jimnoneill/paper-to-field-training huggingface dataset:
Summary of the BioLINK SIG 2013 meeting at ISMB/ECCB 2013

Abstract The ISMB Special Interest Group on Linking Literature, Information and Knowledge for Biology (BioLINK) organized a one-day workshop at ISMB/ECCB 2013 in Berlin, Germany. The theme of the workshop was ‘Roles for text mining in biomedical knowledge discovery and translational medicine’. This summary reviews the outcomes of the workshop. Meeting themes included concept annotation methods and applications, extraction of biological relationships and the use of text-mined data for biological data analysis. Availability and implementation: All articles are available at http://biolinksig.org/proceedings-online/ . Contact: karin.verspoor@unimelb.edu.au

Topic: Biomedical Text Mining and Ontologies
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Comparison of the Treatment Efficacy of Rituximab and Plasmapheresis/Intravenous Immunoglobulin Combination with Historical Control in Chronic Antibody Mediated Rejection

OBJECTIVE: Chronic antibody mediated rejection (CAMR) is a major therapeutic challenge for achieving long-term graft survival; treatment options are limited to several anti-humoral interventions. MATERIAL and METHODS: Efficacy of rituximab combination therapy was retrospectively investigated by comparison with a historical control group for allograft function at six month and overall graft survival/dysfunction. The inclusion criterion was biopsy proven chronic AMR according to the Banff 2007 classification. Nineteen patients found eligible, rituximab group had nine patients (rituximab, plasmapheresis and low dose IVIG); control group had ten recipients. Predictive factors for graft failure also investigated according to Banff scores and renal functions. RESULTS: None of the outcomes were exposed significant efficacy of rituximab, although better treatment response at sixth month (55% vs. 40%, p= 0.51), fewer overall graft failures (33% vs. 60%, p= 0.25) and dysfunctions (66% vs. 80%, p= 0.52). Overall, 47% of patients suffered graft failure. Advanced transplant glomerulopathy was found in 90% of biopsies (all scored = 2). Peritubular capillaritis score (1.67 +/- 0.87 vs. 0.70 +/- 0.94, p= 0.04) and interstitial inflammation score (1.78 +/- 0.44 vs. 1.00 +/- 0.47, p= 0.004) were significantly higher in recipients who suffered graft failure. CONCLUSION: Rituximab could not sufficiently prevent further deterioration of allograft and failed to improve allograft survival in CAMR, especially after settlement of the irreversible transplant glomerulopathy.

Topic: Blood groups and transfusion
Subfield: Hematology
Field: Medicine
Domain: Health Sciences
The emotional labour of prison work

The emotional life in prisons has been described in popular literature in terms of horror and suffering, but the research literature on this topic is sparse and mostly produced in later decades. During this short time, emotion research concerning prisons has focussed on a prison reality under constant change and development. The development of prisons, which is influenced by increased security, technical monitoring, and risk governance but also by centralization, specialization, and efficiency demands, has deeply affected prison work. Not the least of these concerns is the emotional labour performed by the largest group of staff, the prison officers. How this labour is performed in each prison wing or unit is closely connected to the institutional framework, the subculture, and the relationships between officers and prisoners. The aim of this chapter is to describe and discuss the emotional labour of prison staff under today's prevailing conditions of prison life and ongoing changes to prison systems. This is done with reference to research findings from several countries as well as data from our own Swedish research projects. Research and data on prison officer work will be analysed in the light of prison policy changes and organisational theory on the development of public organisations and by using the work of Hochschild and other social theorists.

Topic: Criminal Justice and Corrections Analysis
Subfield: Sociology and Political Science
Field: Social Sciences
Domain: Social Sciences
Reconstruction Legal Culture of Madurese Based on Pancasila Values as Criminal Policy in Tackling Carok (Duel)

This study attempts to uncover carok (duel), a tradition used as a solution to overcome problems related to the humiliation of a man's honor in the Madurese. This homogenous society believes that dying would be better than living enduring shame. It seems that carok becomes a socio-cultural fate for

Topic: Legal Studies and Policies
Subfield: Law
Field: Social Sciences
Domain: Social Sciences
Development of Hodgkin Lymphoma in a Patient with Common Variable Immunodeficiency

