nils-herrmann/clean_scirepeval huggingface dataset:
Reversal of cognitive deficits by an ampakine (CX516) and sertindole in two animal models of schizophrenia—sub-chronic and early postnatal PCP treatment in attentional set-shifting

Therapies treating cognitive impairments in schizophrenia especially deficits in executive functioning are not available at present. The current study evaluated the effect of ampakine CX516 in reversing deficits in executive functioning as represented in two animal models of schizophrenia and assessed by a rodent analog of the intradimensional–extradimensional (ID–ED) attentional set-shifting task. The second generation antipsychotic, sertindole, provided further validation of the schizophrenia-like disease models. Animals were subjected to (a) sub-chronic or (b) early postnatal phencyclidine (PCP) treatment regimes: (a) Administration of either saline or PCP (5 mg/kg, intraperitonally b.i.d. for 7 days) followed by a 7-day washout period and testing on day 8. (b) On postnatal days (PNDs) 7, 9, and 11, rats were subjected to administration of either saline or PCP (20 mg/kg, subcutaneously (s.c.)) and tested on PNDs 56–95, after reaching adulthood. The single test session required rats to dig for food rewards in a series of discriminations following acute administration of either vehicle, or CX516 (5–40 mg/kg, s.c.), or sertindole (1.25 mg/kg, perorally). The specific extradimensional deficits produced by sub-chronic or early postnatal PCP treatment were significantly attenuated by sertindole and dose-dependently by CX516. Findings here further establish PCP treatment as model of executive functioning deficits related to schizophrenia and provide evidence that direct glutamatergic interventions could improve these, when assessed in the ID–ED attentional set-shifting task.
“Coffee plus Honey” versus “topical steroid” in the treatment of Chemotherapy-induced Oral Mucositis: a randomised controlled trial

Oral mucositis is one of the common complications of cancer chemotherapy and about 40% of the patients who take chemotherapy protocols, experience this irritating problem. The purpose of this study was to draw comparison between the therapeutic effects of our treatment modalities (topical steroid, honey, honey plus coffee) in patients suffering from oral mucositis.



This was a double blinded randomised clinical trial of a total of 75 eligible adult participants which they randomly fell into three treatment groups. For all the participants a syrup-like solution was prepared. Each 600 grams of the product consisted of "20 eight-mg Betamethasone solution ampoules" in the Steroid (S) group, "300 grams of honey plus 20 grams of instant coffee" in the Honey plus Coffee (HC) group, and "300 grams of honey" for the Honey (H) group. The participants were told to sip 10 ml of the prescribed product, and then swallow it every three hours for one week. Severity of lesions was clinically evaluated before the treatment and also one week after the initiation of the intervention. This study adhered to the principles of the Declaration of Helsinki and guidelines of Good Clinical Practice.



This study showed that all three treatment regimens reduce the severity of lesions. The best reduction in severity was achieved in HC group. H group and S group took the second and third places. In other words, honey plus coffee regimen was the most effective modality for the treatment of oral mucositis.



Oral mucositis can be successfully treated by a combination of honey and coffee as an alternative medicine in a short time. Further investigations are warranted in this field.
PTV margin definition in hypofractionated IGRT of localized prostate cancer using cone beam CT and orthogonal image pairs with fiducial markers

To evaluate PTV margins for hypofractionated IGRT of prostate comparing kV/kV imaging or CBCT.



Between 2009 and 2012, 20 patients with low- (LR), intermediate- (IR) and high-risk (HR) prostate cancer were treated with VMAT in supine position with fiducial markers (FM), endorectal balloon (ERB) and full bladder. CBCT's and kV/kV imaging were performed before and additional CBCT's after treatment assessing intra-fraction motion. CTVP for 5 patients with LR and CTVPSV for 5 patients with IR/HR prostate cancer were contoured independently by 3 radiation oncologists using MRI. The van Hark formula (PTV margin =2.5Σ +0.7σ) was applied to calculate PTV margins of prostate/seminal vesicles (P/PSV) using CBCT or FM.



