nils-herrmann/clean_scirepeval huggingface dataset:
Biologic therapies and bone loss in rheumatoid arthritis
Venue: Osteoporosis International

IntroductionRheumatoid arthritis (RA) is a common systemic autoimmune disease of unknown cause, characterized by a chronic, symmetric, and progressive inflammatory polyarthritis. One of the most deleterious effects induced by the chronic inflammation of RA is bone loss. During the last 15 years, the better knowledge of the cytokine network involved in RA allowed the development of potent inhibitors of the inflammatory process classified as biological DMARDs. These new drugs are very effective in the inhibition of inflammation, but there are only few studies regarding their role in bone protection. The principal aim of this review was to show the evidence of the principal biologic therapies and bone loss in RA, focusing on their effects on bone mineral density, bone turnover markers, and fragility fractures.MethodsUsing the PICOST methodology, two coauthors (PC, LM S) conducted the search using the following MESH terms: rheumatoid arthritis, osteoporosis, clinical trials, TNF antagonists, infliximab, adalimumab, etanercept, certolizumab, golimumab, IL 6 antagonists, IL 1 antagonists, abatacept, tocilizumab, rituximab, bone mineral density, bone markers, and fractures. The search was conducted electronically and manually from the following databases: Medline and Science Direct. The search period included articles from 2003 to 2015. The selection included only original adult human research written in English. Titles were retrieved and the same two authors independently selected the relevant studies for a full text. The retrieved selected studies were also reviewed completing the search for relevant articles. The first search included 904 titles from which 253 titles were selected. The agreement on the selection among researchers resulted in a Kappa statistic of 0.95 (p 0.000) Only 248 abstracts evaluated were included in the acronym PICOST. The final selection included only 28 studies, derived from the systematic search. Additionally, a manual search in the bibliography of the selected articles was made and included into the text and into the section of "small molecules of new agents."ConclusionTreatment with biologic drugs is associated with the decrease in bone loss. Studies with anti TNF blocking agents show preservation or increase in spine and hip BMD and also a better profile of bone markers. Most of these studies were performed with infliximab. Only three epidemiological studies analyzed the effect on fractures after anti TNF blocking agent's treatment. IL 6 blocking agents also showed improvement in localized bone loss not seen with anti TNF agents. There are a few studies with rituximab and abatacept. Although several studies reported favorable actions of biologic therapies on bone protection, there are still unmet needs for studies regarding their actions on the risk of bone fractures.
Progress Towards Treatment and Cure of Epidermolysis Bullosa: Summary of the DEBRA International Research Symposium EB2015
Venue: The Journal of investigative dermatology

Epidermolysis bullosa (EB) a group of complex heritable blistering diseases, is the topic of triennial research meetings organized by DEBRA International, the umbrella of patient advocacy organizations. The DEBRA 2015 Research Conference, held in May 2015, brought together investigators and clinicians from around the world working at the forefront of EB research. Discussing the state of the art approaches from a wide range of disciplines, there was a palpable excitement at this conference brought about by the optimism about applying new sequencing techniques, genome editing, protein replacement, autologous and allogeneic stem cell therapy, innovations in cancer biology, revertant mosaicism and iPSC techniques, all of which are aimed at developing new therapies for EB. Many in the field who have participated in EB research for many years were especially enthusiastic and felt that, possibly for the first time, the field seems uniquely poised to bring these new tools to effectively tackle EB using multiple complementary approaches towards improved quality of life and eventually a cure for patients suffering from EB, a currently intractable disease.
El cuidado en la teoria del reconocimiento de Honneth. Repercusiones en las personas con diversidad funcional

In the theory of justice as recognition by Honneth, w e find a connection between care and justice. The aim of this article is to study this connection and the repercusion of this theory for people with functional diversity. This article p resents the afective recognition in the primary relationship as it is exposed by Honneth. Furthermore, this article defends to extend it, considering the volunteers and assistant professionals.
Training the trainers: beyond providing a well received course
Venue: Education for primary care an official publication of the Association of Course Organisers, National Association of GP Tutors, World Organisation of Family Doctors

