nils-herrmann/clean_scirepeval huggingface dataset:
Diffuse gastric cancer with Krukenberg tumor: A case report

Diffuse gastric carcinoma (DGC) is histologically characterized by increased intracellular mucin production, leading to a "signet ring cell differentiation" in tumor cells. Signet ring tumor cells are often rapidly progressive in nature, with tumor cells diffusely infiltrating the stomach, leading to desmoplasia and thickening of the gastric wall (linitis plastica) Like intestinal gastric carcinoma (IGC) DGC can be associated with H. pylori infections, among other environmental factors such as smoking, alcohol, and socioeconomic status. DGC, however, is characterized by a higher mortality and poorer prognosis than IGC due to its rapid progression, higher metastatic potential, and delayed diagnosis. Common presentation in those with DGC include weight loss, generalized abdominal pain, nausea and vomiting. In our specific case, the rare presentation of DGC with metastasis to the peritoneum, small intestine, colon, left ovary and fallopian tube can be appreciated. A 54 year old female presented with consistent, generalized abdominal pain, leading to an exploratory laparotomy for suspected adhesions. Examination revealed numerous tumors throughout the abdomen and pelvis, with omental and mesenteric implants. Multiple biopsies of the ovaries, mesenteric implants, and omental implants revealed welldefined glands lined by moderately atypical nuclei and focal luminal necrosis. Diagnosis of DGC with metastatic spread and Krukenberg tumors (KT) was made and treatment was initiated with palliative chemotherapy. DGC with KT is remarkably rare, as only 1% of metastatic ovarian tumors result from gastric primaries. The grim prognosis is due to rapid disease progression, advanced stage at presentation, and late diagnosis. As such, effective treatment for this subset of patients cannot be initiated. (This page in not part of the published article. ]  Khosla et al. 733  A case report and literature review Manraj Khosla, Ali Imran, Panagiotis Fidias
Exploring the Field of Computational Thinking as a 21st Century Skill

Computational Thinking, which entails using analytic and algorithmic approaches to formulate, analyse and solve problems, has increasingly gained attention in the educational field in the past decade, giving rise to a large amount of academic and grey literature, as well as to numerous public and private initiatives to implement it. Despite such widespread interest, its successful integration in school curricula is still facing several open issues and challenges. In order to contribute to the field development, we are carrying out a desk investigation to draw a comprehensive overview of recent findings produced by academic research, grassroots initiatives and policy actions addressing the development of computational thinking in primary and secondary school, as well as to highlight major implications for policy and practice. In this paper we describe the project methodology and a classification of the comprehensive corpus of documents collected. We also present a preliminary picture of the field as it is emerging from our analysis.  Information Society
Synthesis and anticancer activity of novel 3 6 disubstituted 1

