jimnoneill/paper-to-field-training huggingface dataset:
Prioritizing Disease Genes and Understanding Disease Pathways

Genetic factors play a major role in the etiology of many human diseases. Genome-wide experimental methods produce an increasing number of genes associated with such diseases. This chapter introduces data sources, bioinformatics tools, and computational methods for prioritizing disease candidate genes and identifying disease pathways. The main strategy is to examine the similarity among the candidate genes and known disease genes at the functional level. The authors review different similarity measures and prevailing methods for integrating results from different functional aspects. They hope this chapter will help advocate many useful resources that the researchers can use to investigate diseases of their interest.

Topic: Bioinformatics and Genomic Networks
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
The pathological and immunohistochemical profile of tumor angiogenesis in perforated sigmoid carcinoma–Case report and short literature review

&lt;b&gt;Background:&lt;/b&gt; Little is known about the physiopathological factors or mechanisms that underlie tumor invasion of the serosa and lead to perforation in the peritoneal cavity. The aim of the work was to analyze the pathological and immunohistochemical factors of tumor neoangiogenesis which could influence tumor perforation in colorectal cancer.&lt;br /&gt; &lt;b&gt;Results and discussions:&lt;/b&gt; 451 cases of complicated colorectal carcinomas were statistically analyzed, of which 19 cases were perforated sigmoid tumors. The immunohistochemical detection of mutant p53 proteins was the first molecular parameter examined in the context of the search for markers predicting the natural evolution mode in colorectal carcinomas.&lt;br /&gt; &lt;b&gt;Conclusions&lt;/b&gt;: Both loss of p53 and overexpression of bcl-2 proteins confer immortalization on cancer cells by inhibiting the processes leading to apoptosis. The paper proposes a review of the specialized literature, but also the presentation of a clinical case.

Topic: Cancer, Lipids, and Metabolism
Subfield: Cancer Research
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
The Effect of Non-Personalised Tips on the Continued Use of Self-Monitoring mHealth Applications

Chronic tinnitus, the perception of a phantom sound in the absence of corresponding stimulus, is a condition known to affect patients’ quality of life. Recent advances in mHealth have enabled patients to maintain a ‘disease journal’ of ecologically-valid momentary assessments, improving patients’ own awareness of their disease while also providing clinicians valuable data for research. In this study, we investigate the effect of non-personalised tips on patients’ perception of tinnitus, and on their continued use of the application. The data collected from the study involved three groups of patients that used the app for 16 weeks. Groups A &amp; Y were exposed to feedback from the start of the study, while group B only received tips for the second half of the study. Groups A and Y were run by different supervisors and also differed in the number of hospital visits during the study. Users of Group A and B underwent assessment at baseline, mid-study, post-study and follow-up, while users of group Y were only assessed at baseline and post-study. It is seen that the users in group B use the app for longer, and also more often during the day. The answers of the users to the Ecological Momentary Assessments are seen to form clusters where the degree to which the tinnitus distress depends on tinnitus loudness varies. Additionally, cluster-level models were able to predict new unseen data with better accuracy than a single global model. This strengthens the argument that the discovered clusters really do reflect underlying patterns in disease expression.

Topic: Hearing Loss and Rehabilitation
Subfield: Cognitive Neuroscience
Field: Neuroscience
Domain: Life Sciences
Method Westerns: The Left-Handed Gun and One Eyed Jacks

This chapter discusses how the Method style of American film acting was appropriate to the representation of the heroic but psychologically complex protagonists of Hollywood Western films in the 1950s and 1960s. The chapter explains the history of how Method came to the USA, how it was taught at the Actors Studio, and how Hollywood stars used it in their work. The chapter explores the implications of Method for performances by Paul Newman in The Left Handed Gun (1958) and Marlon Brando in One Eyed Jacks (1961).