The Royal College of General Practitioners in partnership with the South African Academy of Family Physicians obtained funding to run a series of 'Training the Trainers' courses for trainers of family medicine registrars, with a view to strengthening clinical supervision of postgraduate registrars. The authors wanted to establish whether it was worthwhile for the course to be provided on an ongoing basis after the funded project was completed.  Development of a pilot tool for evaluation visits after a faculty development course.  The authors developed a pre visit pack and conducted five site visits to registrar trainers who had been on the course between 12 and 24 months earlier. Before the series of visits and after each visit we debriefed and modified our approach.  Optimising the use of the pre visit pack will require greater orientation of the trainer. Administrative support for the visits will be vital. The visits were experienced very positively. However, in a context in which these visits are not the norm, the trainers need support and encouragement to participate in an activity which made them feel quite vulnerable.  The tool enabled course participants to show evidence of their behaviour change, enabled their colleagues to report on the impact on their own teaching practices, and enabled registrars to voice their opinions of their trainer's supervision skills. A post course formative evaluation visit has the potential to catalyse the impact of the training course. It will be necessary to train the family physicians who conduct these visits.
Towards 3D reconstruction of outdoor scenes by mmw radar and a vision sensor fusion

The main goal of this PhD work is to develop 3D mapping methods of large scale environment by combining panoramic radar and cameras. Unlike existing sensor fusion methods, such as SLAM (simultaneous localization and mapping) we want to build a RGB D sensor which directly provides depth measurement enhanced with texture and color information.After modeling the geometry of the radar/camera system, we propose a novel calibration method using points correspondences. To obtain these points correspondences, we designed special targets allowing accurate point detection by both the radar and the camera. The proposed approach has been developed to be implemented by non expert operators and in unconstrained environment.Secondly, a 3D reconstruction method is elaborated based on radar data and image point correspondences. A theoretical analysis is done to study the influence of the uncertainty zone of each sensor on the reconstruction method. This theoretical study, together with the experimental results, show that the proposed method outperforms the conventional stereoscopic triangulation for large scale outdoor scenes.Finally, we propose an efficient strategy for automatic data matching. This strategy uses two calibrated cameras. Taking into account the heterogeneity of cameras and radar data, the developed algorithm starts by segmenting the radar data into polygonal regions. The calibration process allows the restriction of the search by defining a region of interest in the pair of images. A similarity criterion based on both cross correlation and epipolar constraint is applied in order to validate or reject region pairs. While the similarity test is not met, the image regions are re segmented iteratively into polygonal regions, generating thereby a shortlist of candidate matches. This process promotes the matching of large regions first which allows obtaining maps with locally dense patches.The proposed methods were tested on both synthetic and real experimental data. The results are encouraging and prove the feasibility of radar and vision sensor fusion for the 3D mapping of large scale urban environment.
The ability of apolipoprotein E fragments to promote intraneuronal accumulation of amyloid beta peptide 42 is both isoform and size specific
Venue: Scientific reports

The apolipoprotein (apo) E4 isoform is the strongest risk factor for late onset Alzheimer's disease (AD) ApoE4 is more susceptible to proteolysis than apoE2 and apoE3 isoforms and carboxyl terminal truncated apoE4 forms have been found in AD patients' brain. We have previously shown that a specific apoE4 fragment, apoE4 165, promotes amyloid peptide beta 42 (Ab42) accumulation in human neuroblastoma SK N SH cells and increased intracellular reactive oxygen species formation, two events considered to occur early in AD pathogenesis. Here, we show that these effects are allele dependent and absolutely require the apoE4 background. Furthermore, the exact length of the fragment is critical since longer or shorter length carboxyl terminal truncated apoE4 forms do not elicit the same effects. Structural and thermodynamic analyses showed that apoE4 165 has a compact structure, in contrast to other carboxyl terminal truncated apoE4 forms that are instead destabilized. Compared however to other allelic backgrounds, apoE4 165 is structurally distinct and less thermodynamically stable suggesting that the combination of a well folded structure with structural plasticity is a unique characteristic of this fragment. Overall, our findings suggest that the ability of apoE fragments to promote Ab42 intraneuronal accumulation is specific for both the apoE4 isoform and the particular structural and thermodynamic properties of the fragment.
Expression of the Alzheimer's Disease Mutations AbPP695sw and PSEN1M146I in Double Transgenic Gottingen Minipigs.
Venue: Journal of Alzheimer's disease JAD