172 and 52 CBCTs before and after RT and 507 kV/kV images before RT were analysed. Differences between FM in CBCT or in planar kV image pairs were below 1 mm. Accounting for both random and systematic uncertainties anisotropic PTV margins were 5-8 mm for P (LR) and 6-11 mm for PSV (IR/HR). Random uncertainties like intra-fraction and inter-fraction (setup) uncertainties were of similar magnitude (0.9-1.4 mm). Largest uncertainty was introduced by CTV delineation (LR: 1-2 mm, IR/HR: 1.6-3.5 mm). Patient positioning using bone matching or ERB-matching resulted in larger PTV margins.



For IGRT CBCT or kV/kV-image pairs with FM are interchangeable in respect of accuracy. Especially for hypofractionated RT, PTV margins can be kept in the range of 5 mm or below if stringent daily IGRT, ideally including prostate tracking, is applied. MR-based CTV delineation optimization is recommended.
Impact of sinus surgery on pseudomonal airway colonization, bronchiolitis obliterans syndrome and survival in cystic fibrosis lung transplant recipients.

Lung transplantation (LTx) is a therapy for patients with cystic fibrosis (CF) end-stage lung disease. Pseudomonal airway colonization (PAC) is common in CF.



We investigated the influence of post-transplant sinus surgery and daily nasal douching on PAC after LTx and the influence of PAC on survival and bronchiolitis obliterans syndrome (BOS).



CF patients transplanted at our centre were included (November 1992 to December 2009). Clinical data, including microbiological data before and after LTx were collected. Survival and BOS following LTx were compared for CF recipients with and without PAC by Kaplan-Meier statistics and Cox regression analysis.



Ninety-four CF patients were transplanted, of whom 82 (87%) underwent sinus surgery after transplantation, and 65% of 66 patients with pre-transplant PAC had persistent PAC after transplantation. Upper and lower PAC is related. Patients without PAC after transplantation had a significantly better survival rate, and BOS was less frequent with a later onset. PAC was the only significant parameter for the development of BOS stage 2 in the multivariate analysis for cytomegalovirus infection, acute rejection and PAC.



Sinus surgery and daily nasal douching reduced PAC in LTx recipients. Absence of post-transplant PAC had a positive impact on post-transplant survival and the development of BOS.
Measuring Stroke Impact with SIS: Construct Validity of SIS Telephone Administration

The purpose of this study was to examine the construct validity of the Stroke Impact Scale (SIS) using telephone mode of administration.  Stroke patients were identified using national VA administrative data and ICD-9 codes in 13 participating VA hospitals. Stroke was confirmed by reviewing electronic medical records. Patients were administered SIS by telephone at 12-weeks post-stroke, and administered the Functional Independence Measure (FIM) and SF-36V at 16 weeks post-stroke. The instrument’s convergent validity and its ability to differentiate between groups of stroke patients with different disability levels were examined using Pearson’s correlations and Kruskal–Wallis one way ANOVA tests.  All the relevant relationships yielded high correlation coefficients with statistical significance: 0.86 for FIM-motor vs. SIS-ADL, and 0.77 for PF in SF-36V vs. SIS-PHYSICAL. The SIS presented better score discrimination and distribution for different severity of stroke than FIM and SF-36V without severe ceiling and floor effects. Kruskal–Wallis tests showed the Physical Component Score of SF-36V did not discriminate any disability levels. Physical functioning (PF) in SF-36V, FIM-motor, SIS-PHYSICAL, SIS-16, and SIS-ADL showed better discrimination in person’s functioning. The pairwise comparisons showed that SIS-PHYSICAL, SIS-16, and SIS-ADL discriminated more Rankin levels than FIM-motor and PF in SF-36V. Conclusions: SIS telephone survey had superior convergent validity and was better at differentiating between groups of stroke patients with different disability levels than the FIM and SF-36V with no evidence of ceiling and floor effects. Telephone administration of SIS would be a useful and cost-effective method to follow-up community dwelling veterans with stroke.
A phase II trial of prolonged, continuous infusion of low-dose gemcitabine plus cisplatin in patients with advanced malignant pleural mesothelioma

