nils-herrmann/clean_scirepeval huggingface dataset:
Nutrition, oxidative stress and intestinal dysbiosis: Influence of diet on gut microbiota in inflammatory bowel diseases.
Venue: Biomedical papers of the Medical Faculty of the University Palacky, Olomouc, Czechoslovakia

Microbiota refers to the population of microorganisms (bacteria, viruses and fungi) that inhabit the entire gastrointestinal tract, more particularly the colon whose role is to maintain the integrity of the intestinal mucosa and control the proliferation of pathogenic bacteria. Alteration in the composition of the gut microbiota is called dysbiosis. Dysbiosis redisposes to inflammatory bowel diseases such as ulcerative colitis, Crohn disease and indeterminate colitis.  The purpose of this literature review is to elucidate the influence of diet on the composition of the gastrointestinal microbiota in the healthy gut and the role of diet in the development of dysbiosis.  The "Western diet" in particular a low fiber high fat/high carbohydrate diet is one factor that can lead to severe dysbiosis. In contrast, "mediterranean" and vegetarian diets that includes abundant fruits, vegetables, olive oil and oily fish are known for their anti inflammatory effects and could prevent dysbiosis and subsequent inflammatory bowel disease.
Ontogenetic Characterization of the Intestinal Microbiota of Channel Catfish through 16S rRNA Gene Sequencing Reveals Insights on Temporal Shifts and the Influence of Environmental Microbes
Venue: PloS one

Aquaculture recently overtook capture fisheries as the largest producer of food fish, but to continue increasing fish production the industry is in search of better methods of improving fish health and growth. Pre and probiotic supplementation has gained attention as a means of solving these issues, however, for such approaches to be successful, we must first gain a more holistic understanding of the factors influencing the microbial communities present in the intestines of fish. In this study, we characterize the bacterial communities associated with the digestive tract of a highly valuable U.S. aquaculture species, channel catfish Ictalurus punctatus, over the first 193 days of life to evaluate temporal changes that may occur throughout ontogenetic development of the host. Intestinal microbiota were surveyed with high throughput DNA sequencing of 16S rRNA V4 gene amplicons derived from fish at 3, 65, 125, and 193 days post hatch (dph) while also characterizing the environmental microbes derived from the water supply and the administered diets. Microbial communities inhabiting the intestines of catfish early in life were dynamic, with significant shifts occurring up to 125 dph when the microbiota somewhat stabilized, as shifts were less apparent between 125 to 193 dph. Bacterial phyla present in the gut of catfish throughout ontogeny include Bacteroidetes, Firmicutes, Fusobacteria, and Proteobacteria; with the species Cetobacterium somerae and Plesiomonas shigelloides showing the highest abundance in the catfish microbiota after 3 dph. Comparisons of the gut microbiota to the environmental microbes reveals that the fish gut is maintained as a niche habitat, separate from the overall microbial communities present in diets and water supply. Although, there is also evidence that the environmental microbiota serves as an inoculum to the fish gut. Our results have implications for future research related to channel catfish biology and culture, and increase our understanding of ontogenetic effects on the microbiota of teleost fish.
Transcriptomic responses in the fish intestine.
Venue: Developmental and comparative immunology

The intestine, being a multifunctional organ central to both nutrient uptake, pathogen recognition and regulating the intestinal microbiome, has been subjected to intense research. This review will focus on the recent studies carried out using high throughput gene expression approaches, such as microarray and RNA sequencing (RNA seq) These techniques have advanced greatly in recent years, mainly as a result of the massive changes in sequencing methodologies. At the time of writing, there is a transition between relatively well characterised microarray platforms and the developing RNA seq, with the prediction that within a few years as costs decrease and computation power increase, RNA seq related approaches will supersede the microarrays. Comparisons between the approaches are made and specific examples of how the techniques have been used to examine intestinal responses to pathogens, dietary manipulations and osmoregulatory challenges are given.
Security of CCTV and Video Surveillance Systems: Threats, Vulnerabilities, Attacks, and Mitigations
Venue: TrustED@CCS

