Miracle-dz/UniFAR-FTUs huggingface dataset:
On Building a Quantitative Food-Disease-Gene Network

Nutritional genomics is a new science that studies the relationship between foods (or nutrients), diseases, and genes. Large amounts of scientific findings have been published in this area, primarily in unstructured text. Moreover, given a pair of entities, different studies can report different findings. It is hence important to obtain a holistic view of the reported relationships. In this article, we describe an information extraction system aiming to reach this goal. The system integrates natural language processing techniques, domain ontology, statistical, and machine learning methods. It consists of four main modules: (1) entity extraction, which recognizes and extracts five types of entities: foods, chemicals (or nutrients), diseases, proteins and genes; (2) relationship extraction, which extracts binary relationships between entities; (3) relationship polarity analysis, which categorizes relationships into three groups: positive, negative, and neutral; and (4) strength analysis, which rates a relationship as weak, medium, or strong. To the best of our knowledge, we are the first to propose to analyze the polarity and strength of a binary relationship. We have evaluated our system using the GENIA corpus and datasets drawn from the MEDLINE database. The first two modules outperform the reported best results with an average F-score of 0.89 and 0.82, respectively; while the last two also achieve promising results with an accuracy of 0.75-0.84 and ~0.90, respectively. 1 INTRODUCTION Advances in biotechnology and life sciences are leading to an ever-increasing volume of published research data, predominantly in unstructured text (or natural language). At the time of writing, the MEDLINE database consists of 19 million scientific articles with a growth rate of ~400,000 articles per year [8]. This phenomenon becomes even more apparent in nutritional genomics, an emerging new science that studies the relationship between foods (or nutrients), diseases, and genes [16]. For instance, soy products and green tea have been two of the intensively studied foods in this new discipline due to their controversial relationship with cancer. A search to the MEDLINE database on " soy and cancer " renders a total of 1,287 articles, and a search on " green tea and cancer " renders 1,318 articles. Due to the large number of publications every year, it is unrealistic for even the most motivated to manually go through these articles to obtain a full picture of the findings reported to date. This however has become ever more important and necessary due to the following reasons: (1) given a …
THE ACCEPTANCE OF VIRTUAL PLATFORMS FOR PROMOTING KNOWLEDGE SHARING BEHAVIOR – A REVIEW OF THE TECHNOLOGY ACCEPTANCE MODEL ( TAM ) Hairol Adenan Kasim

Knowledge sharing is recognized as an important facet in the Knowledge Management (KM) process. As an essential tool for the successful implementation of KM, knowledge is considered the most important resource that an organization possesses. Presently, people are using virtual platforms and web-based technologies, including Internet, Intranet, social media and other online technologies, through which knowledge can be extracted, shared and distributed globally. Apparently, there are wide ranges of web-based platforms and technologies that can be utilized to support knowledge sharing initiatives. The purpose of this study is to evaluate the acceptance of virtual platforms to inculcate the knowledge sharing behavior for the selected respondents. Therefore, this study adopted Technology Acceptance Model (TAM) to investigate the key factors on this sharing behavior. The TAM model adopted in this paper is empirically tested on a sample of 510 respondents, and significant relationships among these constructs were found.
The Nottingham Fatigue After Stroke (NotFAST) study: results from follow-up six months after stroke

Abstract Background Post-stroke fatigue is common and disabling. Objectives The aim of NotFAST was to examine factors associated with fatigue in stroke survivors without depression, six months after stroke. Methods Participants were recruited from four UK stroke units. Those with high levels of depressive symptoms (score ≥7 on Brief Assessment Schedule Depression Cards) or aphasia were excluded. Follow-up assessment was conducted at six months after stroke. They were assessed on the Fatigue Severity Scale, Rivermead Mobility Index, Nottingham Extended Activities of Daily Living scale, Barthel Index, Beck Anxiety Index, Brief Assessment Schedule Depression Cards, Impact of Event Scale-Revised, and Sleep Hygiene Index. Results Of the 371 participants recruited, 263 (71%) were contacted at six months after stroke and 213 (57%) returned questionnaires. Approximately half (n = 109, 51%) reported fatigue at six months. Of those reporting fatigue initially (n = 88), 61 (69%) continued to report fatigue. ‘De novo’ (new) fatigue was reported by 48 (38%) of those not fatigued initially. Lower Nottingham Extended Activities of Daily Living scores and higher Beck Anxiety Index scores were independently associated with fatigue at six months. Conclusions Half the stroke survivors reported fatigue at six months post-stroke. Reduced independence in activities of daily living and higher anxiety levels were associated with the level of fatigue. Persistent and delayed onset fatigue may affect independence and participation in rehabilitation, and these findings should be used to inform the development of appropriate interventions.
Nuclear thymidylate synthase expression, p53 expression and 5FU response in colorectal carcinoma