Common variable immunodeficiency (CVID) is a primary immunodeficiency, which is characterized by insufficiency in the synthesis of immunoglobulins due to the disruption of B cell differentiation.The term "variable" in its name describes the heterogeneous clinical picture (infections, chronic lung disease, autoimmune diseases, gastrointestinal disorders, and malignancy) in this disease.Although the risk of developing malignancy in children with primary immunodeficiency is reported to be 4%, this rate is 10.000 times higher than healthy subjects of similar age.Non-Hodgkin lymphoma (NHL) accounts for 60% of malignancy in primary immunodeficiency patients (1).In the cohorts, the incidence of cancer in CVID patients was 15-21%.The most common malignancy was reported to be NHL, followed by gastric, breast, bladder, and cervix tumors (2-4).Our case shows that Hodgkin lymphoma may rarely develop in CVID and is presented to raise awareness.

Topic: Immunodeficiency and Autoimmune Disorders
Subfield: Immunology
Field: Immunology and Microbiology
Domain: Life Sciences
γ-Aminobutyric Acid-producing Lactic Acid Bacteria from Kimchi : Potential Psychobiotics

γ-Aminobutyric acid (GABA) functions as the primary inhibitory neurotransmitter in mammals, numerous studies have demonstrated that direct ingestion of GABA effectively induces natural sleep and alleviates stress. Low doses of GABA reduce stress by modulating the autonomic nervous system, while high doses do so by modulating the central nervous system. The oral administration of GABA-producing lactic acid bacteria (LAB) to experimental animals has been shown to promote mental health and ameliorate neurological disorders, such as essential tremor and depression, and to have positive effects on diabetes, fibromyalgia, chronic fatigue, and pain in experimental animals. Consequently, diet supplementation with GABA-producing LAB offers a potential means of treating mental health and neurological disorders in humans. Furthermore, supplementation with GABA-producing LAB might have sleep-inducing and stress-relieving effects akin to those observed after GABA consumption. Numerous LAB strains in kimchi produce diverse metabolites, and a significant proportion generate GABA. Although further animal and clinical studies are required, kimchi-sourced GABA-producing LAB appear to be potential psychobiotics.

Topic: GABA and Rice Research
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Pre History Cultures and Setting Identity Gayo Community (Knowledge for Power)

Gayo is the name of the ethnic group that occupies the plateau region of Aceh, Sumatra Island. Archaeological data showed that there was a prehistoric activity of two different human races that Australomelanesoid and Mongoloid. Both of these races acculturated at around 5000 BP. Of the remains suggests that they have a fairly advanced culture . It is known from deskrifsion on artifacts , ecofact and features that are found to then interpreted. The result of the prehistoric culture continued until before the arrival of Islam to the region. Archaeological research results are then used to amplify the desire Gayo community forming the Province of Aceh Leuser Antara Keywords : Archaeologycal data, ethnic identity, Aceh Leuser Antara Province

Topic: Hermeneutics and Narrative Identity
Subfield: Philosophy
Field: Arts and Humanities
Domain: Social Sciences
Vacancy-stabilized crystalline order in hard cubes

We examine the effect of vacancies on the phase behavior and structure of systems consisting of hard cubes using event-driven molecular dynamics and Monte Carlo simulations. We find a first-order phase transition between a fluid and a simple cubic crystal phase that is stabilized by a surprisingly large number of vacancies, reaching a net vacancy concentration of approximately 6.4% near bulk coexistence. Remarkably, we find that vacancies increase the positional order in the system. Finally, we show that the vacancies are delocalized and therefore hard to detect.