Mutations in the amyloid b protein precursor gene (AbPP) the presenilin 1 gene (PSEN1) or the presenilin 2 gene (PSEN2) that increase production of the AbPP derived peptide Ab42 cause early onset Alzheimer's disease. Rodent models of the disease show that further increase in Ab42 production and earlier brain pathology can be obtained by coexpressing AbPP and PSEN1 mutations. To generate such elevated Ab42 level in a large animal model, we produced Gottingen minipigs carrying in their genome one copy of a human PSEN1 cDNA with the Met146Ile (PSEN1M146I) mutation and three copies of a human AbPP695 cDNA with the Lys670Asn/Met671Leu (AbPPsw) double mutation. Both transgenes were expressed in fibroblasts and in the brain, and their respective proteins were processed normally. Immunohistochemical staining with Ab42 specific antibodies detected intraneuronal accumulation of Ab42 in brains from a 10 and an 18 month old pig. Such accumulation may represent an early event in the pathogenesis of Alzheimer's disease.
An Evolutionary Discrete Firefly Algorithm with Novel Operators for Solving the Vehicle Routing Problem with Time Windows
Venue: Nature Inspired Computation in Engineering

An evolutionary discrete version of the Firefly Algorithm (EDFA) is presented in this chapter for solving the well known Vehicle Routing Problem with Time Windows (VRPTW) The contribution of this work is not only the adaptation of the EDFA to the VRPTW, but also with some novel route optimization operators. These operators incorporate the process of minimizing the number of routes for a solution in the search process where node selective extractions and subsequent reinsertion are performed. The new operators analyze all routes of the current solution and thus increase the diversification capacity of the search process (in contrast with the traditional node and arc exchange based operators) With the aim of proving that the proposed EDFA and operators are effective, some different versions of the EDFA are compared. The present work includes the experimentation with all the 56 instances of the well known VRPTW set. In order to obtain rigorous and fair conclusions, two different statistical tests have been conducted.
Phosphorus in the coarse soil fraction is related to soil organic phosphorus mineralization measured by isotopic dilution

A sound prediction of soil organic phosphorus (Po) mineralization would be helpful to improve fertilizer recommendations. However, in most mineral soils expensive and time consuming isotopic dilution experiments are required to assess Po mineralization. A proposed method to estimate Po mineralization is the quantification of P in the coarse fraction (CF, >53 mm) of the soil. The aim of this study was to evaluate if P in the CF can effectively predict Po mineralization. Soil samples from three North American long term arable field experiments >10 years) with different textures (sand content 15 82% and different fertilization treatments (non P fertilized, mineral P fertilizer, poultry litter) were analyzed. Soil samples were physically fractioned into CF and fine fraction (FF, <53 mm) Total P (Pt) Po, and total carbon (Ct) were determined in each fraction. Gross and net Po mineralization rates as well as soil respiration were determined in a 13 day incubation experiment. The cumulative gross Po mineralization over 13 days ranged from 8.3 to 38.6 mg P kg 1, while Pt in CF varied between 9.7 and 90.7 mg P kg 1 and Po in CF between 6.1 and 17.7 mg kg 1. No association between Pt in CF and gross or net mineralized Po was observed. However, a significant linear relationship between Po in CF and net (R2:0.68, p 0.01) and gross mineralized Po (R2:0.72, p 0.01) was observed after 6 days and 13 days of incubation. Additionally, gross and net mineralized Po could also be predicted from C respiration, and these models were significantly improved by incorporating the Ct:Po ratio of the CF. Our results suggest that the quantification of Po in the CF as well as the measurement of respiration corrected by the Ct:Po ratio of the CF are promising non isotopic indicators of Po mineralization rates.
3D pharmacophore based virtual screening, docking and density functional theory approach towards the discovery of novel human epidermal growth factor receptor 2 (HER2) inhibitors.
Venue: Journal of theoretical biology

