nils-herrmann/clean_scirepeval huggingface dataset:
Evaluation of Expression Profiles of Hematopoietic Stem Cell, Endothelial Cell, and Myeloid Cell Antigens in Spontaneous and Chemically Induced Hemangiosarcomas and Hemangiomas in Mice
Venue: Toxicologic pathology
Year: 2013

It is unclear whether the process of spontaneous and chemically induced hemangiosarcoma and hemangioma formation in mice involves the transformation of differentiated endothelial cells (ECs) or recruitment of multipotential bone marrow derived hematopoietic stem cells or endothelial progenitor cells (EPCs) which show some degree of endothelial differentiation. In the present study, immunohistochemical staining for hematopoietic stem cell markers (CD45 and CD34) EC markers (vascular endothelial growth factor receptor 2 [VEGFR2] CD31, and factor VIII related antigen) and a myeloid lineage marker (CD14) was employed to better define the origin of hemangiosarcomas and hemangiomas in mice. Staining was negative for CD45, factor VIII related antigen, and CD14 and positive for CD34, VEGFR2, and CD31, indicating that mouse hemangiosarcomas and hemangiomas are composed of cells derived from EPCs expressing CD34, VEGFR2, and CD31 but not factor VIII related antigen. The lack of CD45 expression suggests that mouse vascular tumors may arise from EPCs that are at a stage later than hematopoietic stem cells. Since factor VIII related antigen expression is known to occur later than CD31 expression in EPCs, our observations may indicate that these tumor cells are arrested at a stage prior to complete differentiation. In addition, myeloid lineage cells do not appear to contribute to hemangiosarcoma and hemangioma formation in mice.
Human Rights in the Council of Europe and the EU: Towards 'Individual' 'Constitutional' or 'Institutional' Justice?
Year: 2009

The European Convention on Human Rights, promulgated by the Council of Europe in 1950, is widely regarded as the world's most successful experiment in the trans national judicial protection of human rights. The EU's much more recent judicial and political interest in human rights has also been widely welcomed. Yet, while the crisis currently afflicting the Convention system has not gone unnoticed, the same cannot equally be said of the difficulties presented by the increasing interpenetration of the two systems. Amongst the few who have shown some interest in these problems, the dominant view is that good will and common sense will provide adequate solutions. We disagree. Instead, we detect a gathering crisis which, unless properly analysed and effectively tackled, will only deepen as the EU's interest in human rights develops further. In our view, the problem is essentially conceptual and that, ultimately, it boils down to a much neglected question, simple to state but not so easy to answer: is the trans national protection of human rights in Europe a matter of 'individual' 'constitutional' or 'institutional' justice?
RESPONSIVENESS CAPABILITY IN THE INTERNATIONAL CLOTHING INDUSTRY: GLOBAL QUICK RESPONSE AND PLANNING POSTPONEMENT CAPABILITIES
Year: 2013

Responsiveness has been recognized as an essential strategy to enhance the capabilities of organizations as well as supply networks in the clothing industry to quickly and accurately respond to the changing market requirements. Although responsiveness embedded with several aspects including social concern, it has mostly been studied in terms of Quick Response (QR) initiatives in the clothing industry. However, as contemporary clothing industry operates globally, QR strategies need to be considered in the global context. With this wider context in mind, the concept of Global Quick Response (GQR) has been introduced. In order to make normative suggestions and to confirm this new theoretical concept of GQR, a measurement scale for GQR should be built up though none has paid the attention in the literature so far. Therefore, the first objective of this paper is to develop a measurement scale for GQR; and to validate the measurement properties of the same. Then, as responsiveness can also be enhanced through the planning postponement strategies, the second objective of this paper is to examine the association between the GQR and planning postponement capabilities. Data was collected from both strategic and operational level personnel in the clothing industry at the supply network level using mix research approach. A Multiple Discriminant Analysis was carried out taking the degree of GQR capability and Planning Postponement capability on board. The results uncovers that there is an association between GQR and Planning Postponement. The degree of GQR capability discriminates the Planning Postponement capability though the discriminating power is weak. Finally the paper makes important implications and suggestions for practitioners as well as for academics in order to enhance the responsiveness not only through GQR but also through planning postponement.  Clothing Industry, Global Quick Response, Postponement,
Optimising the mandatory reporting process for drivers admitted to an inpatient stroke rehabilitation unit
Venue: BMJ open quality
Year: 2018