Please cite this article in press as: Charitos, G. et al. Synthesis and anticancer activity of novel 3,6 disubstituted 1,2,4 triazolo [3,4 b] 1,3, 4 thiadiazole der Arabian Journal of Chemistry (2016) http:/dx.doi.org/10.1016/j.arabjc.2016.09.015 Georgios Charitos Dimitrios T. Trafalis Panayiotis Dalezis Constantinos Potamitis Vasiliki Sarli Panagiotis Zoumpoulakis Charalambos Camoutsis
Abstract 1240: Targeting epigenetic regulation in clear cell renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) the most common subtype of renal cell cancer, is highly resistant to traditional radiation and chemotherapy. Recently, targeted therapies have extended progression free survival, but responses are variable and no significant overall survival benefit has been achieved; thus, treatment options are scarce for patients bearing this disease. The majority of ccRCC cases ~90% are characterized by bi allelic loss of the von Hippel Lindau (VHL) gene, followed by mutations in the epigenetic regulators PBRM1 (23% SETD2 (8.4% BAP1 (7.1% and KDM5C (4.7% The latter four genes implicate an integral role for chromatin remodeling in ccRCC, and thus signify a new realm of exploration and therapeutic targeting for this disease. Given the limited number of commercially available ccRCC cell lines, and reports that they may not accurately reflect primary tumors at the molecular level, our lab developed a novel method to generate primary patient derived ccRCC (VHLmut) cells and matched normal renal proximal tubular epithelial (VHLwt) cells from human surgical specimens with high efficiency. This involved fluorescence activated cell sorting of primary tumor single cell suspensions using the cell surface marker carbonic anhydrase IX (CA9) a HIF target which is upregulated upon VHL loss, to establish CA9+ VHLmut and CA9 VHLwt cells. Transcriptional profiling of VHLmut and VHLwt pairs found gene signatures that corresponded with patient matched primary ccRCC tumors and adjacent normal tissues in The Cancer Genome Atlas, demonstrating that these cells represent novel models for interrogation of ccRCC biology and testing of therapeutic strategies. Here, in the current study, these newly established cells were utilized to screen a focused library of 30 well characterized drug like compounds targeting specific components of chromatin remodeling complexes to determine the effect on cell growth in culture. At Day 0, 786 0 VHL) cells and VHLmut cells corresponding to four patient primary ccRCC tumors were plated at 2,500 cells/well in 96 well black clear bottom plates (n 5) Cells were then treated with the library of chromatin targeting drugs on Day 1 and monitored until control treated cells were 90 95% confluent. At endpoint, cells were fixed and stained with DRAQ5, a DNA intercalating dye that stains DNA stoichiometrically, for visualization on the LI COR Odyssey CLx Imaging System. Across all five samples, there was a significant reduction in growth observed among cells treated with drugs targeting: i) BET bromodomains (BRD2, BRD3, BRD4 and BRDT) ii) EZH1/2, and iii) JMJD3, UTX and JARID1B. Ongoing work will determine mechanisms of action and whether these targets are also affected in matching VHLwt cells in order to identify compounds that may translate well in the clinic to treat patients with ccRCC.  Targeting epigenetic regulation in clear cell renal cell carcinoma.
Characterization of pellets from mixing olive pomace and olive tree pruning.

Olive pomace is an interesting agro industrial byproduct that can be a potential raw material for densified biomass products. At first, 2 phase (2 PH) and 3 phase (3 PH) olive pomace pellets were analyzed in order to evaluate their quality in terms of the main parameters required by the European Standard EN 17225 6. The characterization of the pure pellets has shown important problems because of out of limits values of nitrogen, durability and copper in the two olive pomace. To improve the properties of olive pomace pellets, the possibility of manufacturing pellets by mixing olive pomace and olive tree pruning (PR) was investigated. Several blends at different weight ratios were analyzed in order to verify the effect of mixing on the pellet properties. It can be concluded that the physical properties of all mixtures are in compliance with the requirements of the standard. In particular, two best blends in terms of physical, chemical and mechanical characteristics were identified as becoming potential fuel for combustion and gasification applications: 75PR252 PH (75% pruning and 25% 2 phase pomace) and 50PR503 PH (50% pruning and 50% 3 phase pomace)
Aerobic bacteria and fungi from skin lesions of fish in Khartoum state

This cross sectional study was conducted from April to July 2014 in Khartoum state, the Sudan, to investigate aerobic bacteria and fungi of skin lesions of fish in 3 different areas in Khartoum.  A total of 50 samples were collected from the skin lesions of different types of fish including Synodontis species (n=17) Tilapia niloticus (n=15) Labeo niloticus (n=10) Hydrocynus species (n=4) and Clarias species (n=4) Liquid, semi solid, and solid culture media like nutrient broth, blood agar, MacConkey agar, sabouraud dextrose agar (SDA) and Simmon's citrate medium were used for the isolation and identification of bacteria and fungi. Besides, Gram staining and biochemical characterization were also conducted.  Culturing of the collected samples revealed growth of bacteria from all (100% and growth of fungi could be found from 32% samples. A number of 188 bacteria were isolated, mainly Staphylococcus species, Bacillus species, Aeromonas species, Pseudomonas species, and Vibrio species. Besides, 16 fungi could be identified containing Aspergillus niger A. flavus A. fumigatus and Phycomycete.  Fishes with skin lesions are harboring many pathogenic bacteria and fungi and may act as a source of zoonotic infections and can transmit several pathogens to workers in fish industry and consumers. Therefore, thorough and strict routine inspection of fish is recommended to ensure safety and that there are no serious risks to consumers. http:/doi.org/10.5455/javar.2016.c176
Communication: Mode specific quantum dynamics of the F CHD3 HF CD3 reaction.
Venue: The Journal of chemical physics