Topic: Cinema and Media Studies
Subfield: Economics and Econometrics
Field: Economics, Econometrics and Finance
Domain: Social Sciences
Micro-Raman spectroscopic characterization of ZnO quantum dots, nanocrystals and nanowires

Nanostructures, such as quantum dots, nanocrystals and nanowires, made of wurtzite ZnO have recently attracted attention due to their proposed applications in optoelectronic devices. Raman spectroscopy has been widely used to study the optical phonon spectrum modification in ZnO nanostructures as compared to bulk crystals. Understanding the phonon spectrum change in wurtzite nanostructures is important because the optical phonons affect the light emission and absorption. The interpretation of the phonon peaks in the Raman spectrum from ZnO nanostructures continues to be the subject of debates. Here we present a comparative study of micro-Raman spectra from ZnO quantum dots, nanocrystals and nanowires. Several possible mechanisms for the peak position shifts, i.e., optical phonon confinement, phonon localization on defects and laser-induced heating, are discussed in details. We show that the shifts of ~2 cm<sup>-1</sup> in non-Resonant spectra are likely due to the optical phonon confinement in ZnO quantum dots with the average diameter of 4 nm. The small shifts in the non-Resonant spectra from ZnO nanowires with the diameter ~20 nm - 50 nm can be attributed to either defects or large size dispersion, which results in a substantial contribution from nanowires with smaller diameters. The large red-shifts of ~10 cm<sup>-1</sup> in the resonant Raman spectrum from nanocrystals were proved to be due to local laser heating.

Topic: ZnO doping and properties
Subfield: Materials Chemistry
Field: Materials Science
Domain: Physical Sciences
Characterization of Methotrexate Loaded Fucoidan/Chitosan Nanoparticles

Methotrexate is one of the most popular and safe anti-inflammatory drugs which is an antifolate-type antimetabolite and is used as an anticancer drug. In this study, oppositely charged chitosan and fucoidan have been non-covalently bonded using their electrostatic interactions with the methotrexate drug loaded into these nanoparticles. Fucoidan is obtained from marine algae which are composed of l-fucose and sulfate groups in various types of brown seaweeds; whereas chitosan is a naturally occurring biopolymer obtained through the N-deacetylation of chitin. Depending on the fucoidan / chitosan (F / C) weight ratio, three distinct nanoparticles (1F / 1C; 3F / 1C; 5F / 1C) are synthesized and characterized. Nanoparticles were prepared using cross linkers EDC and NHS at a constant pH to reduce the conjugate size. The prepared conjugates were characterized for their size and zeta potential using DLS analysis and the functional groups were analysed using FTIR. DLS results proclaimed that there was size reduction in particle size with cross linker and without the drug methotrexate. The 5:1 F/C nanoparticles was seen to be 441.5 nm, the difference being considerable larger in the 5:1 formulation. Hence for further analysis 5:1 F/C nanoparticles were preferred. Maximum entrapment efficiency was observed in 5:1 F/C nanoparticle with and without cross linkers. To understand the structural morphology of nanoparticles electromagnetic magnification like SEM and TEM were taken in account.

Topic: Seaweed-derived Bioactive Compounds
Subfield: Aquatic Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Black and white and read all over The constraints and opportunities of monochrome cartography in newspapers

AbstractNewspapers have traditionally appeared in monochrome, thus newspaper map designers have for most of their careers needed to exploit the opportunities available with black and white cartography, and although aware of the constraints this imposes, they have been unable to experiment with the possibilities that colour holds. In recent years however this has changed. Advances in technology have allowed newspapers to print in four-colour — most noticeable in the use of colour photography — facilitating the use of colour maps. This paper discusses with examples how and why black and white maps are used in newspapers and what colour can add.

Topic: Geographic Information Systems Studies
Subfield: Geography, Planning and Development
Field: Social Sciences
Domain: Social Sciences
How does priming influence people's decision? Quantitative analysis of EEG and eye movement II