Ontario physicians are legally obligated to report patients who may be medically unfit to drive to the Ministry of Transportation of Ontario (MTO) Currently at Toronto Rehabilitation Institute (TRI) there are no standardised processes for MTO reporting, resulting in inconsistent communication regarding driving with patients and between healthcare providers, redundant assessments and ultimately reduced patient satisfaction. TRI received 10 patient complaints regarding the driving reporting process in the 5 years prior to this project and a large number of patients were not being reported appropriately. The project aim was to use Lean Methods to achieve 100% reporting and optimise communication and education of drivers admitted to a 23 bed inpatient stroke rehabilitation unit. Interventions included process mapping, identification of wasteful steps and implementation of a standard work. Chart audits before and after implementation were performed. Value stream process mapping identified inconsistent reporting procedures and lack of use of the government issued driver reporting form. Following implementation of standard work processes, use of the MTO Medical Conditions Report Form increased from 0% to 100% Indication of whether drivers were reported to the MTO in Physical Medicine Rehabilitation consultation notes increased from 50% to 91% Identifying reported drivers in the discharge summary, of which patients receive a copy at the time of discharge, increased from 0% to 90% Physician satisfaction with the new standard work process was qualitatively assessed to be high, with no negative impacts reported. Lean methodology was effective for increasing the usage of the MTO Medical Conditions Report Form, documenting driver status in the initial Physical Medicine Rehabilitation consultation and indicating MTO reporting status in the discharge summary. Communication between healthcare providers regarding patients' driving status has been successfully standardised, resulting in improved coordination of care and a reduction in patient complaints to zero in the 14 months since implementation.
TOPCONS: consensus prediction of membrane protein topology
Venue: Nucleic Acids Res.
Year: 2009

TOPCONS (http:/topcons.net/ is a web server for consensus prediction of membrane protein topology. The underlying algorithm combines an arbitrary number of topology predictions into one consensus prediction and quantifies the reliability of the prediction based on the level of agreement between the underlying methods, both on the protein level and on the level of individual TM regions. Benchmarking the method shows that overall performance levels match the best available topology prediction methods, and for sequences with high reliability scores, performance is increased by ~10 percentage points. The web interface allows for constraining parts of the sequence to a known inside/outside location, and detailed results are displayed both graphically and in text format.
From crizotinib to lorlatinib: continuous improvement in precision treatment of ALK positive non small cell lung cancer
Venue: ESMO Open
Year: 2019

Patients with advanced non small cell lung cancer (NSCLC) have received first line chemotherapy with a platin based doublet in case of good performance status and with a single agent or well tolerated doublet in case of older age for many  3 Chemotherapy has been combined with bevacizumab or necitumumab in selected patients. Two major advances have changed this therapeutic landscape. The first change refers to the identification of driver mutations and the establishment of corresponding tyrosine kinase inhibitors (TKIs) as preferred first line therapy for patients harbouring these mutations in their tumours. The second change refers to the establishment of immune checkpoint inhibitors in routine clinical practice. Patients with driver negative NSCLC and good performance status nowadays receive first line therapies with either chemotherapy plus pembrolizumab or atezolizumab, pembrolizumab as single agent in case of PD L1 expression in =50% of tumour cells, or nivolumab plus ipilimumab in case of high tumour mutational load. Second line therapies are docetaxel (plus/minus nintedanib or ramucirumab) pemetrexed, erlotinib, afatinib or immune checkpoint inhibitors. The identification of driver mutations has affected both diagnosis and therapy of NSCLC.4 5 Advanced NSCLC is currently classified based on histology, immunohistochemistry and driver mutation status. Adenocarcinomas are routinely assessed for the presence of EGFR mutations, anaplastic lymphoma kinase (ALK) or ROS1 re arrangements, and BRAF mutations. Additional tests are performed based on both their availability and access to corresponding targeted drugs. Patients with driver mutation positive NSCLC receive corresponding TKIs as preferred first line therapy. ALK positive NSCLC is a representative example on how continuous improvements in precision treatment have been achieved. Here, we summarise the clinical establishment of ALK inhibitors for the treatment of patients with advanced NSCLC with focus on phase III trials. In 2007, a transforming ALK fusion gene was described in NSCLC.6 ALK fusion genes can be detected in approximately 4% of
Developing an Emergency Physician Productivity Index Using Descriptive Health Analytics
Venue: ICIMTH
Year: 2015

Emergency department (ED) crowding became a major barrier to receiving timely emergency care. At King Faisal Specialist Hospital and Research Center, Saudi Arabia, we identified variables and factors affecting crowding and performance to develop indicators to help evaluation and improvement. Measuring efficiency of work and activity of throughput processes; it was important to develop an ED physician productivity index. Data on all ED patients' encounters over the last six months of 2014 were retrieved and descriptive health analytics methods were used. Three variables were identified for their influence on productivity and performance; Number of Treated Patients per Physician, Patient Acuity Level and Treatment Time. The study suggested a formula to calculate the productivity index of each physician through dividing the Number of Treated Patients by Patient Acuity Level squared and Treatment Time to identify physicians with low productivity index and investigate causes and factors.
Mechatronics, Identification Tehnology, Industry 4.0 and Education
Venue: 2019 18th International Symposium INFOTEH JAHORINA (INFOTEH)
Year: 2019