Video surveillance, closed circuit TV and IP camera systems became virtually omnipresent and indispensable for many organizations, businesses, and users. Their main purpose is to provide physical security, increase safety, and prevent crime. They also became increasingly complex, comprising many communication means, embedded hardware and non trivial firmware. However, most research to date focused mainly on the privacy aspects of such systems, and did not fully address their issues related to cyber security in general, and visual layer (i.e. imagery semantics) attacks in particular. In this paper, we conduct a systematic review of existing and novel threats in video surveillance, closed circuit TV and IP camera systems based on publicly available data. The insights can then be used to better understand and identify the security and the privacy risks associated with the development, deployment and use of these systems. We study existing and novel threats, along with their existing or possible countermeasures, and summarize this knowledge into a comprehensive table that can be used in a practical way as a security checklist when assessing cyber security level of existing or new CCTV designs and deployments. We also provide a set of recommendations and mitigations that can help improve the security and privacy levels provided by the hardware, the firmware, the network communications and the operation of video surveillance systems. We hope the findings in this paper will provide a valuable knowledge of the threat landscape that such systems are exposed to, as well as promote further research and widen the scope of this field beyond its current boundaries.
The Concept of Smart Hotels as an Innovation on the Hospitality Industry Market Case Study of Puro Hotel in Wroclaw

Market observation indicates the development of a new model for running a business in hospitality industry, referred to as smart hotels. This model is specifically distinguished by the new information and communication technologies. The concept of smart hotels is relatively new and can be regarded as an innovative solution in tourism. The presented article discusses the essence of a smart hotel category and identifies the attributes of an intelligent hotel. The theoretical discussion based on the subject literature in the theory of organization and management, as well as hospitality business economics and management was also illustrated using the case study of PURO hotel in Wroclaw. The necessary information was collected from both secondary and primary sources. The most important information gathering method was interpersonal in depth interview with the aforementioned hotel's manager.
From Smart Rooms to Smart Hotels

This paper gives an overview of a potential path that new hotels have to satisfy to improve their status from a hotel with smart rooms towards a full scale smart hotel facility. It presents a possible transitional way including innovative applications based on modern information technology for ambient settings in the domain of hotel industry that aims to improve the quality of offered services towards clients, starting from the present level of smart rooms. The main objective is to pose the basis that hotels must satisfy by utilizing sophisticated information technologies for direct interaction with the guest, as well as to accommodate hotel services depending on guest's wishes and needs in order to make their stay as pleasant as possible. Accordingly, the paper concludes that the desired future of the hotel industry is within the concept of being a smart establishment aiming to leverage the disadvantages of being away from home and offering a unique guest experience.
Hierarchical Attention Networks for Document Classification
Venue: NAACL

We propose a hierarchical attention network for document classification. Our model has two distinctive characteristics: (i) it has a hierarchical structure that mirrors the hierarchical structure of documents; (ii) it has two levels of attention mechanisms applied at the wordand sentence level, enabling it to attend differentially to more and less important content when constructing the document representation. Experiments conducted on six large scale text classification tasks demonstrate that the proposed architecture outperform previous methods by a substantial margin. Visualization of the attention layers illustrates that the model selects qualitatively informative words and sentences.
Improved protein protein interactions prediction via weighted sparse representation model combining continuous wavelet descriptor and PseAA composition
Venue: BMC Systems Biology

BackgroundProtein protein interactions (PPIs) are essential to most biological processes. Since bioscience has entered into the era of genome and proteome, there is a growing demand for the knowledge about PPI network. High throughput biological technologies can be used to identify new PPIs, but they are expensive, time consuming, and tedious. Therefore, computational methods for predicting PPIs have an important role. For the past years, an increasing number of computational methods such as protein structure based approaches have been proposed for predicting PPIs. The major limitation in principle of these methods lies in the prior information of the protein to infer PPIs. Therefore, it is of much significance to develop computational methods which only use the information of protein amino acids sequence.ResultsHere, we report a highly efficient approach for predicting PPIs. The main improvements come from the use of a novel protein sequence representation by combining continuous wavelet descriptor and Chou's pseudo amino acid composition (PseAAC) and from adopting weighted sparse representation based classifier (WSRC) This method, cross validated on the PPIs datasets of Saccharomyces cerevisiae, Human and H. pylori, achieves an excellent results with accuracies as high as 92.50% 95.54% and 84.28% respectively, significantly better than previously proposed methods. Extensive experiments are performed to compare the proposed method with state of the art Support Vector Machine (SVM) classifier.ConclusionsThe outstanding results yield by our model that the proposed feature extraction method combing two kinds of descriptors have strong expression ability and are expected to provide comprehensive and effective information for machine learning based classification models. In addition, the prediction performance in the comparison experiments shows the well cooperation between the combined feature and WSRC. Thus, the proposed method is a very efficient method to predict PPIs and may be a useful supplementary tool for future proteomics studies.
A Robotic Home Assistant with Memory Aid Functionality
Venue: KI