Low-dose, prolonged infusion of gemcitabine has effects similar to standard doses in several cancers. We evaluated the toxicity and efficacy of low-dose gemcitabine in prolonged infusion plus cisplatin in patients with advanced pleural mesothelioma. Patients with mesothelioma received gemcitabine (250 mg/m2) in a 6-h infusion plus cisplatin (35 mg/m2) on days 1 and 8 every three weeks. We used the modified response evaluation criteria in solid tumours.  We included 39 patients; 82.1 % were low risk according to the European Organisation for Research and Treatment of Cancer prognostic group. Partial response was observed in 53.8 % (21/39), stable disease in 33.3 % (13/39) and progression in 12.8 % (5/39). The median progression-free survival was 6.9 months (95 % CI 3.2–10.6 months), and the associated factors were the EORTC risk and histology. The median overall survival was 20.7 months (95 % CI 10.7–30.8 months). The functional, physical and emotional roles and dyspnoea, insomnia and pain symptom scales improved. The most commonly graded 3/4 side effects were neutropenia (24.4 %), lymphopenia (14.6 %), thrombocytopenia (14.7 %) and anaemia (12.2 %). Low-dose, prolonged gemcitabine infusion plus cisplatin has acceptable toxicity and high efficacy with improved quality of life, representing an affordable regimen for the low-income population.
Serum procalcitonin and CRP levels in non-alcoholic fatty liver disease: a case control study

Both C reactive protein (CRP) and procalcitonin (PCT) are well known acute phase reactant proteins. CRP was reported to increase in metabolic syndrome and type-2 diabetes. Similarly altered level of serum PCT was found in chronic liver diseases and cirrhosis. The liver is considered the main source of CRP and a source of PCT, however, the serum PCT and CRP levels in non-alcoholic fatty liver disease (NAFLD) were not compared previously. Therefore we aimed to study the diagnostic and discriminative role of serum PCT and CRP in NAFLD.



Fifty NAFLD cases and 50 healthy controls were included to the study. Liver function tests were measured, body mass index was calculated, and insulin resistance was determined by using a homeostasis model assessment (HOMA-IR). Ultrasound evaluation was performed for each subject. Serum CRP was measured with nephalometric method. Serum PCT was measured with Kryptor based system.



Serum PCT levels were similar in steatohepatitis (n 20) and simple steatosis (n 27) patients, and were not different than the control group (0.06 +/- 0.01, 0.04 +/- 0.01 versus 0.06 +/- 0.01 ng/ml respectively). Serum CRP levels were significantly higher in simple steatosis, and steatohepatitis groups compared to healthy controls (7.5 +/- 1.6 and 5.2 +/- 2.5 versus 2.9 +/- 0.5 mg/dl respectively p < 0.01). CRP could not differentiate steatohepatitis from simple steatosis. Beside, three patients with focal fatty liver disease had normal serum CRP levels.



Serum PCT was within normal ranges in patients with simple steatosis or steatohepatitis and has no diagnostic value. Serum CRP level was increased in NAFLD compared to controls. CRP can be used as an additional marker for diagnosis of NAFLD but it has no value in discrimination of steatohepatitis from simple steatosis.
Factors in the Efficacy, Safety, and Impact on Quality of Life for Treatment of Drooling with Botulinum Toxin Type A in Patients with Cerebral Palsy.

To assess the efficacy and safety of botulinum toxin A (BoNT-A) injected in both submandibular and parotid versus only in parotid glands as a treatment for drooling in patients with spastic and dyskinetic cerebral palsy (CP), including an assessment of impact on quality of life (QoL) based on items from the International Classification of Functioning, Disability, and Health (ICF) core set.



Forty patients with CP 18 years or older (mean, 21.8 years) participated in a prospective, single-center, randomized controlled interventional study. All participants were classified as Gross Motor Function Classification System level III or higher and all had significant drooling as defined in prior studies. One group (group A) was treated with 100 U of BoNT-A, and another group (group B) served as control. In the treatment group, all patients first received combined parotid and submandibular injections, and then parotid injections only. The main outcome variables were a postinjection decrease in the drooling quotient (DQ) of 50% or more, total flow of 30% or more, and QoL as assessed by a set of 10 items related to drooling from the ICF.



