jimnoneill/paper-to-field-training huggingface dataset:
LncBook: a curated knowledgebase of human long non-coding RNAs

This FAIRsharing record describes: LncBook is a curated knowledgebase of human lncRNAs that features a comprehensive collection of human lncRNAs and systematic curation of lncRNAs by multi-omics data integration, functional annotation and disease association. It integrates multi-omics data from expression, methylation, genome variation and lncRNA-miRNA interaction. A core component of LncBook is the community-curated LncRNAWiki portal, which a wiki-based, publicly editable and open-content platform for community curation of human long non-coding RNAs (lncRNAs).

Topic: Cancer-related molecular mechanisms research
Subfield: Cancer Research
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Validation of HPLC method for quantitative determination of active compounds in Thai traditional herbal medicine to treat gastrointestinal disease

Quality control is essential for determining the quality and consistency of medicinal plant products before their use. Thatbunjob is a Thai herbal formulation included in the National List of Essential Medicines for treating gastrointestinal diseases. This study aimed to develop and validate a high-performance liquid chromatography method for determining active compounds in Thatbunjob. The main compounds, gallic acid, chebulagic acid, rutin, and eugenol, were determined following the International Conference on Harmonization (ICH) guidelines. The method was validated in terms of linearity, accuracy, precision, limit of detection (LOD), and limit of quantitation (LOQ), and found to be linear, with a correlation coefficient (R2) ranging from 0.9995 to 0.9998. The LOD and LOQ values calculated from the calibration curve ranged from 7.29 to 20.29 and 22.09 to 61.48 µg/mL, respectively. The method also exhibited acceptable precision, with relative standard deviation values lower than 2%. The accuracy of the method was evaluated based on the recovery percentages, and found to be within an acceptable range (90.12–105.39%). The validated protocol developed in this study was employed to analyze the concentration levels of gallic acid, chebulagic acid, rutin, and eugenol in eight different Thatbunjob products commercially available in Thailand. The performance parameters show that the developed and validated method is appropriate for the quantitative determination of gallic acid, chebulagic acid, rutin, and eugenol in Thatbunjob.

Topic: Natural product bioactivities and synthesis
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
[Strategies of genome-wide association study based on high-throughput sequencing].

Genome-wide association studies (GWASs) have been playing an important role on human complex diseases. Generally speaking, GWAS tries to detect the relationship between genome-wide genetic variants and measurable traits in the population level. Although fruitful, array-based GWASs still exist some problems, for example, the so-called missing heritability--significantly associated SNPs can only explain a small part of phenotypic variation. Other problems include that, in some traits, significantly associated SNPs in one study are hard to be repeated by other studies; and that the functions of significantly associated SNPs are often difficult to interpret. High-throughput sequencing, also known as next-generation sequencing (NGS), could be one of the most promising technologies to solve those problems by quickly producing accurate variations in a high-throughput way. NGS-based GWASs (NGS-GWAS), to some extent, provide a better solution compared with traditional array-based GWASs. We systematically review the strategies and methods for NGS-GWASs, pick out the most feasible and efficient strategies and methods for NGS-GWASs, and discuss their applications in personalized medicine.

Topic: Genetic Associations and Epidemiology
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Relationship Between the Effect of Immune Checkpoint Inhibitors and Peripheral Differential Leukocyte Counts

目的．肺癌患者の腫瘍微小環境（TME）の免疫状態が免疫チェックポイント阻害剤（ICI）の効果に影響している．末梢血白血球分画とTMEでの腫瘍浸潤白血球分画との関係を文献的に調べ，末梢血白血球分画でICIの有効な免疫状態を探索した．方法．2016年2月～2019年10月までに当院にてICI単剤を投与された非小細胞肺癌83症例において，ICI投与時（Day 1）とICI投与後42日（Day 43）の末梢血白血球分画を無増悪生存期間（PFS）と全生存期間（OS）に対してCox回帰解析を行った．結果．Day 1の末梢血において，好酸球数が高いほどPFSを有意に良好にし，単球数が高いほどPFSとOSを有意に不良にした．Day 43の末梢血において，好酸球数とリンパ球数が高いほどPFSとOSを有意に良好にし，好塩基球数と単球数が高いほどPFSとOSを有意に不良にした．Day 1に比べDay 43の末梢血好中球数が高いほど，PFSとOSを有意に不良にした．結論．ICI治療の効果と末梢血白血球分画は関連している．