We present the robotic system IRMA Interactive Robotic Memory Aid that assists humans in their search for misplaced belongings within a natural home like environment. Our stand alone system integrates state of the art approaches in a novel manner to achieve a seamless and intuitive human robot interaction. IRMA directs its gaze toward the speaker and understands the person's verbal instructions independent of specific grammatical constructions. It determines the positions of relevant objects and navigates collision free within the environment. In addition, IRMA produces natural language descriptions for the objects' positions by using furniture as reference points. To evaluate IRMA's usefulness, a user study with 20 participants has been conducted. IRMA achieves an overall user satisfaction score of 4.05 and a perceived accuracy rating of 4.15 on a scale from 1 5 with 5 being the best.
Poster: Comparative study of EM MAC and TSCH/orchestra for IoT
Venue: 2016 Symposium on Communications and Vehicular Technologies (SCVT)

Multichannel Medium Access Control (MAC) protocols for IoT can potentially improve network performance. Therefore, a considerable number of such protocols have been proposed in the last decade, ranging from slotted synchronous to contention based asynchronous multichannel protocols. In this paper two of the most representative multichannel MAC layer protocols are compared: Time Slotted Channel Hopping (TSCH) using the Orchestra scheduling algorithm, and Energy Efficient Multichannel MAC (EM MAC) The performance of these protocols is assessed under different traffic loads and node densities using the standard IPv6 Routing Protocol for Low Power and Lossy Networks (LLNs) i.e. RPL. The results show the cross layer interaction between the RPL protocol and the multichannel MAC schemes under study. Moreover, it can be generally appreciated that TSCH/Orchestra performs better in terms of Packet Delivery Ratio (PDR) whereas EM MAC exhibits lower power consumption. These characteristics reveal the suitability of these protocols for different IoT applications.
Exocyst SEC3 and Phosphoinositides Define Sites of Exocytosis in Pollen Tube Initiation and Growth1[OPEN]
Venue: Plant Physiology

The SEC3 exocyst subunit serves as a landmark for secretory vesicles, and its localization and differential regulation by membrane lipids determine pollen tube initiation and polar growth. Polarized exocytosis is critical for pollen tube growth, but its localization and function are still under debate. The exocyst vesicle tethering complex functions in polarized exocytosis. Here, we show that a sec3a exocyst subunit null mutant cannot be transmitted through the male gametophyte due to a defect in pollen tube growth. The green fluorescent protein (GFP) SEC3a fusion protein is functional and accumulates at or proximal to the pollen tube tip plasma membrane. Partial complementation of sec3a resulted in the development of pollen with multiple tips, indicating that SEC3 is required to determine the site of pollen germination pore formation. Time lapse imaging demonstrated that SEC3a and SEC8 were highly dynamic and that SEC3a localization on the apical plasma membrane predicts the direction of growth. At the tip, polar SEC3a domains coincided with cell wall deposition. Labeling of GFP SEC3a expressing pollen with the endocytic marker FM4 64 revealed the presence of subdomains on the apical membrane characterized by extensive exocytosis. In steady state growing tobacco (Nicotiana tabacum) pollen tubes, SEC3a displayed amino terminal Pleckstrin homology like domain (SEC3a N) dependent subapical membrane localization. In agreement, SEC3a N interacted with phosphoinositides in vitro and colocalized with a phosphatidylinositol 4,5 bisphosphate (PIP2) marker in pollen tubes. Correspondingly, molecular dynamics simulations indicated that SEC3a N associates with the membrane by interacting with PIP2. However, the interaction with PIP2 is not required for polar localization and the function of SEC3a in Arabidopsis (Arabidopsis thaliana) Taken together, our findings indicate that SEC3a is a critical determinant of polar exocytosis during tip growth and suggest differential regulation of the exocytotic machinery depending on pollen tube growth modes.
Establishing cycle times in a high variety manufacturing environment using DMAIC Procedure

Today many competitive manufacturing companies use a variety of quantitative metrics to provide them with the means to track and identify problems with performance, and to make good decisions. This explains the need for a weaving and dyeing plant based in Cape Town, South Africa, to establish production performance metrics in general, and the cycle times at various workstations in particular. Also, this research assumes that the establishment of the cycle times at various workstations of the weaving and dyeing plant constitutes an important step toward the adequate management of the manufacturing lead times. While there exist many generic techniques for establishing the cycle times in a manufacturing environment, there is limited literature on how to establish the cycle times in a high variety production environment, such as a weaving and dyeing plant. Consequently, this research focuses on establishing cycle times at various workstations of a weaving and dyeing plant, while taking into account the entire population of products that has to be produced at each workstation. Furthermore, following the establishment of the cycle times, this research creates a cycle time control sheet to be used by the weaving and dyeing department's managers, in order to better control the manufacturing lead times. Lastly this research identifies the DMAIC procedure as a viable quality management approach, which can be used to realign the weaving and dyeing production performance measurements with the requirements of its ISO 9001:2008 certification. Therefore DMAIC is used as the most suitable technique for carrying out this research. Stellenbosch University https:/scholar.sun.ac.za
Productivity Improvement Using Industrial Engineering Tools Case Study Of a Typical Spinning Mill