Computing infrastructure is an ever changing category which influence of technology advancements is so obviously that can be see almost on daily level. This influence is very important especially in the fields of Mechatronics and Identification technology in creating environments for introducing concept of Industry 4.0. One of the approaches to overcoming this difference in the speed of the process in education and production services is continuously improving curricula with a particular emphasis on the introduction of identification technologies as one of the main features of the concept Industry 4.0. In this paper are described some of the experiences in applying this approach to study programs carried out at the Faculty of Technical Sciences, University of Novi Sad and College of Information and Electrical Engineering, China Agricultural University.
T cell and NK cell lymphomas in the lung.
Venue: Seminars in diagnostic pathology
Year: 2020

While the lung is frequently involved by systemic lymphoma, primary pulmonary lymphoma accounts for less than 1% of all extranodal ymphomas. In particular, T cell lymphoma is very rare in the lung, as a primary or secondary lesion. Patients with pulmonary T cell lymphoma usually present with cough, dyspnea, pain, fever, recurrent infections, and hemoptysis. Typical radiologic features include pulmonary nodules, consolidation, solid pulmonary opacities, cystic changes, hilar adenopathy, and pleural effusions. Patients with these clinical and radiologic findings are frequently presumed to have pneumonia and initially treated with empirical antibiotics. Therefore, CT guided needle biopsy, bronchoscopic examination, or even wedge biopsy should be considered when clinical symptoms show deterioration despite adequate antibiotic therapy. Precise pathologic diagnosis and molecular characterization are recommended in all cases, following the World Health Organization (WHO) classification. Principles of treatment typically vary with the different histologic types of T cell lymphoma.
Learning Tree based Deep Model for Recommender Systems
Venue: KDD
Year: 2018

Model based methods for recommender systems have been studied extensively in recent years. In systems with large corpus, however, the calculation cost for the learnt model to predict all user item preferences is tremendous, which makes full corpus retrieval extremely difficult. To overcome the calculation barriers, models such as matrix factorization resort to inner product form (i.e. model user item preference as the inner product of user, item latent factors) and indexes to facilitate efficient approximate k nearest neighbor searches. However, it still remains challenging to incorporate more expressive interaction forms between user and item features, e.g. interactions through deep neural networks, because of the calculation cost. In this paper, we focus on the problem of introducing arbitrary advanced models to recommender systems with large corpus. We propose a novel tree based method which can provide logarithmic complexity w.r.t. corpus size even with more expressive models such as deep neural networks. Our main idea is to predict user interests from coarse to fine by traversing tree nodes in a top down fashion and making decisions for each user node pair. We also show that the tree structure can be jointly learnt towards better compatibility with users' interest distribution and hence facilitate both training and prediction. Experimental evaluations with two large scale real world datasets show that the proposed method significantly outperforms traditional methods. Online A/B test results in Taobao display advertising platform also demonstrate the effectiveness of the proposed method in production environments.
The Herculean Echoes in Frankenstein
Year: 2018

Many critics have discussed the echoes of Faust and Prometheus in Mary Shelley's masterpiece Frankenstein, the Modern Prometheus, exploring the limits of ambition and rebelliousness and their moral implications. However, there is a mythological resemblance in this novel that has received almost no critical comment. In many ways, Victor's forlorn and unnatural creature offers poignant echoes of Hercules, the greatest and most fearsome of all the heroes in the Greek mythology, yet also one of the loneliest and most tragic figures in the Western canon.  Hercules; misfit; self sacrifice; majestic
An Open Source Robotic Platform for Ambient Assisted Living
Venue: AIRO@AI*IA
Year: 2015

Last years have seen a worldwide lengthening of life expectancy  and, as a consequence, an increment of advanced assistive solutions for integrated care models. In this context, ICT can enhance home assistance services for elderly people and thus, the economical burden for health care institutions. Indeed, recent studies report that 89% wish to stay at home for sentimental reasons or because they cannot afford nursing homes  In addition, the shortage of professional caregivers is a well known issue and relatives or friends must face with emotional distress negatively impacting also their productivity at work  In this perspective, home robots will play a crucial role. Not only they will keep their house safe by monitoring and detecting anomalies or sources of hazards but they can also be companions able to enhance their social life, e.g. by better connecting them with their relatives and friends. Examples of recent projects that have tried to develop such a kind of systems are Hobbit [4, 5] Astro [6, 7] and Giraffplus  The difficulties in creating a robust and reliable prototype and the encountered challenges in computer vision and autonomous robotics have been well explained in  This work aims at presenting an open source and practical solution for an autonomous robotic platform for home care. The final goal is to develop a set of artificial intelligence services for indoor autonomous and safe navigation, fall detection, people recognition, speech interaction and telepresence. In Section 2 and 3 respectively, the prototype and the tasks currently implemented are described. We have developed these functions in ROS: Robot Operating System [9] which provides many algorithms and a standard communication framework. The need for standards and open solutions have been already pointed out in  Future works are reported in Section 4: this project enables research in many fields like scene understanding, human robot interaction, socially assistive/intelligent robotics and sensor integration.
Negative effects on postural control after anterior cruciate ligament reconstruction as measured by the balance error scoring system.
Venue: Journal of sport rehabilitation
Year: 2013