Topic: Immune cells in cancer
Subfield: Immunology
Field: Immunology and Microbiology
Domain: Life Sciences
OPTIMIZED U-NET SEGMENTATION MODEL AND DEEP MAXOUT CLASSIFIER FOR BRAIN TUMOR CLASSIFICATION

The most serious nervous system ailment, a brain tumor impairs one’s health seriously and ultimately results in death. MRI, one of the most frequently used medical imaging modalities for brain tumors, has emerged as the main diagnostic system for the treatment and study of brain tumors. It was challenging to segment and classify the many kinds of brain tumors. The swarm intelligence approach has the potential to more efficiently and effectively tackle a number of issues. Therefore, this work develops a novel model for the classification of brain tumors that includes various phases. Primarily, the input image is preprocessed via the proposed median filtering that aids in removing noises. Subsequently, segmentation is done via optimal U-Net. For precise segmentation, the weights are tuned optimally by battle royale optimization with the Bernoulli randomization (BROBR) algorithm. Then, features like the proposed local Gabor XOR pattern (PLGXP), texton features, gray level co-occurrence matrix (GLCM), and correlation features are extracted. Finally, BTC is done using a deep maxout network (DMO) that provides the final output on the absence or presence of a brain tumor.

Topic: Brain Tumor Detection and Classification
Subfield: Neurology
Field: Neuroscience
Domain: Life Sciences
Five new taxa of Nepenthes (Nepenthaceae) from North and West Sumatra.

From our studies we concluded to describe five new taxa of Nepenthaceae including four new species. From the Lake Toba region in North Sumatra we describe a new species, which is closely related to Nepenthes carunculata, but differs in some morphological features that justify the establishment of a new taxon. Two new species related to Nepenthes dubio and Nepenthes inermis, and one, which is related to Nepenthe rafflesiana and Nepenthes sumatrana, all from West Sumatra are dscribed. From our studies on Nepenthes carunculata at different locations we further decided to describe a new variety.

Topic: Plant and Biological Electrophysiology Studies
Subfield: Plant Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Pengaruh Praktik Kesetaraan Gender dan Status Gizi (IMT/U) Terhadap Usia Menarche pada Remaja Putri di Yayasan Perguruan Ki Hajar Dewantara

Menarche is a menstrual event that occurs for the first time in women. Each adolescent has a variety of ages in reaching sexual maturity. Many factors cause differences in the age of menarche, including nutritional status. This study aims to analyze the effect of gender equality practices and nutritional status (BMI / U) on the age of menarche in young women of Yayasan Perguruan Ki Hajar Dewantara. This type of research is observational analytic with a cross-sectional study design. The data analysis method is path analysis. The population was 784 female students. The sampling technique used simple random sampling, namely 58 students. The results of the study had no direct effect on nutritional status (BMI / U) on the age of menarche. There is a direct influence of intake on nutritional status, namely ρ-value = 0.049 &lt;0.05 and gender equality practice on intake, namely the path coefficient value that ρ-value = 0.003 &lt;0.05. The conclusion is that there is an indirect effect of gender equality practices on status nutrition and gender equality practice on the age of menarche with beta value on the indirect effect is greater than the beta value on the direct effect. It is recommended to further increase knowledge of gender equality practices, growth and development of young women about the age of menarche and improve diet and see the nutritional status of young women with counseling.

Topic: Adolescent Health and Behaviors
Subfield: General Health Professions
Field: Health Professions
Domain: Health Sciences
Impact of grape juice press fractioning on polysaccharide and oligosaccharide composition of Pinot meunier Champagne base wines

Impact of press fractioning on polysaccharide and oligosaccharide composition of Pinot meunier Champagne base wines. 10. Symposium International d’Œnologie de Bordeaux, Œno2015

Topic: Fermentation and Sensory Analysis
Subfield: Food Science
Field: Agricultural and Biological Sciences
Domain: Life Sciences
The Effect Of Discipline, Motivation And Work Environment On Employee Job Satisfaction

The aim of this research is to determine the influence of work discipline, motivation, and work environment on the employees of PT. Energy Logistic Balikpapan. This research was conducted at PT. Energy Logistic Balikpapan, with 60 respondents, using quantitative research methods. Data collection was carried out through observation and questionnaires. The data analysis technique used was multiple linear regression with the Partial Least Square (PLS) program. The research results indicate that the variables of work discipline, motivation, and work environment have a significant positive influence on employee job satisfaction at PT. Energy Logistic Balikpapan.