The proportion of patients who achieved at least 50% reduction in DQ was 45% in group A versus 0.0% in group B; 0.0% (P = 0.0012); and of those who achieved at least 30% reduction in total flow was 90% in group A versus 10% in group B (P < 0.0001). Within group A, 42.1% of the dyskinetic patients versus 58.0% of the spastic ones showed 50% or better response in DQ, which is not a statistically significant difference (P = 0.8045). With regard to ICF questions, group A showed statistically significant improvements in several related items. There did not seem to be a significant difference in overall response for providing parotid-only injections. Additional correlations and uncommon adverse effect experiences are also reviewed.



Botulinum toxin A injection of the salivary glands is frequently effective and generally safe for the treatment of drooling in patients with either spastic or dyskinetic CP, both in objective measurement of saliva production and subjective symptoms related to the condition. There does not seem to be a significant advantage of injecting both submandibular and parotid glands over injecting parotid glands alone.
Long-term treatment of pulmonary hypertension with aerosolized iloprost.

Pulmonary arterial hypertension (PAH), defined as elevated pulmonary arterial pressure and pulmonary vascular resistance, is an end-point of a variety of conditions. The only therapy that has been shown to improve both quality of life and survival is intravenous prostacyclin (prostaglandin I2 (PGI2), epoprostenol). The effect of long-term aerosolized iloprost (Ilomedin, Schering, Berlin, Germany and Vienna, Austria), a stable prostacyclin analogue and potent vasodilator, on haemodynamics and functional status was investigated in 12 patients with severe pulmonary hypertension. Haemodynamic measurements and vasodilator testing by right heart catheterization were performed prior to and after long-term iloprost inhalation therapy. Haemodynamic improvement or increased exercise tolerance was not observed in any of the patients. After a mean+/-SD treatment period of 10+/-5 months, mean+/-SD pulmonary vascular resistance had increased from 11+/-3 Wood Units (mmHg.L(-1).min) to 13+/-4 Wood Units, with unchanged arterial oxygen saturation (92+/-4%, versus 91+/-4%). Within the study period, three patients went into right heart failure and had to be placed on intravenous epoprostenol. The authors conclude that inhaled iloprost in addition to conventional therapy in the presently recommended dose of 100 microg.day(-1) delivered in 8-10 2 h portions, is not an efficient vasodilator therapy in severe pulmonary hypertension. It remains to be shown whether dose increases and/or combination protocols will be effective, or whether inhalation of iloprost may be safe for selected cases of pulmonary hypertension.
Initial and long-term evaluation of patients with Alzheimer’s after hospitalization in cognitive and behavioural units: the EVITAL study design

Alzheimer's disease and related disorders are characterized by cognitive impairment associated with behavioral and psychological symptoms of dementia. These symptoms have significant consequences for both the patient and his family environment. While risk factors for behavioral disorders have been identified in several studies, few studies have focused on the evolution of these disorders. Moreover, it is important to identify factors linked to the long-term evolution of behavioral disorders, as well as patients' and caregivers' quality of life. Our purpose is to present the methodology of the EVITAL study, which primary objective is to determine the factors associated with the evolution of behavioral disorders among patients with Alzheimer's disease and related disorders during the year following their hospitalization in cognitive and behavioral units. Secondary objectives were 1) to assess the factors related to the evolution of behavioral disorders during hospitalization in cognitive and behavioral units; 2) to identify the factors linked to patients' and caregivers' quality of life, as well as caregivers' burden; 3) to assess the factors associated with rehospitalization of the patients for behavioral disorders in the year following their hospitalization in cognitive and behavioral units.