The mode specific reactivity of the F CHD3 HF CD3 reaction is investigated using an eight dimensional quantum dynamical model on a recently developed ab initio based full dimensional potential energy surface. Our results indicate prominent resonance structures at low collision energies and absence of an energy threshold in reaction probabilities. It was also found that excitation of the C D stretching or CD3 umbrella mode has a relatively small impact on reactivity. On the other hand, the excitation of the C H vibration (v1) in CHD3 is shown to significantly increase the reactivity, which, like several recent quasi classical trajectory studies, is at odds with the available experimental data. Possible sources of the disagreement are discussed.
TAXONOMIC STUDY OF SYRPHIDAE (DIPTERA) OF NORTHERN DRY MOUNTAINS REGION OF PAKISTAN

The current study deals with the taxonomic study of family Syrphidae of Northern Dry Mountains of Pakistan. Extensive field survey to collect syrphid fauna in one of the Agro Ecological Zones (AEZ's) of Pakistan (Northern Dry Mountains) was conducted during 2012 2014. More than 500 specimens of the family Syrphidae were examined. A total of 10 genera and 24 species under two subfamilies (Syrphinae and Eristalinae) are recognized in the present study. Three species, viz, Eristalinus (Eristalodes) paria, Spilomyia manicata (Rondani) and Chrysotoxum antiquum Walker are reported first time from Pakistan. Subfamily Eristalinae includes genus Eristalinus Rondani, Eristalis Latreille and Spilomyia Meigen while Syrphinae consist of Chrysotoxum Meigen, Episyrphus Matsumura, Ischiodon Sack, Eupeodes Osten Sacken, Paragus Latreille, Scaeva Fabricius, and Sphaerophoria Lepeletier and Serville. Genus Eristalinus Rondani is represented by three species namely, Eristalinus (Eristalodes) paria (Bigot) Eristalinus (Lathyrophthalmus) aeneus (Scopoli) and E. (Lathyrophthalmus) obscuritarsis (de Meijere) Eristalis Latreille is represented by three species i.e. Eristalis (Eoseristalis) arbustorum (Linnaeus) E. (Eoseristalis) cerealis Fabricius and E. (Eristalis) tenax (Linnaeus) Genus Spilomyia Meigen is very rare and represented by single species, Spilomyia manicata (Rondani) which had not previously been collected from Pakistan. The Subfamily Syrphinae include the following species: Chrysotoxum antiquum Walker, C. baphyrum Walker and C. Intermedium Meigen; Episyrphus balteatus De Geer) Episyrphus viridaureus (Wiedemann) Ischiodon scutellaris (Fabricius) Eupeodes (Metasyrphus) bucculatus (Rondani) Eupeodes (Macrosyrphus) confrater (Wiedemann) Eupeodes (Metasyrphus) corollae (Fabricius) Paragus (Pandasyopthalmus) politus Wiedemann and Paragus (Serratoparagus) serratus (Fabricius) Scaeva albomaculata (Macquart) Scaeva latimaculata (Brunetti) and Scaeva pyrastri (Linnaeus) Sphaerophoria bengalensis Macquart, Sphaerophoria indiana Bigot and Sphaerophoria scripta (Linnaeus) Almost all species are newly recorded to the said region. Illustrated keys, bibliography and synonymy are provided for each species. The distribution, host range, male and female description and economic importance of these syrphids are also given. The male genitalia of almost all the species are figured. Species identifications were confirm by male genitalic dissection of the species.
Taxonomic study of genus Sphaerophoria Le Peletier et Serville (Diptera: Syrphidae) with three species from Northern Dry Mountains region of Pakistan