Spinning mill industries continue to face the challenges of improving productivity, in order to remain successful, in a highly competitive industry. As year on year, every input cost goes higher, it is important to provide better products at lower costs to the end consumer by improving the efficiency of the plant. The project site is a spinning and weaving mill. Today the company has a production capacity of almost 85680 spindles per day. This capacity cannot be utilized properly due to various losses. The project aims at identifying the root cause of these losses and to propose methods to increase the productivity. DMAIC technique is used for productivity increase with why why analysis in the analysis stage to find out the root causes of losses. Pareto chart is used to plot various factors that affect productivity. This project mainly focuses on reasons for power failure and absenteeism, which is a threat to the organization. In order to improve the productivity of the organization, suggestions were made to manage the power failure and absenteeism, thus a better system was proposed for the organization under study.
Association of type 1 diabetes mellitus and autoimmune disorders in Brazilian children and adolescents
Venue: Indian journal of endocrinology and metabolism

Type 1 diabetes mellitus (T1DM) is caused by an immune mediated destruction of pancreatic beta cells. Other autoimmune diseases can be observed in association with T1DM. The screening for celiac disease (CD) and Hashimoto's thyroiditis is necessary due to the increased prevalence of these pathologies in T1DM patients.  This study aimed to investigate the prevalence of autoimmune markers for pancreatitis, thyroiditis, and CD in racially admixtured children and adolescents with T1DM.   Seventy one patients with T1DM (average: 11.6 5.1 years) In all patients, the following antibodies were surveyed: Anti glutamic acid decarboxylase (anti GAD) immunoglobulin A (IgA) anti transglutaminase (anti tTG) Antithyroglobulin (AAT) anti thyroid peroxidase (anti TPO) and IgA. Statistical Analysis Used: The quantitative variables were expressed as a mean and standard deviation and the qualitative variables in contingency tables. Student's t test and kh2 tests were used to assess the differences between the groups. The level of significance was established as P 0.05.  The prevalence of anti GAD antibodies was 5.9% anti tTG IgA, 7.4% anti TPO, 11.8% and AAT, 11.8%  Children and adolescents with T1DM have increased the prevalence of antithyroid and CD related antibodies. The positivity for anti GAD and antithyroid antibodies was less frequent than in other studies. The prevalence of anti tTG antibodies was similar to the literature.
Pancreatic exocrine insufficiency: Comparing fecal elastase 1 with 72 h stool for fecal fat estimation
Venue: Indian Journal of Gastroenterology

IntroductionIdentification of pancreatic exocrine insufficiency (PEI) is important in the management of chronic pancreatitis. The 72 h stool for fecal fat estimation (FFE) has long been considered a gold standard indirect test for the diagnosis of PEI. However, the test is cumbersome for both patients and laboratory personnel alike. In this study, we aimed to assess fecal elastase 1 (FE1) as an alternate to FFE for the diagnosis of PEI.MethodsIn all, 87 consecutive patients diagnosed with chronic pancreatitis were included in this study. FFE and FE1 estimation was done for all the patients. For FE1, two cutoffs <100 and <200 mg) were selected to define pancreatic exocrine insufficiency. The sensitivity, specificity, and positive and negative predictive values for the two cutoffs were estimated. Kappa statistics was used to assess degree of agreement between both tests.ResultsAll patients completed the study and were included in the analysis. The sensitivity, specificity, and positive and negative predictive value and PABAK (prevalence and bias adjusted kappa) for FE1 <100 mg was 84.9, 47.6, 83.6, 50, and 0.52, respectively. For FE1 <200 mg, it was 90.9, 9.5, 75.95, 25, and 0.43, respectively.ConclusionFE1 is a sensitive test; however, it does not have a good agreement with FFE. FE1 may be used as screening test for PEI in patients with chronic pancreatitis.
Big data visualization: Tools and challenges
Venue: 2016 2nd International Conference on Contemporary Computing and Informatics (IC3I)

In today's world where everything is recorded digitally, right from our web surfing patterns to our medical records, we are generating and processing petabytes of data every day. Big data will be transformative in every sphere of life. But just to process and analyze those data is not enough, human brain tends to find pattern more efficiently when data is represented visually. Data Visualization and Analytics plays important role in decision making in various sectors. It also leads to new opportunities in the visualization domain representing the innovative ideation for solving the big data problem via visual means. It is quite a challenge to visualize such a mammoth amount of data in real time or in static form. In this paper, we discuss why big data visualization is of utmost importance, what are the challenges related to it and review some big data visualization tools.