A multicenter, prospective cohort of patients with Alzheimer's disease and related disorders as well as behavioral disorders who are hospitalized in cognitive and behavioral units. The patients will be included in the study for a period of 24 months and followed-up for 12 months. Socio-demographic and environmental data, behavioral disorders, medications, patients and caregivers quality of life as well as caregivers burden will be assessed throughout hospitalization in cognitive and behavioral units. Follow-up will be performed at months 3, 6 and 12 after hospitalization. Socio-demographic and environmental data, behavioral disorders, medications, patients and caregivers quality of life, unplanned rehospitalization as well as caregivers burden will also be assessed at each follow-up interview.



The present study should help better identify the factors associated with reduction or stabilization of the behavioral and psychological symptoms of dementia in patients with Alzheimer's disease. It could therefore help clinicians to better manage these symptoms.
Concept-Based Relevance Models for Medical and Semantic Information Retrieval

Relevance models provide an important approach for estimating probabilities of words in the relevant class. However, the associated bag-of-words assumption breaks dependencies between words, especially between those within a phrase. If such dependencies could be preserved, it would permit matching the query terms with document terms having the same dependencies. Additionally, during the estimation of relevance, relevance models are unable to distinguish relevant and non-relevant information in a feedback document, and hence take the entire document into account, which potentially hurts the accuracy of estimation. In this paper, we define the notion of "concept", and design a concept-based information retrieval framework. Using this framework, we transform documents and queries from term space into concept space, and propose a concept-based relevance model for improved estimation of relevance. Our approach has three advantages. First, this approach only assumes independence between concepts, so is able to keep the strong dependencies between the words of a concept. Second, it unifies synonyms or different surface forms of a concept, leading to reduced dimensionality of the space, increased sample size of a concept, and consequently more accurate and reliable estimates of the relevance. Third, when knowledge bases are available, our approach enables the semantic analysis of query concepts, and thus identifies concepts related to the query, from which a more accurate distribution of relevance can be estimated. This work is aligned with semantic search methods.
 We apply our concept-based relevance model to information retrieval in the medical domain, where concepts are abundant and their variations are numerous. We compare with relevance models, BM25 with pseudo relevance feedback, and the state of the art conceptual language models, on several data collections. The proposed model demonstrates consistent and statistically significant improvements across collections, outperforming top benchmark conceptual language models by at least 9% and up to 20% on a number of metrics.
A multicenter, retrospective study of acute kidney injury in adult patients with nonmyeloablative hematopoietic SCT

Acute kidney injury (AKI) is a common early complication in patients with hematopoietic SCT (HSCT). However, there are limited data about the incidence and risk factors of AKI in patients with nonmyeloablative HSCT. We conducted a multicenter, retrospective cohort study of 62 patients from three institutions who were treated with similar protocols for nonmyeloablative HSCT. AKI was classified according to the Acute Kidney Injury Network criteria. It was shown that 29% of the patients developed AKI in the first 100 days after nonmyeloablative HSCT. The risk factor at baseline for AKI was incomplete HLA-matched transplant (odds ratio (OR) 3.6; 95% confidence interval (CI) 1.1–13.0). Complications such as acute GVHD, veno-occlusive disease of liver and sepsis were also associated with the development of AKI (OR 12.1; 95% CI 2.4–62.4). AKI was significantly associated with mortality (OR=4.7; 95% CI 1.9–11.5). We concluded that AKI is a very common complication in patients with nonmyeloablative HSCT, which is associated with incomplete HLA-matched transplant and complications, and has an important impact on the patients’ first year of survival.
Local Tree-Width, Excluded Minors, and Approximation Algorithms

The local tree-width of a graphG = (V, E) is the function ltw : N → N that associates with every∈ N the maximal tree-width of an r-neighborhood in G. Our main graph theoretic result is a decomposition theorem for graphs with excluded minors that essentially says that such graphs can b e decomposed into trees of graphs of bounded local tree-width. As an application of this theorem, we show that a number of com binatorial optimization problems, such as M INIMUM VERTEX COVER, M INIMUM DOMINATING SET, and MAXIMUM INDEPENDENTSET have a polynomial time approximation scheme when restricted to a class of graphs with an excluded minor.