Topic: Employee Performance and Management
Subfield: Human Factors and Ergonomics
Field: Social Sciences
Domain: Social Sciences
Formulation of the Generalized Backward-Projection Method for Acoustical Imaging

Absmct-Reconstruction algorithms have become a major component in acoustical imaging. Special-purpose methods have been developed and successfully applied to various systems. They are similar in terms of concepts and approaches, but they differ in terms of objectives and structures. This paper introduces the formulation of the generalized backward-projection method which is applicable to all linear imaging systems. Both the analog and discrete forms of the algorithm are pre sented for theoretical analysis and practical computation considerations. The main purpose of the paper is to provide a fundamental structure and to serve as a reference for future development of algorithms in acoustic image reconstruction.

Topic: Ultrasonics and Acoustic Wave Propagation
Subfield: Mechanics of Materials
Field: Engineering
Domain: Physical Sciences
The Quality Of Public Services In Administration

Is to show a model of good practice in public management by implementing a quality system in Prefecture. The national context in which change and reforming government is synthesized in any government program, based on new principles, which includes the following objectives: Public administration reform, based on increasing local autonomy and the financial and economic; restructure the central and local government, aiming to achieve an effective organizational model of administrative structures, while drastically reducing public expenditure; reducing bureaucracy and streamlining public services. The Prefecture aims to provide citizens, high-quality public services, in accordance with the needs, requirements and expectations, as well as those established by law. Thus, the institution will sustain a strong culture of quality, to ensure continuous improvement of services and to increase its customer satisfaction; The paper introduces a new concept: "Citizen – customer”, public service consumer.

Topic: Management, Economics, and Public Policy
Subfield: Marketing
Field: Business, Management and Accounting
Domain: Social Sciences
Neural aspects of prostaglandin involvement in gastric mucosal defense.

In rats, central vagal stimulation by thyrotropin-releasing hormone protects against ethanol-induced gastric damage by muscarinic release of prostaglandins. In contrast, gastroprotection following capsaicin-induced stimulation of afferent neurons is prostaglandin-independent. Capsaicin-evoked protection is abolished by blockade of calcitonin gene-related peptide (CGRP) receptors and inhibition of nitric oxide (NO) synthase. Various peptides including gastrin 17, cholecystokinin octapeptide, thyrotropin-releasing hormone, bombesin, corticotropin-releasing factor, epidermal growth factor, peptide YY, neurokinin A analogs and intragastric peptone exert gastroprotection that is abolished by afferent nerve denervation, blockade of CGRP receptors and inhibition of NO synthase. Indomethacin attenuates the protection of some peptides but has no effect with others. The hyperemic response to peptides is mediated by the afferent nerve/CGRP/NO system without contribution of prostaglandins. Furthermore, it was shown that NKA analogs exert afferent nerve-, CGRP- and NO-dependent gastroprotection in the face of substantial reduction of gastric mucosal blood flow indicating that gastroprotection is not necessarily mediated by mucosal hyperemia. In the rat stomach with functioning afferent nerves neither selective inhibition of cyclooxygenase (COX)-1 nor COX-2 is ulcerogenic and only simultaneous inhibition of both COX isoenzymes induees mucosal lesions. In the face of pending injury such as intragastric acid a COX-1 inhibitor evokes dose-dependent damage whereas COX-2 inhibitors are not injurious as long as the function of afferent nerves is not impaired. After afferent nerve denervation, however, COX-2 inhibitors or dexamethasone which suppresses the acid-induced up-regulation of COX-2 are highly ulcerogenic. In conclusion, release of prostaglandins following nerve stimulation can mediate protective effects under certain conditions but is not a prerequisite for neurally mediated mucosal defense. Prostaglandins are of particular importance for the maintenance of gastric mucosal integrity when neuronal defense mechanisms are impaired.