Topic: Theoretical and Computational Physics
Subfield: Condensed Matter Physics
Field: Physics and Astronomy
Domain: Physical Sciences
Comparative analysis of modern tendencies in the development of the lexical level of the language system based on the Russian and the English languages

Tendencies in the development and changes of the language, as well as the current state of the language and the forms of its existence in the 21st century have been undergoing various changes, while being conditioned by the internal patterns of the development of the relevant language systems. The main feature of language development of the modern period is the speed and intensity of language processes, the main dominants of language development including the influence of socio-political factors on the development of the language system, the predominance of quantitative changes over qualitative, functional over systemic. Since language, and its lexical composition in particular, plays the key role of a means of communication, language is being refined, differentiated and rebuilt in order to adequately and expediently reproduce, display and consolidate new concepts and phenomena in appropriate words and expressions. Form the point of view of demonstrating the tendency towards saving linguistic resources, we can turn to borrowings. In addition, an interesting development is the tendency to save linguistic resources in the process of new words formation based on abbreviations of existing words. An important characteristic of the modern language lexical level is also the tendency to analyticism and the law of emphase manifested in both Russian and English.

Topic: Lexicography and Language Studies
Subfield: Language and Linguistics
Field: Arts and Humanities
Domain: Social Sciences
Supplementary Materials from Breast Cancer Detection by B7-H3–Targeted Ultrasound Molecular Imaging

&lt;p&gt;Supplementary Table 1. Summary of B7-H3 Immunohistochemistry Scores in Human Tissue Samples. Supplementary Table 2. Subanalysis of B7-H3 IHC Scores in Cancer and Surrounding Normal, Benign and Precursor Lesions&lt;/p&gt;

Topic: Cancer Research and Treatments
Subfield: Biotechnology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Room temperature electrically pumped silicon nano-light source at telecommunication wavelengths

We demonstrate electrically pumped silicon nano-light source at room temperature, having very narrow emission line (&#60;0.5nm) at 1500nm wavelength, by enhancing the electroluminescence (EL) via combination of hydrogen plasma treatment and Purcell effect. The measured output power spectral density is 0.8mW/nm/cm2, which is highest ever reported value from any silicon light emitter.

Topic: Nanowire Synthesis and Applications
Subfield: Biomedical Engineering
Field: Engineering
Domain: Physical Sciences
How the Dutch deal with demographic decline

For the past few years, there has been much attention paid to demographic decline in the Netherlands. Initially, the shrinkage of an area’s population was considered as a marginal phenomenon in the peripheral regions, such as Limburg, Groningen and Zeeland. However, now, it is recognized as an omnipresent phenomenon. According to the Netherlands Environmental Assessment Agency, up to 2030 a quarter of the Dutch municipalities will experience a population decline of more than 2.5% (PBL 2014). Furthermore, this decline will not remain limited to areas on the edges of the Netherlands. For example, villages within the Randstad conurbation are already having to deal with that now. There is also a demographic decline in the large cities such as Rotterdam and Almere. Here, we usually see that one district is growing at the expense of another.

Topic: Migration, Aging, and Tourism Studies
Subfield: Demography
Field: Social Sciences
Domain: Social Sciences
Effect of Body Mass Index on Eruption Time of Permanent First Molars and Incisors among a Group of 6- 8 Year Old Iraqi School Children

Tooth Eruption is the process that involves the movement or change of position of the tooth from the deeper portion of the jaws into the oral cavity until it achieves occlusal contact with adjacent and opposing teeth. Many factors that affect the eruption time of the teeth. Nutrition is the science of food and its relationship to health. The aims of the study were to count the number of teeth erupted in 6 -8 years old children and see the effect of BMI on the eruption time and level of eruption in those children. Body mass index is an index which its use as growth indicator is also controversial but it has been widely used in the field of dentistry, especially in studies about obesity and dental caries. It's used to classify children into healthy, underweight and overweight. The total sample consisted of 50 primary school children between 6 -8 years old girls and boys. The erupted permanent incisors and first molars were recorded and their level of eruption was also recorded. Nutritional status of each child was assessed by measuring height and weight to calculate body mass index according to formula recorded by Worlds Health Organization, 2000. The higher number of erupted permanent teeth was seen in girls of 6 -7 and 7 -8 years old. Girls 7 -8 years old show highest weight values. The number of erupted teeth in healthy children was higher than other children. There was a significant difference in the number of erupted permanent teeth between the healthy and the over weighted children. The highest stage of eruption (stage 4) was seen for the mandibular central incisors, the maxillary and mandibular first molars. It can be concluded that BMI affected the eruption time of permanent first molars and incisors which was seen mostly in girls.