Thymidylate synthase (TS) is a key enzyme in DNA synthesis and is inhibited by metabolites of the chemotherapeutic agent 5-fluorouracil (5FU). Nuclear expression of TS in human tissue in vivo has not been characterised and its clinicopathological correlates in malignancy are unknown. 52 cases of primary colorectal carcinoma (CRC) and 24 cases of matched metastatic carcinoma were studied immunohistochemically using the monoclonal antibody TS106. The degree of nuclear TS immunostaining correlated closely with levels of TS mRNA expression amongst 10 CRCs studied. Strong nuclear immunostaining was seen in normal basal crypt colonocytes and germinal centre cells, and in a varying proportion of adenocarcinoma cells. Amongst the primary carcinomas, higher TS nuclear expression was associated with prominent extracellular mucin production and right-sided location. Higher TS nuclear expression also showed a significant association with poorer response to protracted venous infusional 5FU therapy. There was no clear association between TS nuclear expression and Ki67 or p53 expression assessed immunohistochemically. There was a strong positive correlation between TS nuclear expression in primary and metastatic CRC but the latter generally showed higher expression than matched primary tumour tissue. These findings confirm the nuclear expression of TS protein in human cells in vivo and provide new insight into how such expression may relate to the behaviour of CRCs. © 2001 Cancer Research Campaign http://www.bjcancer. com
The Natural History of Root Entrapment Syndrome

An attempt was made to recognize entrapment of the lumbar root within the root canal using four criteria; (1) severe, constant root pain to the lower leg, (2) pain unrelieved by bed rest, (3) minimal tension signs, and (4) patients over 40 years of age. Two hundred forty-nine patients fulfilled the criteria, representing 11% of patients attending a back pain clinic. Most had restricted spinal extension, but few had abnormal neurologic signs. Degenerative change was common, especially disc space reduction. Central canal size measured by ultrasound was normal, compatible with a variable past history of back pain. Patients with a long history of back pain numbered 80%, and 90.4% were managed by nonoperative means. Although 78% of these still had some root pain between 1 and 4 years after first attendance, most of them were not troubled sufficiently to have sought alternative help.
Cytokines, Treatment Responses, and Body Weight Changes in Major Depressive Patients Treated with Antidepressants

Objectives: Serum cytokine levels are implicated in the action of mechanism for acute-phase major depression. In this study, we intended to investigate the relationships between cytokine serum levels and treatment responses as well as body weight changes after a four-week antidepressant treatment in patients with major depressive disorders. Methods: Fifty-four major depressive patients were recruited. Their serum cytokine levels of interferon-γ (IFN-γ), tumor necrosis factor-α (TNF-α), interleukin-10 (IL-10), and transforming growth factor β1 (TGF-β1) were examined using ELISA kits. Psychiatric diagnoses were made using the DSM-IV criteria. Severity of major depression was assessed using the 17-item Hamilton Depression Rating Scale. Results: We found significantly lower baseline serum IL-10 level (p = 0.001) and significantly lower baseline IL-10/TGF-β1 ratio (p ＜ 0.01) in responders compared to those in non-responders. In all patients after antidepressant treatment, we found a significant positive correlation between body weight change and TNF-α/TGF-β1 ratio change (p ＜ 0.05). In responders alone, a significant positive correlation between body weight change and TNF-α/ TGF-β1 ratio change (p ＜ 0.05) was found. In non-responders, a significant negative correlation between body weight change and IL-10/TGF-β1 ratio change (p ＜ 0.01) was found. Conclusion: Serum levels of TNF-α, IL-10 and TGF-β1 could be used to predict the treatment response and body weight change in patients with major depression.
Bilateral Histogram Equalization for Contrast Enhancement

As image enhancement is a well discussed issue, various methods have already been proposed till to date. Some of these methods perform well for specific applications but most of the techniques suffer from artifacts due to the over or under enhancement. To mitigate this problem a new technique namely Bilateral Histogram Equalization for contrast enhancement BHE which uses Harmonic mean of the image to divide the histogram is introduced. BHE is evaluated in both qualitative and quantitative manner and the results show that BHE creates less artifacts on several standard images than other existing state-of-the-art image enhancement techniques.
Capturing Cultural Differences in Expressions of Intentions