Topic: Neuropeptides and Animal Physiology
Subfield: Cellular and Molecular Neuroscience
Field: Neuroscience
Domain: Life Sciences
Dose-dependent differences in the profile of mutations induced by (+)-7R,8S-dihydroxy-9S,10R-epoxy-7,8,9,10-tetrahydrobenzo(a)pyrene in the coding region of the hypoxanthine (guanine) phosphoribosyltransferase gene in Chinese hamster V-79 cells.

Chinese hamster V-79 cells were exposed to a high dose (0.30-0.48 microM; 32% cell survival), an intermediate dose (0.04-0.10 microM; 100% cell survival) or a low dose (0.01-0.02 microM; 97% cell survival) of (+)-7R,8S-dihydroxy-9S,10R-epoxy-7,8,9,10-tetrahydrobenzo(a)pyrene [(+)-BPDE] which is the ultimate carcinogenic metabolite of benzo(a)pyrene. The mutation frequency for cells treated with dimethyl sulfoxide vehicle or with low, intermediate or high dose of (+)-BPDE were 1, 10, 52 or 514 8-azaguanine-resistant colonies/10(5) survivors, respectively. Independent 8-azaguanine-resistant clones were isolated, and complementary DNAs were prepared by reverse transcription. The coding region of the hypoxanthine (guanine) phosphoribosyltransferase (HPRT) gene was amplified by the polymerase chain reaction and sequenced. Altogether, 368 (+)-BPDE-induced mutant clones were examined. At all doses, base substitutions were the most prevalent mutations observed (about 72% of the mutant clones), followed by exon deletions (about 26% of the mutant clones) and frame-shift mutations (about 6% of the mutant clones). At the high cytotoxic dose, 7 of 120 base substitutions occurred at AT base pairs (6%) and 113 at GC base pairs (94%). At the intermediate noncytotoxic dose, 20 of 82 base substitutions occurred at AT base pairs (24%) and 62 at GC base pairs (76%). At the low noncytotoxic dose, 27 of 76 base substitutions were at AT base pairs (36%) and 49 were at GC base pairs (64%). The results indicated that decreasing the dose of (+)-BPDE decreased the proportion of mutations at GC base pairs and increased the proportion of mutations at AT base pairs. At the dose of (+)-BPDE was decreased, there was a dose-dependent decrease in the proportion of GC-->TA transversions (from 69% to 42% of the base substitutions) and a dose-dependent increase in the proportion of AT-->CG transversions (from 1% to 25% of the base substitutions). The data also indicated dose-dependent differences in (+)-BPDE-induced exon deletions and hot spots for base substitutions at GC and AT base pairs. Although more than 99% of the (+)-BPDE-induced mutations at guanine occurred on the nontranscribed strand of DNA, (+)-BPDE-induced mutations at adenine occurred on both the transcribed and nontranscribed strands. The ratio of mutations at adenine on the transcribed strand to mutations at adenine on the nontranscribed strand was 35:19 in (+)-BPDE-treated V-79 cells.(ABSTRACT TRUNCATED AT 400 WORDS)

Topic: DNA Repair Mechanisms
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Compact and robust fiber optic components using integrated optics with silica waveguides

With flame hydrolysis deposition (FHD) and photolithography & dry etching, integrated silica waveguide circuits are mass produced on planar substrates. Based on this technology, compact and reliable integrated fiber optic devices are manufactured to further span the use of fiber optics in communication.

Topic: Semiconductor Lasers and Optical Devices
Subfield: Electrical and Electronic Engineering
Field: Engineering
Domain: Physical Sciences
Mammalia, Didelphimorphia, Didelphidae, Glironia venusta Thomas, 1912 and Chironectes minimus (Zimmermann, 1780): distribution extension for eastern Amazonia

We report a new record for the bushy-tailed opossum Glironia venusta Thomas, 1912 and the water opossum Chironectes minimus (Zimmermann, 1780) in the Floresta Nacional de Carajás, municipality of Parauapebas, state of Pará, Brazil (06°03’00” S, 50°15’00” W). This study represents the second record of Glironia venusta, but the first voucher specimen for eastern Brazilian Amazon. For Chironectes minimus, this record extends the range of the species 558 km southeastwards from the closest known locality in Pará.

