy for 4 weeks and serum pepsinogen I concentrations were significantly decreased from 129.8 +/- 43.0 to 82.4 +/- 24.0 ng/ml after eradication of the organism. (p < 0.0001) In contrast, H. pylori-positive patients who had not received antibacterial therapy were still infected at the completion of the study and there was no significant change in the serum pepsinogen I concentrations after the treatment (120.8 +/- 40.9 vs 126.3 +/- 40.4 ng/ml). (p > 0.57) None of the patients who were initially H. pylori-negative has been reinfected during the period of the study and their serum pepsinogen I concentrations were not changed. (pre-treatment value 75.1 +/- 8.0; post-treatment value 77.3 +/- 24.5 mg/ml) (p < 0.75) Four-to six-week therapy of H2-receptor antagonist and antacid did not exert any influence on serum pepsinogen I concentrations.



On the basis of our results, we have confirmed that the chronic infection of H. pylori of gastric antrum in peptic ulcer patients causes increased pepsinogen I release into the circulation, and eradication of the organism results in significant fall in serum pepsinogen I concentrations.
Safety behaviour does not necessarily interfere with exposure therapy.

There has been much recent controversy regarding whether or not the use of safety and other neutralizing behaviour interferes with exposure-based therapy. The aim of this study was to examine the role of safety behaviour in the treatment of specific phobia. Sixty-two snake-fearful participants were randomized to a 45-min exposure session with or without the use of safety gear, such as gloves and goggles. During the treatment, participants in the safety behaviour group were able to achieve a significantly closer initial distance of approach to the snake compared to controls. When tested post-treatment without any safety gear, both groups demonstrated comparable treatment gains involving significant reductions in fearful cognitions and subjective anxiety, as well as significant improvements in distance of approach. Results suggest that reliance on safety behaviour during exposure therapy for anxiety disorders may not interfere with treatment outcome.
Effect of combined multiple contexts and multiple stimuli exposure in spider phobia: A randomized clinical trial in virtual reality.

Our previous study indicated that treatment in multiple contexts (MC) improved the outcome of exposure treatment by reducing return of fear. This effect was evident when the test was conducted immediately post treatment. In the present study, we conducted a treatment analogue study where we investigated whether an exposure to multiple stimuli (MS) and a combination of both MS and MC would further improve treatment efficacy in the short and long terms.



Spider-phobic patients (N = 58) were randomly allocated to one of four groups. Each group received virtual reality (VR) exposure treatment in either one or four different contexts and was exposed to either one or four different spiders. All participants completed both a VR test with a novel spider in a novel context and an in vivo behavioral avoidance test (BAT) pre-, post-treatment and at follow-up.



Short-term but not long-term return of fear was attenuated by multiple context exposure in VR. Long-term effect of fear attenuation was observed only in the MS single context group. In the BAT, the multiple stimuli condition seemed to be more beneficial in both the short and long term. Notably, there was no evidence for superiority of the combined multiple stimuli and contexts condition.



Change of contexts during exposure significantly reduced return of fear post treatment; however, similar results could not be observed with a follow-up test. The implementation of multiple stimuli during exposure seems to have both short-term and long-lasting beneficial effects on the treatment outcome. We recommend further investigation of this phenomenon and introduce further possible improvements to our paradigm.
Impact of mannose-binding lectin deficiency on radiocontrast-induced renal dysfunction: a post-hoc analysis of a multicenter randomized controlled trial

Local renal ischemia is regarded as an important factor in the development of contrast-induced nephropathy (CIN). Mannose-binding lectin (MBL) is involved in the tissue damage during experimental ischemia/reperfusion injury of the kidneys. The aim of the present study was to investigate the association of MBL deficiency with radiocontrast-induced renal dysfunction in a large prospective cohort.



246 patients with advanced non-dialysis-dependent renal dysfunction who underwent radiographic contrast procedures were included in the study. Baseline serum MBL levels were analyzed according to the occurrence of a creatinine-based (increase of ≥ 0.5 mg/dL or ≥ 25% within 48 hours) or cystatin C-based (increase of ≥ 10% within 24 hours) CIN.



The incidence of creatinine-based and cystatin C-based CIN was 6.5% and 24%, respectively. MBL levels were not associated with the occurrence of creatinine-based CIN. However, patients that experienced a cystatin C increase of ≥ 10% showed significantly higher MBL levels than patients with a rise of <10% (median 2885 (IQR 1193-4471) vs. 1997 (IQR 439-3504)ng/mL, p = 0.01). In logistic regression analysis MBL deficiency (MBL levels ≤ 500 ng/ml) was identified as an inverse predictor of a cystatin C increase ≥ 10% (OR 0.34, 95% CI 0.15-0.8, p = 0.01).



MBL deficiency was associated with a reduced radiocontrast-induced renal dysfunction as reflected by the course of cystatin C. Our findings support a possible role of MBL in the pathogenesis of CIN.