The intersection of psychology and computational linguistics is capable of providing novel automated insight into the language of everyday cognition through analysis of micro-blogs. While Twitter is often seen as banal or focused only on thewho,what,when orwhere tweets can actually serve as a source for learning about the language people use to express complex cogntive states and their cultural identity. In this contribution we introduce a novel model which captures latent cultural dimensions through an individual’s expressions of intentionality. We then show how these latent cultures can be used to create a culturally-sensitive model which provides enahnced detection of signals of intentionality in tweets. Finally, we demonstrate how these models reveal interesting cross-cultural differences in the goals and motivations of individuals from different cultures.
Aberrant splicing of the type III procollagen mRNA leads to intracellular degradation of the protein in a patient with ehlers‐danlos type IV

Ehlers‐Danlos syndrome type IV (EDS IV) is an autosomal dominant disorder characterized by fragile skin, blood vessels, and internal organs and associated with decreased production, secretion, or thermal stability of type III procollagen. Mutations in the gene for type III procollagen have been identified in patients exhibiting decreased secretion or thermal stability of the protein, but no defect has been elucidated to explain the decreased production of type III procollagen in some patients with EDS IV. We report on a patient with a moderate case of EDS IV who produced decreased amounts of type III procollagen despite normal levels of translatable type III procollagen mRNA. SI nuclease analysis of the type III procollagen mRNA indicated a defect in the region encoding exon 27. Sequence analysis of cDNA clones and genomic fragments generated by polymerase chpin reaction amplification revealed that sequences encoded by exon 27 were absent from 3 out of 5 cDNA clones and that a G at the +5 position of the splce donor site in intron 27 was changed to an A in one allcle of the patient's type III procollagen gene. Using a cDNA genomic DNA hybrid probe in Si nuclease analysis, fragments consistent with mRNA species containing and lacking exon 27 were detected in a 1:1 ratio. Pulse label and chase experiments in the presence or absenci: of brefeldin A indicated that most of the type III procollagen molecules synthesized by the patient'; fibroblasts were not secreted into the medium but were degraded in the endoplasmic reticulum‐Golgi compartment by a nonlysosomal mechanism. © 1995 Wiley‐Liss, Inc.
Quality of life in high-functioning adults with autism spectrum disorder

Although the concept of quality of life has increasingly been used in the field of intellectual disabilities over the past three decades, the factors contributing to quality of life of persons with autism spectrum disorder (ASD) have received relatively little attention. In this study, disability and support characteristics associated with variations in the level of quality of life among adults with ASD are identified, using self-report measures. Fifty-eight high-functioning adults with ASD participated in the study. The results of a multiple linear regression analysis reveal that support characteristics are related to quality of life in adults with ASD, whereas disability characteristics are not. The R2 effect size (0.620) is large and significant. The results reinforce the significance of an available supportive social network, the importance of a substantial needs assessment and effective professional support.
Nonparametric approaches to estimation problems for demand and supply functions in Power Exchange markets

In this paper, we demonstrate two approaches to estimate supply and demand functions in the Japan Electric Power Exchange (JEPX) spot market based on the sell and buy matching rates (SMRs and BMRs) and the nonparametric simultaneous equations. In the first approach, we apply the generalized additive model (GAM) of the contract price on the SMR and the BMR to derive the volume rate functions, where the SMR and the BMR are defined using the contract volume divided by the total selling and buying volumes. We demonstrate that supply and demand functions are obtained by performing the coordinate transformations for the volume rate functions. In the nonparametric simultaneous equations approach, we use the total selling and buying volumes as exogenous variables and show that supply and demand functions may be constructed based on parametric representations using GAMs. An empirical analysis is also included to compare the two approaches.
A Web-Based Sign Language Translator Using 3D Video Processing

The American Sign Language (ASL) is used by hearing-impaired people in North America, as well as in other parts of the world to supplement indigenous sign language. A proof-of-concept ASL Translator has been designed and developed using 3D video processing techniques. Foreseeing its potential as a Web-based application, the Translator must have a portable input device to capture gestures and its cost must be kept low. The recently introduced Xbox Kinect is a versatile gesture input device and fits the low-cost requirement as well. 3D data of the joints of a user captured by the Kinect are analyzed and matched to a library of pre-recorded signs. The matched signs are then transcribed to word or phrase, and output to a suitable user interface. The implemented prototype works with excellent accuracy for a limited vocabulary. Using the Web and a server to archive the pre-recorded signs and to process recorded gesture via a motion capture device, there are many potential applications. The Translator can be utilized as an assistive tool for the hearing impaired to communicate or as a teaching tool for those who want to learn the sign language.
The role of the CA3 subregion of the dorsal hippocampus in spatial pattern completion in the rat