Human epidermal growth factor receptor 2 (HER2) is one of the four members of the epidermal growth factor receptor (EGFR) family and is expressed to facilitate cellular proliferation across various tissue types. Therapies targeting HER2, which is a transmembrane glycoprotein with tyrosine kinase activity, offer promising prospects especially in breast and gastric/gastroesophageal cancer patients. Persistence of both primary and acquired resistance to various routine drugs/antibodies is a disappointing outcome in the treatment of many HER2 positive cancer patients and is a challenge that requires formulation of new and improved strategies to overcome the same. Identification of novel HER2 inhibitors with improved therapeutics index was performed with a highly correlating (r=0.975) ligand based pharmacophore model (Hypo1) in this study. Hypo1 was generated from a training set of 22 compounds with HER2 inhibitory activity and this well validated hypothesis was subsequently used as a 3D query to screen compounds in a total of four databases of which two were natural product databases. Further, these compounds were analyzed for compliance with Veber's drug likeness rule and optimum ADMET parameters. The selected compounds were then subjected to molecular docking and Density Functional Theory (DFT) analysis to discern their molecular interactions at the active site of HER2. The findings thus presented would be an important starting point towards the development of novel HER2 inhibitors using well validated computational techniques.
KONUT VE YERLESIM ALANI KULLANICI ALGISININ MEMNUNIYET VE TERCIH DAVRANISINA ETKISI UZERINE BIR ARASTIRMADA AMASYA ORNEGI

Konut ve cevresinden memnuniyet, insanlarin yasadiklari cevreye verdikleri yanitlarini yansitmaktadir. Bu calismada konut cevresi ve konut seciminde, kullanicilarin tercihinde etkili olan degiskenlerin bireylerin davranislarina ne olcude yansidigi konu edinilmistir. orneklem alani olarak Amasya kenti secilmis ve analiz calismalari bes farkli konut alaninda 9 konut sitesinde anket calismasi ve alanda yapilan gozlemler ile gerceklestirilmistir. Elde edilen verilerin analizleri sonucunda kullanicilarin sosyal, ekonomik ve kulturel degismelerine bagli tepki olarak kabul edilebilecek memnuniyet duygusunda anlamlanan kavramsal bir model olusturulmustur. Anket verileri SPSS 20.0 (Statistical Package for Social Sciences) ile elde edilen ampirik bulgular, kentsel mekandaki hane halkinin, sosyo ekonomik ve demografik gostergelerine gore konut yer seciminde, tercihinin de degistigini ortaya koymustur. Arastirmada olusturulan kavramsal modelin gelecekte konut ve cevresel kalite memnuniyeti konusunda calisma yapacak diger arastirmacilara isik tutacagi dusunulmektedir.
Neural speech recognition: continuous phoneme decoding using spatiotemporal representations of human cortical activity.
Venue: Journal of neural engineering

The superior temporal gyrus (STG) and neighboring brain regions play a key role in human language processing. Previous studies have attempted to reconstruct speech information from brain activity in the STG, but few of them incorporate the probabilistic framework and engineering methodology used in modern speech recognition systems. In this work, we describe the initial efforts toward the design of a neural speech recognition (NSR) system that performs continuous phoneme recognition on English stimuli with arbitrary vocabulary sizes using the high gamma band power of local field potentials in the STG and neighboring cortical areas obtained via electrocorticography.  The system implements a Viterbi decoder that incorporates phoneme likelihood estimates from a linear discriminant analysis model and transition probabilities from an n gram phonemic language model. Grid searches were used in an attempt to determine optimal parameterizations of the feature vectors and Viterbi decoder.  The performance of the system was significantly improved by using spatiotemporal representations of the neural activity (as opposed to purely spatial representations) and by including language modeling and Viterbi decoding in the NSR system.  These results emphasize the importance of modeling the temporal dynamics of neural responses when analyzing their variations with respect to varying stimuli and demonstrate that speech recognition techniques can be successfully leveraged when decoding speech from neural signals. Guided by the results detailed in this work, further development of the NSR system could have applications in the fields of automatic speech recognition and neural prosthetics.
Environment and evolution modulate plant virus pathogenesis.
Venue: Current opinion in virology