To explore the syrphid flies of Northern Dry Mountains Region of Pakistan, collection survey was conducted from 2012 2014 each month in different localities of the study area during active season. Species identification of collected specimen was performed with the help of relevant literature. Three species of genus Sphaerophoria Le Peletier et Serville, 1828 i.e. Sphaerophoria bengalensis Macquart, 1842, Sphaerophoria indiana Bigot, 1884 and Sphaerophoria scripta (Linnaeus, 1758) were recorded in the said region. Diagnostic character with distribution, flower records, illustrations and synonymy are provided for each species. The male genitalia of all the species were figured.
A Visual Approach for Interactive Co Training

Co training is a popular semi supervised method to build classifiers by combining labeled and unlabeled data. It trains two classifiers with a small amount of initially labeled data and iteratively retrains them after exchanging their high confidence instances. As the initial amount of labels is very small, however, the performance can suffer from the label pollution problem. We therefore propose an interactive visual approach that improves the stability of co training through user inspection of transferred instances. It includes a visualization of classifier uncertainties and disagreement. It further helps users to quickly identify possible mistakes of the automatic approach by guiding user's attention to the instances which are labeled differently than the majority of their nearest neighbors and instances which are labeled differently by the two base classifiers. To help users examine such instances, we also include a visual explanation which shows important features of an instance along with its raw data. We show the effectiveness of our approach with a usage scenario and by comparing it with the classical cotraining approach through experiments. Finally, we discuss limitations and propose several possibilities for future improvement.
Visual Presence: Viewing Geometry Visual Information of UHD S3D Entertainment
Venue: IEEE Transactions on Image Processing

To maximize the presence experienced by humans, visual content has evolved to achieve a higher visual presence in a series of high definition (HD) ultra HD (UHD) 8K UHD, and 8K stereoscopic 3D (S3D) Several studies have introduced visual presence delivered from content when viewing UHD S3D from a content analysis perspective. Nevertheless, no clear definition has been presented for visual presence, and only a subjective evaluation has been relied upon. The main reason for this is that there is a limitation to defining visual presence via the use of content information itself. In this paper, we define the visual presence for each viewing environment, and investigate a novel methodology to measure the experienced visual presence when viewing both 2D and 3D via the definition of a new metric termed volume of visual information by quantifying the influence of the viewing geometry between the display and viewer. To achieve this goal, the viewing geometry and display parameters for both flat and atypical displays are analyzed in terms of human perception by introducing a novel concept of pixel wise geometry. In addition, perceptual weighting through analysis of content information is performed in accordance with monocular and binocular vision characteristics. In the experimental results, it is shown that the constructed model based on the viewing geometry, content, and perceptual characteristics has a high correlation of about 84% with subjective evaluations.
Visual Presence: Viewing Geometry Visual Information of UHD S3D Entertainment.
Venue: IEEE transactions on image processing a publication of the IEEE Signal Processing Society

To maximize the presence experienced by humans, visual content has evolved to achieve a higher visual presence in a series of high definition (HD) ultra HD (UHD) 8K UHD, and 8K stereoscopic 3D (S3D) Several studies have introduced visual presence delivered from content when viewing UHD S3D from a content analysis perspective. Nevertheless, no clear definition has been presented for visual presence, and only a subjective evaluation has been relied upon. The main reason for this is that there is a limitation to defining visual presence via the use of content information itself. In this paper, we define the visual presence for each viewing environment, and investigate a novel methodology to measure the experienced visual presence when viewing both 2D and 3D via the definition of a new metric termed volume of visual information by quantifying the influence of the viewing geometry between the display and viewer. To achieve this goal, the viewing geometry and display parameters for both flat and atypical displays are analyzed in terms of human perception by introducing a novel concept of pixel wise geometry. In addition, perceptual weighting through analysis of content information is performed in accordance with monocular and binocular vision characteristics. In the experimental results, it is shown that the constructed model based on the viewing geometry, content, and perceptual characteristics has a high correlation of about 84% with subjective evaluations.
Is health related quality of life between 90 and 180 days following stroke associated with long term unmet needs?
Venue: Quality of Life Research