Rats were trained on a delayed matching‐to‐sample for a spatial location task to examine spatial pattern completion. On the sample phase of the task, rats were trained to move a small black block covering a food well that could appear in one of five possible spatial locations. During the choice phase of the task, rats were required to find the same food well, with the block removed so as to receive reinforcement. After reaching stable performance in terms of accuracy to find the correct location, rats received neurotoxic injections into the CA3 subregion of the hippocampus. The control group received vehicle injections into the CA3 subregion. After surgery, four extramaze cues were always available during the sample phase, but during the choice phase zero, one, two, three, or four cues were removed. The results indicate that normal vehicle control injected rats display excellent pattern completion across all reductions in the availability of cues, whereas rats with CA3 lesions are impaired in pattern completion as indicated by a linear increase in errors as the number of available cues is reduced. It appears that the CA3 subregion of the hippocampus plays an important role in spatial pattern completion. ©2005 Wiley‐Liss, Inc.
An Improved Culture Method for Selective Isolation of Campylobacter jejuni from Wastewater

Campylobacter jejuni is one of the leading foodborne pathogens worldwide. C. jejuni is isolated from a wide range of foods, domestic animals, wildlife, and environmental sources. The currently available culture-based isolation methods are not highly effective for wastewater samples due to the low number of C. jejuni in the midst of competing bacteria. To detect and isolate C. jejuni from wastewater samples, in this study, we evaluated a few different enrichment conditions using five different antibiotics (i.e., cefoperazone, vancomycin, trimethoprim, polymyxin B, and rifampicin), to which C. jejuni is intrinsically resistant. The selectivity of each enrichment condition was measured with Ct value using quantitative real-time PCR, and multiplex PCR to determine Campylobacter species. In addition, the efficacy of Campylobacter isolation on different culture media after selective enrichment was examined by growing on Bolton and Preston agar plates. The addition of polymyxin B, rifampicin, or both to the Bolton selective supplements enhanced the selective isolation of C. jejuni. The results of 16S rDNA sequencing also revealed that Enterococcus spp. and Pseudomonas aeruginosa are major competing bacteria in the enrichment conditions. Although it is known to be difficult to isolate Campylobacter from samples with heavy contamination, this study well exhibited that the manipulation of antibiotic selective pressure improves the isolation efficiency of fastidious Campylobacter from wastewater.
Undetectable communication: The Online Social Networks case

Online Social Networks (OSNs) provide users with an easy way to share content, communicate, and update others about their activities. They also play an increasingly fundamental role in coordinating and amplifying grassroots movements, as demonstrated by recent uprisings in, e.g., Egypt, Tunisia, and Turkey. At the same time, OSNs have become primary targets of tracking, profiling, as well as censorship and surveillance. In this paper, we explore the notion of undetectable communication in OSNs and introduce formal definitions, alongside system and adversarial models, that complement better understood notions of anonymity and confidentiality. We present a novel scheme for secure covert information sharing that, to the best of our knowledge, is the first to achieve undetectable communication in OSNs. We demonstrate, via an open-source prototype, that additional costs are tolerably low.
Dentin etch chemistry investigated by Raman and infrared spectroscopy

Micro-Raman and infrared spectroscopy were used to investigate the influence of surface treatment on the diffusion of a dental adhesive into dentin. The commercial dentin adhesive Scotchbond MultiPurpose Plus (3M) was placed on coronal dentin substrates that were cut from extracted, unerupted third molars. Prior to placement of the adhesive, one surface was treated with a phosphoric acid etch and the other with a citric acid–iron(III) chloride etch. Thin sections, ∼3 μm in thickness, were prepared and mounted on silver chloride disks for infrared spectroscopic studies with the remaining bulk sample being used for the Raman studies. The infrared studies were performed at the Aladdin Synchrotron radiation source at the Synchrotron Radiation Center, Stoughton, WI, USA. The Raman studies employed a krypton ion laser in conjunction with a microscope equipped with a 100× objective and confocal aperture. In both studies the sample was translated in 1 μm steps at the focus of the respective radiation, providing a line scan across the interface. The infrared results clearly show the interface but owing to the diffraction limit of ∼15 μm, accurate dimensional information could not be obtained. The Raman results clearly indicate a broad interface associated with the sample etched with phosphoric acid and the presence of a much more abrupt interface with the citric acid etch. Additionally, a thin layer of exposed collagen exists at the dentin–adhesive interface. Copyright  2000 John Wiley & Sons, Ltd.