The basic principle of priming involves stimulation of sensitivity to certain stimuli due to previous exposure to related stimulus. Such priming effects could possibly influence attitude and evaluation towards an image. In the realm of advertising, a successful product evaluation would likely depend on careful selection of primes. Current popular methods in evaluating priming effect of consumers’ attitude and intention, such as self-evaluation questionnaires, are not standardized and effective. In this project, the influence of subliminal priming on subjects’ perception of visual stimuli and decision-making by quantitative analysis of ERPs was studied. EEG data was acquired from forty subjects across three different priming conditions. The data mining process, includes signal enhancement, component analysis, feature selection and discriminant analysis, was applied in the study. The study compared normal averaging and Woody averaging techniques to investigate the latency jitters effect. In particular, windowed mean amplitude was applied for component analysis. The study focused on latency at early window, N100, and late window, P300 for evaluation involved in perception and decision-making process respectively. In particular, normal averaged ERP yielded significant results in the component analysis. Further study was carried out using SVM binary and multi-class classifier. Highest results of classification of priming conditions were obtained from the features selection studied earlier. Hence, it is evident that priming effect is influential to subjects’ evaluation of image or advertisement with the encouraging results of the component analysis and classification in line with previous literature.

Topic: Hermeneutics and Narrative Identity
Subfield: Philosophy
Field: Arts and Humanities
Domain: Social Sciences
Occurrence Download

A dataset containing 149 species occurrences available in GBIF matching the query: { "TaxonKey" : [ "is Pongo abelii Lesson, 1827" ] } The dataset includes 149 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003605-190307172214381/datasets/export for details. Data from some individual datasets included in this download may be licensed under less restrictive terms.

Topic: Mind wandering and attention
Subfield: Cognitive Neuroscience
Field: Neuroscience
Domain: Life Sciences
Application of Turbo Codes in a Radio Data-transmitting System

An overview of the apparent improvement of the system dependability from error correcting coding and decoding and its developments is made.On this basis,the application of Turbo codes in a specific radio data transmitting system is proposed.After analyzing and comparing,the design of Turbo codes is given to meet the system performance and parameter target.

Topic: Wireless Communication Networks Research
Subfield: Computer Networks and Communications
Field: Computer Science
Domain: Physical Sciences
Aspects of cohesion and coherence in translation

This book deals with the (re)production of cohesion and coherence in translation. Building on the theories and methods of Translation Studies and Discourse Analysis it answers some basic, still much debated questions related to translational discourse production. Such a question is whether it is possible to analyse the (re)production of coherence, and if yes, how? Can the models devised for the study of English original (not translated) and independent texts (unlike translations and their sources) be applied for the analysis of translation? How do cohesive, rhetorical and generic structure “behave” in translation? How do particular components of coherence relate to translation universals? The volume proposes a complex translational discourse analysis model and presents findings that bring new insights primarily for the study of news translation, translation strategies and translation universals. It is recommended for translation researchers, discourse analysts, practicing translators, as well as professionals and students involved in translator training.

Topic: Translation Studies and Practices
Subfield: Language and Linguistics
Field: Arts and Humanities
Domain: Social Sciences
Primary and Secondary Progressive Aphasia in Posterior Cortical Atrophy

Background: Posterior cortical atrophy (PCA) is a clinico-radiological syndrome characterized by a progressive decline in visuospatial/visuoperceptual processing. PCA is accompanied by the impairment of other cognitive functions, including language abilities. Methods: The present study focused on three patients presenting with language complaints and a clinical profile that was compatible with PCA. In addition to neurological and neuroimaging examinations, they were assessed with comprehensive batteries of neuropsychological and neurolinguistic tests. Results: The general medical profile of the three patients is consistent with PCA, although they presented with confounding factors, making diagnosis less clear. The cognitive profile of the three patients was marked by Balint and Gerstmann’s syndromes as well as impairments affecting executive functions, short-term and working memory, visuospatial and visuoperceptual abilities, and sensorimotor execution abilities. Their language ability was characterized by word-finding difficulties and impairments of sentence comprehension, sentence repetition, verbal fluency, narrative speech, reading, and writing. Conclusions: This study confirmed that PCA is marked by visuospatial and visuoperceptual deficits and reported evidence of primary and secondary language impairments in the three patients. The similarities of some of their language impairments with those found in the logopenic variant of primary progressive aphasia is discussed from neurolinguistic and neuroanatomical points of view.