Topic: Forensic Anthropology and Bioarchaeology Studies
Subfield: Archeology
Field: Arts and Humanities
Domain: Social Sciences
Diltiazem Inhibits the Spontaneous Platelet Aggregation in Essential Hypertension

Plasma beta-thromboglobulin, initial (spontaneous) and total platelet aggregation, induced by adrenaline or ADP, were determined in 15 patients with essential hypertension before and after 1 week of diltiazem therapy. Diltiazem significantly decreased the spontaneous platelet aggregation in a therapeutic dose of 3 x 60 mg/day. This antiaggregatory effect is the further advantage of the antihypertensive therapy with diltiazem that may be of importance for the inhibition of atherosclerotic and thrombotic complications in essential hypertension.

Topic: Cholesterol and Lipid Metabolism
Subfield: Surgery
Field: Medicine
Domain: Health Sciences
Draft Genome Sequence of Rhizobium sp. Strain PDO1-076, a Bacterium Isolated from Populus deltoides

ABSTRACT Rhizobium sp. strain PDO1-076 is a plant-associated bacterium isolated from Populus deltoides , and its draft genome sequence is reported.

Topic: Legume Nitrogen Fixing Symbiosis
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
The Improving Management of Hospital Business Process Pattern in Nosocomical Infections Control by Means of Clinical Pharmacy Intervene Route

The inspect and contral of nosocomical infection(NI)is an important component of hospital quality.By means of clinical pharmacy intervene route which regards as key process of hospital Improving Management of Hospi- tal Business Process in our hospital,through process reconstruction and sustain improving over one year,the level of rationaliazing antibiotics in clinical was improved,the rate of NI decreased,the rate of delivering test ascended.

Topic: Pharmacy and Medical Practices
Subfield: Pharmacology
Field: Pharmacology, Toxicology and Pharmaceutics
Domain: Life Sciences
Acute viral hepatitis (C - genotype 6a and B) acquired during kidney transplantation by two patients and review of the literature.

Two patients were contaminated by hepatitis during kidney transplantation from unrelated living donors, performed abroad in 2006. One patient died from fulminant hepatitis C (the first case of virus genotype 6a diagnosed in Israel) 2 months after transplantation and the other developed acute hepatitis B with YMDD to YVDD mutation necessitating life-long antiviral therapy. The dilemma of antiviral therapy in transplant recipients is discussed in this paper. Patients awaiting kidney transplantation by far outnumber the kidneys available for cadaver transplantation. International trade with living non-related kidneys has therefore become common. Comorbid conditions, although significant, are often ignored. After transplantation, the first patient presented with a picture of fulminant hepatitis C; immunosuppressive medication was tapered rapidly. This patient subsequently died from hepatic failure. The patient with active hepatitis B with YVDD mutation is receiving ongoing treatment by lamivudine and adefovir.

Topic: Hepatitis C virus research
Subfield: Hepatology
Field: Medicine
Domain: Health Sciences
Third-Generation High-Vision Ultrathin Endoscopy Using Texture and Color Enhancement Imaging and Narrow-Band Imaging to Evaluate Barrett’s Esophagus

It remains unclear whether texture- and color-enhancement imaging (TXI) and narrow-band imaging (NBI) provide an advantage over white-light imaging (WLI) in Barrett’s esophagus. We compared endoscopic findings and color differences between WLI and image-enhanced endoscopy (IEE) using a third-generation ultrathin endoscope. We retrospectively enrolled 40 patients who evaluated Barrett’s esophagus using WLI, TXI, and NBI. Color differences determined using the International Commission on Illumination 1976 (L∗, a∗, b∗) color space among Barrett’s epithelium, esophageal, and gastric mucosa were compared among the endoscopic findings. As the secondary outcome, we assessed the subjective visibility score among three kinds of endoscopic findings. The prevalence of Barrett’s esophagus and gastroesophageal reflux disease (GERD) in WLI was 82.5% and 47.5%, respectively, and similar among WLI, TXI, and NBI. Color differences between Barrett’s epithelium and esophageal or gastric mucosa on NBI were significantly greater than on WLI (all p &lt; 0.05). However, the color difference between Barrett’s epithelium and esophageal mucosa was significantly greater on NBI than TXI (p &lt; 0.001), and the visibility score of Barrett’s epithelium detection was significantly greater on TXI than NBI (p = 0.022), and WLI (p = 0.016). High-vision, third-generation ultrathin endoscopy using NBI and TXI is useful for evaluating Barrett’s epithelium and GERD compared with WLI alone.