The study of plant viruses has focussed on those causing diseases in crops and, only recently, in wild plants. However, increasing evidence shows that plant viruses often are neutral, or even beneficial, for their hosts. Thus, plant viruses can be conditional mutualists, although the underlying mechanisms have been seldom analyzed. Little is known about what environmental factors modulate virus pathogenesis, and how. A major factor can be higher horizontal transmission rates in agricultural than in wild ecosystems. However, ecosystem simplification in human managed habitats may result in changed epidemiological factors that influence pathogenesis. The interplay between ecology, evolution and pathogenesis awaits further research.
Students' perceptions of teachers' interpersonal behaviour across four different school subjects: control is good but affiliation is better

Many researchers have pointed out that teachers' interpersonal behaviour relates to students' positive attitudes towards schooling. However, only few studies have examined whether students' perceptions of their teachers' interpersonal behaviour relates to students' subject related attitudes across different school subjects. In this study, it was investigated to what extent the interpersonal behaviours of secondary school teachers are perceived differently by the students as a function of the school subject being taught and whether such perceptions coincide with students' attitudes towards the subject matter, after controlling for students' achievement. To address these research questions, 2305 adolescent students (47.1% males; Mage 17.85; SD 1.09) from grades 9 to 11 and their teachers (N 42; 38.1% males; mean years of teaching 14.2; SD 1.25) from one urban high school in Turkey were surveyed. The students completed the Questionnaire on Teacher Interaction and attitude questions. Multilevel data analysis showed that Control related to positive attitudes among students in classes grouped under the science, and literature and language domains, but not in classes grouped under the arts and sports domain. Perceived Affiliation, on the other hand, was positively associated with all the four subject domains (science, social sciences, literature and language, and arts and sports) These results show the importance of taking a multidisciplinary perspective in in service training programmes for secondary school science teachers as they emphasise the differential roles that control as an interpersonal behavioural style may play on students' attitudes in certain subject matters.
Bifidobacteria Abundance Featured Gut Microbiota Compositional Change in Patients with Behcet's Disease
Venue: PloS one

Gut microbiota compositional alteration may have an association with immune dysfunction in patients with Behcet's disease (BD) We conducted a fecal metagenomic analysis of BD patients. We analyzed fecal microbiota obtained from 12 patients with BD and 12 normal individuals by sequencing of 16S ribosomal RNA gene. We compared the relative abundance of bacterial taxa. Direct comparison of the relative abundance of bacterial taxa demonstrated that the genera Bifidobacterium and Eggerthella increased significantly and the genera Megamonas and Prevotella decreased significantly in BD patients compared with normal individuals. A linear discriminant analysis of bacterial taxa showed that the phylum Actinobacteria, including Bifidobacterium, and the family Lactobacillaceae exhibited larger positive effect sizes than other bacteria in patients with BD. The phylum Firmicutes and the class Clostridia had large effect sizes in normal individuals. There was no significant difference in annotated species numbers (as numbers of operational taxonomic unit; OTU) and bacterial diversity of each sample (alpha diversity) between BD patients and normal individuals. We next assigned each sample to a position using three axes by principal coordinates analysis of the OTU table. The two groups had a significant distance as beta diversity in the 3 axis space. Fecal sIgA concentrations increased significantly in BD patients but did not correlate with any bacterial taxonomic abundance. These data suggest that the compositional changes of gut microbes may be one type of dysbiosis (unfavorable microbiota alteration) in patients with BD. The dysbiosis may have an association with the pathophysiology of BD.