AbstractPurpose Understanding the relationship between health related quality of life (HRQoL) and long term unmet needs is important for guiding services to optimise life following stroke. We investigated whether HRQoL between 90 and 180 days following stroke was associated with long term unmet needs.MethodsData from Australian Stroke Clinical Registry (AuSCR) registrants who participated in the Australian Stroke Survivor Needs Survey were used. Outcome data, including the EQ 5D, are routinely collected in AuSCR between 90 and 180 days post stroke. Unmet needs were assessed at a median of 2 years and categorised into: health; everyday living; work/leisure; and support domains. Multivariable regression was used to determine associations between the EQ 5D dimensions and the likelihood of experiencing unmet needs and the visual analogue scale (VAS) (rating 0 100) and number of reported unmet needs.ResultsIn total, 173 AuSCR registrants completed the Needs Survey (median age 69 years, 67 male; 77 ischaemic stroke) VAS scores were negatively associated with the number of reported long term unmet needs [irr 0.98, (95 CI 0.97, 0 99) p 0.001] Having EQ 5D activity limitations was associated with unmet living needs (aOR 4.5, 95 CI 1.1, 18.8) Requiring living supports at 90 180 days was associated with unmet health needs (aOR 4.9, 95 CI 1.5, 16.1) Those with pain at 90 180 days were less likely to report unmet health (aOR 0.09, 95 CI 0.02, 0.4) and support needs (aOR 0.2, 95 CI 0.06, 0.6).ConclusionRoutinely collected HRQoL data can identify survivors at risk of experiencing long term unmet needs. This information is important for targeting service delivery to optimise outcomes following stroke.
Interpreting process data of wet pressing process. Part 1: Theoretical approach

The wet pressing process represents a new production method for carbon fibre reinforced plastics components. Due to the low cycle times, it is suitable for use in the automotive industry. Therefore, a sufficient degree of industrialisation needs to be achieved, which is characterised by a stable process. The knowledge about relevant process parameters, their interactions, and influence on the part quality builds the basis of an economic process. This is a major challenge, since in the early stage of process development the available amount of recorded process data is small and the data sets are not complete. As the implementation of time material and cost intensive experiments represents no acceptable alternative, a theoretical approach is chosen. This article describes a theoretical procedure to define the critical factors of the wet pressing process with significantly less resource input.
Interpreting process data of wet pressing process. Part 2: Verification with real values

For the analysis of the wet pressing process, which was presented in the first part of this paper, a theoretical approach was chosen. This enabled the pre definition of three quality related priorities which now will be considered in detail in the second part. For further analysis, real process data, recorded in an early phase of the process implementation, are used. The challenge is that in this process status, the availability of data is limited or the data sets are incomplete. Supported by the theoretical approach, an easier interpretation of the process data, and in case of ambiguous issues, an accelerated decision making is expected. The objective is to show that this combination is suitable for the process analysis in an early production phase.
A cluster of salivirus A1 (Picornaviridae) infections in newborn babies with acute gastroenteritis in a neonatal hospital unit in Hungary
Venue: Archives of Virology

Salivirus (family Picornaviridae) may be associated with acute gastroenteritis in humans, but there have been no reports of salivirus outbreaks. Salivirus A1 infection with faecal virus concentrations of 2.1 2.6 x 109/g were identified retrospectively in newborn babies, between the ages of 1.5 and 5 days, with apparent clinical symptoms of diarrhea (100 fever (40 vomiting (40 and loss of appetite (40 in a neonatal hospital unit in Hungary in July 2013. The complete genome sequence of the salivirus (including the 5' terminal end) was determined. Salivirus mono infection may be associated with gastroenteritis in babies who are a few days old. Salivirus testing should be done in public health laboratories in gastroenteritis outbreaks with unknown etiology.
A Survey on Software Fault Localization
Venue: IEEE Transactions on Software Engineering

Software fault localization, the act of identifying the locations of faults in a program, is widely recognized to be one of the most tedious, time consuming, and expensive yet equally critical activities in program debugging. Due to the increasing scale and complexity of software today, manually locating faults when failures occur is rapidly becoming infeasible, and consequently, there is a strong demand for techniques that can guide software developers to the locations of faults in a program with minimal human intervention. This demand in turn has fueled the proposal and development of a broad spectrum of fault localization techniques, each of which aims to streamline the fault localization process and make it more effective by attacking the problem in a unique way. In this article, we catalog and provide a comprehensive overview of such techniques and discuss key issues and concerns that are pertinent to software fault localization as a whole.