Topic: Bat Biology and Ecology Studies
Subfield: Ecology, Evolution, Behavior and Systematics
Field: Agricultural and Biological Sciences
Domain: Life Sciences
Quantitative Evaluation Method for Liver Fibrosis in Clinical Ultrasound B-Mode Image Based on Optimized Multi-Rayleigh Model

We have proposed an evaluation method for liver fibrosis using an ultrasound B-mode image. We proposed a multi-Rayleigh (MRA) distribution model to express a probability density function of ultrasound echo envelope obtained from a fibrotic liver tissue. The MRA model enabled us to estimate quantitative liver fibrosis parameters such as amount of fibrotic tissue and fibrosis progressive ratio, and to quantitatively visualize the fibrotic tissue in the B-mode image. In previous studies, we addressed several challenges to quantitatively and correctly evaluate liver fibrosis using the MRA model in clinical condition. In the present study, we integrated past achievements as the optimized MRA model and evaluated the clinical ultrasound B-mode image of fibrotic liver. Using the optimized MRA model, the change of estimated fibrotic tissue characteristics according to the liver fibrosis stage well reflected the tissue structural change caused by liver fibrosis. We concluded that the fibrotic tissue characteristics can be quantitatively and correctly estimated in clinical condition by using the optimized MRA model.

Topic: Ultrasound Imaging and Elastography
Subfield: Radiology, Nuclear Medicine and Imaging
Field: Medicine
Domain: Health Sciences
Rapid polymerase chain reaction assays for <i>Brevibacillus laterosporus</i> detection

Abstract The identification of the ubiquitous spore‐forming bacterium Brevibacillus laterosporus , whose interest in pharma, agriculture, and other industrial sectors is raising, mostly relies on 16S ribosomal RNA gene sequence analysis. However, due to bacterial gene homology, this method appears insufficient for a proper discrimination of this species, so that the availability of other target genes is necessary. Leveraging the morphological and genetic feature uniqueness of B. laterosporus , a sensitive and reliable detection and quantification method based on polymerase chain reaction (PCR) and quantitative PCR assays, respectively, was developed. Targeting a highly conserved spore surface protein‐related gene, B. laterosporus could be easily found in different matrices including soil, food, and insect body. Primer set selectivity was confirmed to be very specific and no false positives or negatives were observed using DNA of different bacterial species as a template. The method developed is also suitable for the rapid identification of newly isolated B. laterosporus strains.

Topic: Bacteriophages and microbial interactions
Subfield: Ecology
Field: Environmental Science
Domain: Physical Sciences
Research and Application of Sun Shadow Location Technology in Video Big Data

This paper presents a sun shadow location model for quickly determining and analyzing the location and time of the photographed object in video big data. Because the length of the object's shadow usually changed, it is related to some factors, such as the solar zenith angle, the solar azimuth angle and the geographical latitude of the object. So it proposes building the location information fingerprint database, which shows mainly the relation between the length of the object’s shadow and time by reasonable assumptions for the interception of the video data. Then, it is very convenient to predict the location and time of the taken object by indexing the target in database. Finally, some experimental results show that the proposed model can accurately locate the object.

Topic: Video Analysis and Summarization
Subfield: Computer Vision and Pattern Recognition
Field: Computer Science
Domain: Physical Sciences
Physical principles of microwave assisted magnetic recording

While the basic physics of Microwave Assisted Magnetization Reversal (MAMR) phenomenon is well established both theoretically and experimentally, its application in a practical magnetic recording environment was so far studied primarily with the help of micromagnetic recording models. In this work, we instead attempt to use analytical formulation and simple numerical models to understand the main challenges as well as benefits that are associated with such a system. It appears that the main difference between the previously introduced theory [G. Bertotti et al., Phys. Rev. Lett. 86, 724 (2001); K. Rivkin et al., Appl. Phys. Lett. 92, 153104 (2008); S. Okamoto et al., J. Appl. Phys. 107, 123914 (2010).] and recording environment is that both the RF and DC magnetic fields are applied at a substantial angle to the anisotropy axis. While the associated symmetry breaking prevents one from describing the reversal process explicitly, it is possible to approximate the solutions well enough to satisfactorily match numerical models both in the case of wire and Spin Torque Oscillator generated RF fields. This approach allows for physical explanation of various effects associated with MAMR such as high gradient of writeable anisotropy and reduction of track width, and offers a clear guidance regarding future optimization of MAMR recording.

Topic: Magnetic properties of thin films
Subfield: Atomic and Molecular Physics, and Optics
Field: Physics and Astronomy
Domain: Physical Sciences