Topic: Neurobiology of Language and Bilingualism
Subfield: Cognitive Neuroscience
Field: Neuroscience
Domain: Life Sciences
Modelling charge transfer reactions with the frozen density embedding formalism

The frozen density embedding (FDE) subsystem formulation of density–functional theory is a useful tool for studying charge transfer reactions. In this work charge-localized, diabatic states are generated directly with FDE and used to calculate electronic couplings of hole transfer reactions in two π-stacked nucleobase dimers of B-DNA: 5′-GG-3′ and 5′-GT-3′. The calculations rely on two assumptions: the two–state model, and a small differential overlap between donor and acceptor subsystem densities. The resulting electronic couplings agree well with benchmark values for those exchange-correlation functionals that contain a high percentage of exact exchange. Instead, when semilocal GGA functionals are used the electronic couplings are grossly overestimated.

Topic: DNA and Nucleic Acid Chemistry
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Detection and analysis systems for microsatellite markers in wheat

This paper describes and discusses strategies for screening microsatellites for use in plant genetic research and illustrates how a subset of useful microsatellites can be optimised for implementation on breeding and research using a range of techniques. Beginning with the initial screening of microsatellites for potential polymorphisms in a core set of potential parental lines, through to scaling up for mapping or breeding purposes, we present a time- and cost-effective approach to microsatellite analysis in wheat lines of interest. Each stage of this process benefits from a fresh examination of the techniques applied in order to increase the efficiency with which key markers can be identified and implemented. For the primary screening we use primers without modification to prime PCRs in the presence of f-dNTP (fluorescently labelled nucleotide) to provide the basis for high resolution screening for polymorphisms. As markers are defined for use in a breeding program, the focus changes to a smaller set of primer pairs that will be used to screen large numbers of DNA samples either from the analysis of progeny from a cross or the routine checking of cultivar identity in the industry. We then examine appropriate analysis platforms and refinement of PCR primers and conditions in order to identify procedures that can be implemented widely, not just in specialised well-equipped laboratories. In many cases we are able to use lower cost agarose analysis for identified polymorphisms. Where this is not feasable we examine primers for potential redesign to optimise their application either by altering the sequence of the primer itself, based on available sequence information, or by adding tails to the primers. The latter is shown to alter the ‘stutter’ pattern that is commonly observed with wheat microsatellites so that a single band is prominent and thus allows size polymorphisms to be more readily scored. The addition of a generic 5' tail also provides a method of using a generic fluorescent primer that can be applied to multiple tagged markers in a costeffective fashion. The potential of alternative analytical systems and further refinement of primers to show plus/minus reactions with wheat lines in order to produce simple tests for use in breeding programs are also discussed.

Topic: Wheat and Barley Genetics and Pathology
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Can the Number of Coagulase-negative Staphylococci Specimens Detected be an Alternative Quality Indicator to the Blood Culture Contamination Rate?

Abstract Purpose: Coagulase-negative staphylococci (CoNS) are the most frequent contaminating bacteria; hence, we aimed to investigate an indicator of CoNS to predict the increase in blood culture contamination rate (ConR). Methods : We performed a retrospective study of selected patients who underwent blood culture testing. Results: Cases with CoNS-positive blood cultures correlated with ConR (r=0.85). The area under the receiver operating characteristic curves for the number of cases with ConR ≥ 2.5 did not differ statistically from that of the number of cases contaminated by CoNS. Conclusion: The number of CoNS-positive cases could help predict an increase in ConR ≥2.5.

Topic: Bacterial Identification and Susceptibility Testing
Subfield: Clinical Biochemistry
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Effect of natural sedimentation on the structure of tropical rocky sponge assemblages