Topic: Esophageal Cancer Research and Treatment
Subfield: Surgery
Field: Medicine
Domain: Health Sciences
[Mixed tumor in cervical salivary heterotopy].

This paper presents a case, infrequent and clinically unsuspected, of pleomorphic adenoma in the upper region of the neck in front of the sternocleidomastoid, independent of the salivary glands. The tumor developed within an heterotopic salivary gland of seromucose type, the histopathologic study of the surgical piece being decisive in the diagnosis. The characteristics of salivary heterotopias of the neck, and their diagnostic difficulties and histogenetic problems are reviewed.

Topic: Salivary Gland Tumors Diagnosis and Treatment
Subfield: Surgery
Field: Medicine
Domain: Health Sciences
Spontaneous Chromosome Breakage in Lilium Endosperm

Abnormal mitoses, resulting from chromosome breakage and reunion, occurred in Lilium regale and in the hybrid L. ‘Phyllis Cox’ 4 weeks after fertilization. The abnormalities appeared to commence with a single chromatid bridge and in ‘Phyllis Cox’ abnormalities accumulated resulting in the formation of multiple bridges, ring chromosomes, fragments, dicentric chromosomes, and micronuclei. Failure of anaphase separation followed by restitution resulted in the formation of highly polyploid nuclei in which mass spontaneous chromosome breakage occurred. The accumulation of abnormalities in the hybrid endosperm reduced the mitotic activity and culminated in the failure of the endosperm. This led to the death of the otherwise normal embryo. This sequence of events is probably of wide importance in the failure of interspecific hybridization.

Topic: Flowering Plant Growth and Cultivation
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
How Well Can Spaceborne Digital Elevation Models Represent a Man-Made Structure: A Runway Case Study

In this case study, an active runway of a civilian airport in Zonguldak, Turkey, is used to assess the suitability of spaceborne digital elevation models (DEMs) to model an anthropogenic structure. The tested DEMs include the ASTER, the AW3D30 m, the SRTM-1&amp;rdquo;, the SRTM-3&amp;rdquo;, the SRTM-X, the TanDEM-3&amp;rdquo;, and the WorldDEMTM. A photogrammetric high accuracy DEM was also available for the tests. As a reference dataset, a line leveling survey of the runway using a Leica Sprinter 150/150M instrument was performed. The selection of a runway as a testbed for this type of investigation is justified by its unique characteristics, including its flat surface, homogenous surface material, and availability for a ground survey. These characteristics are significant because DEMs over similar structures are free from environment- and target-induced error sources. The most accurate DEM is the WorldDEMTM followed by the SRTM-3&amp;rdquo; and TanDEM-3&amp;rdquo;, with vertical errors (LE90) equal to 1.291 m, 1.542 m, and 1.56 m, respectively. This investigation uses a method for identifying the vertical errors in DEMs that is known as the runway method.

Topic: 3D Surveying and Cultural Heritage
Subfield: Geology
Field: Earth and Planetary Sciences
Domain: Physical Sciences
The Evolution of Housing Typologies for Older Adults in The Netherlands From 1945 to 2016: An Analysis in the Context of Policy, Societal, and Technological Developments

This study aims to examine housing typologies for older adults in the light of three qualitatively examined exogenous factors: policy, societal and technological changes. The developments in inpatient and semi-residential care facilities for older adults have been mapped from 1945-2016 using quantitative data. Using this data five transition periods can be distinguished. This research shows that the classification of inpatient, semi-residential and outpatient living may no longer be applicable in its current form. Through exogenous factors new typologies have emerged and this paper proposes a classification as a foundation for further research into housing typologies for older adults.

Topic: Migration, Aging, and Tourism Studies
Subfield: Demography
Field: Social Sciences
Domain: Social Sciences