Anterior cruciate ligament (ACL) reconstruction is the standard of care for individuals with ACL rupture. Balance deficits have been observed in patients with ACL reconstruction (ACLR) using advanced posturography, which is the current gold standard. It is unclear if postural control deficits exist when assessed by the Balance Error Scoring System (BESS) which is a clinical assessment of balance.  The purpose of this study is to determine if postural control deficits are present in individuals with ACLR as measured by the BESS.  Thirty participants were included in this study. Fifteen had a history of unilateral ACLR and were compared with 15 matched controls.  The BESS consists of 3 stances (double limb, single limb, and tandem) on 2 surfaces (firm and foam) Participants begin in each stance with hands on their hips and eyes closed while trying to stand as still as possible for 20 s. MAIN OUTCOME MEASURES Each participant performed 3 trials of each stance (18 total) and errors were assessed during each trial and summed to create a total score.  We observed a significant group x stance interaction (P .004) and a significant main effect for stance (P .001) Post hoc analysis revealed that the ACLR group had worse balance on the single leg foam stance than did controls. Finally, the reconstructed group had more errors when total BESS score was examined (P .02) CONCLUSIONS Balance deficits exist in individuals with ACLR as measured by the BESS. Total BESS score was different between groups. The only condition that differed between groups was the single leg stance on the unstable foam surface.
Word Embedding based Generalized Language Model for Information Retrieval
Venue: SIGIR
Year: 2015

Word2vec, a state of the art word embedding technique has gained a lot of interest in the NLP community. The embedding of the word vectors helps to retrieve a list of words that are used in similar contexts with respect to a given word. In this paper, we focus on using the word embeddings for enhancing retrieval effectiveness. In particular, we construct a generalized language model, where the mutual independence between a pair of words (say t and t' no longer holds. Instead, we make use of the vector embeddings of the words to derive the transformation probabilities between words. Specifically, the event of observing a term t in the query from a document d is modeled by two distinct events, that of generating a different term t' either from the document itself or from the collection, respectively, and then eventually transforming it to the observed query term t. The first event of generating an intermediate term from the document intends to capture how well does a term contextually fit within a document, whereas the second one of generating it from the collection aims to address the vocabulary mismatch problem by taking into account other related terms in the collection. Our experiments, conducted on the standard TREC collection, show that our proposed method yields significant improvements over LM and LDA smoothed LM baselines.
MiR 21 is an EGFR regulated anti apoptotic factor in lung cancer in never smokers
Venue: Proceedings of the National Academy of Sciences
Year: 2009

Fifteen percent of lung cancer cases occur in never smokers and show characteristics that are molecularly and clinically distinct from those in smokers. Epidermal growth factor receptor (EGFR) gene mutations, which are correlated with sensitivity to EGFR tyrosine kinase inhibitors (EGFR TKIs) are more frequent in never smoker lung cancers. In this study, microRNA (miRNA) expression profiling of 28 cases of never smoker lung cancer identified aberrantly expressed miRNAs, which were much fewer than in lung cancers of smokers and included miRNAs previously identified (e.g. up regulated miR 21) and unidentified (e.g. down regulated miR 138) in those smoker cases. The changes in expression of some of these miRNAs, including miR 21, were more remarkable in cases with EGFR mutations than in those without these mutations. A significant correlation between phosphorylated EGFR (p EGFR) and miR 21 levels in lung carcinoma cell lines and the suppression of miR 21 by an EGFR TKI, AG1478, suggest that the EGFR signaling is a pathway positively regulating miR 21 expression. In the never smoker derived lung adenocarcinoma cell line H3255 with mutant EGFR and high levels of p EGFR and miR 21, antisense inhibition of miR 21 enhanced AG1478 induced apoptosis. In a never smoker derived adenocarcinoma cell line H441 with wild type EGFR, the antisense miR 21 not only showed the additive effect with AG1478 but also induced apoptosis by itself. These results suggest that aberrantly increased expression of miR 21, which is enhanced further by the activated EGFR signaling pathway, plays a significant role in lung carcinogenesis in never smokers, as well as in smokers, and is a potential therapeutic target in both EGFR mutant and wild type cases.