Abstract Sediment deposition and resuspension of particulate material are key factors in the functioning of coastal ecosystems. This paper reports the results of a study from February 2001 to June 2002 of a rocky sublittoral sponge community influenced by seasonal sand deposition. The largest impacts on the assemblages were a reduction in diversity, losses and substitution of species, and a shift from a relatively mature and stable community to a more unstable, less diverse community dominated by encrusting species more adapted to the local environmental conditions. These observations are consistent with studies that show that morphological diversity of sponge communities decreases when perturbation increases. Encrusting sponges such as Microciona sp. and Spirastrella decumbens were the most abundant and persistent throughout the study, followed by boring sponges of the genus Cliona. Massive species such as Haliclona caerulea, massive branching species such as Mycalesp., and cushion-shaped species such as Callyspongia californica were present only before deposition events. The general fluctuation in the patterns was consistent with the environmental conditions in this bay; the results suggest that the changes in the sponge assemblages may be due partly to great fluctuations in sediment deposition produced by a change in the direction of the dominant winds (from north to south) during the transition from the drought to the rainy season. This change provoked an increase in sedimentation/resuspension (up to 13 kg·m−2·d−1 in May 2001) and water movement in the zone, which were key factors influencing the structure and composition of sponge assemblages.

Topic: Marine Sponges and Natural Products
Subfield: Biotechnology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Stunting Amongst Pakistani Children Under Five: Status of Knowledge, Attitude and Practice of Health Care Workers at Basic Health Units and Rural Health Centers in Raiwind, Lahore

Background: One of the major public health problem amongst children of Pakistan is lack of proper nutrition. Health care workers (HCWs) at primary level have a pivotal role in promoting good nutrition. Objective: To assess the knowledge, attitude and practice of health care workers regarding stunting in under five children, at Basic Health Units and Rural Health Centers of Raiwind, Lahore. Methodology: Cross-sectional descriptive study including all HCWs (15 doctors and 15 nurses) in the selected 3 Rural Health Centers (RHC) and 9 Basic Health Units (BHU) in Raiwind, Lahore, from March 2019 to March 2020. A structured questionnaire was used for assessing Knowledge, Attitude and Practice (KAP) of HCWs regarding stunting in children under- five. Descriptive statistics were used to analyze data, P-values (p ≤ 0.05) were considered to see if the difference is statistically significant between doctors and nurses. Results: The HCWs’ mean percent score of doctors versus nurses, for knowledge related to major childhood illnesses was 48±22 vs 46±21, common nutritional problems 35±19 vs 26±16, and nutritional assessment methods 22±12 vs 42±23, in children under 5 years was found to be suboptimal. Total mean percent score for HCW ‘practices regarding health education of mothers was below 50 i-e 46±16 vs 40±18 in doctors vs nurses. The practice regarding breast feeding was higher 65±20 in nurses. All the doctors and 11 (73%) nurses reported correct practice regarding iron and folic acid supplementation to pregnant mothers. Conclusion: Despite having positive attitude towards stunting, HCWs’ had suboptimal knowledge and practice score in most of the items.

Topic: Child Nutrition and Water Access
Subfield: Nutrition and Dietetics
Field: Nursing
Domain: Health Sciences
EFFECT OF RAM MASS AND BASE AREA ON RAM IMPACT ACCELERATION AND PENETRATION OF SANDY GROUND

重錘を落下させて衝撃的に地盤を締固める際の締固め効果は, 重錘の打撃エネルギーではなく, 運動量に依存することを実験的に示してきた. また打撃時の重錘挙動を調べるために重錘加速度測定の室内実験を行ってきたが, 実規模の現場実験で確かめる必要がある. 今回, 25tから1.25kgの幅広い質量と底面積を有する重錘を用いた現場, 室内打撃試験を砂地盤に対して行い, 打撃時の重錘加速度と重錘の地盤への貫入量を調べた. その結果, これまでの室内試験と同様に, 加速度波形形状は重錘の質量と底面積の大きさによらず, 重錘の単位面積当たりの質量に依存し, 落下高の影響は小さく, 最大加速度, 最大打撃応力および重錘貫入量は提案式で説明できることがわかった.

Topic: Structural Response to Dynamic Loads
Subfield: Civil and Structural Engineering
Field: Engineering
Domain: Physical Sciences
Supplemental Figure S1 from Evolutionary Action Score of &lt;i&gt;TP53&lt;/i&gt; Identifies High-Risk Mutations Associated with Decreased Survival and Increased Distant Metastases in Head and Neck Cancer

&lt;p&gt;Supplemental Figure S1. The mutational status of the TP53 constructs.&lt;/p&gt;

Topic: Cancer Genomics and Diagnostics
Subfield: Cancer Research
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences