jimnoneill/paper-to-field-training huggingface dataset:
Bottom‐up and top‐down proteomic approaches for the identification, characterization, and quantification of the low molecular weight proteome with focus on short open reading frame‐encoded peptides

Abstract The recent discovery of alternative open reading frames creates a need for suitable analytical approaches to verify their translation and to characterize the corresponding gene products at the molecular level. As the analysis of small proteins within a background proteome by means of classical bottom‐up proteomics is challenging, method development for the analysis of small open reading frame encoded peptides (SEPs) have become a focal point for research. Here, we highlight bottom‐up and top‐down proteomics approaches established for the analysis of SEPs in both pro‐ and eukaryotes. Major steps of analysis, including sample preparation and (small) proteome isolation, separation and mass spectrometry, data interpretation and quality control, quantification, the analysis of post‐translational modifications, and exploration of functional aspects of the SEPs by means of proteomics technologies are described. These methods do not exclusively cover the analytics of SEPs but simultaneously include the low molecular weight proteome, and moreover, can also be used for the proteome‐wide analysis of proteolytic processing events.

Topic: RNA and protein synthesis mechanisms
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Computing network-based features from physiological time series: Application to sepsis detection

Sepsis is a systemic deleterious host response to infection. It is a major healthcare problem that affects millions of patients every year in the intensive care units (ICUs) worldwide. Despite the fact that ICU patients are heavily instrumented with physiological sensors, early sepsis detection remains challenging, perhaps because clinicians identify sepsis by using static scores derived from bed-side measurements individually, i.e., without systematically accounting for potential interactions between these signals and their dynamics. In this study, we apply network-based data analysis to take into account interactions between bed-side physiological time series (PTS) data collected in ICU patients, and we investigate features to distinguish between sepsis and non-sepsis conditions. We treated each PTS source as a node on a graph and we retrieved the graph connectivity matrix over time by tracking the correlation between each pair of sources' signals over consecutive time windows. Then, for each connectivity matrix, we computed the eigenvalue decomposition. We found that, even though raw PTS measurements may have indistinguishable distributions in non-sepsis and early sepsis states, the median /I of the eigenvalues computed from the same data is statistically different (p <; 0.001) in the two states and the evolution of /I may reflect the disease progression. Although preliminary, these findings suggest that network-based features computed from continuous PTS data may be useful for early sepsis detection.

Topic: Heart Rate Variability and Autonomic Control
Subfield: Cardiology and Cardiovascular Medicine
Field: Medicine
Domain: Health Sciences
A Study on the Improvement of 3D Building Data Format for Spatial Information Open Platform

공간정보 오픈플랫폼에서는 국가공간정보를 공개하여 국민이 자유롭게 활용할 수 있는 서비스를 제공하고 있다. 최근 고품질의 3차원 공간정보와 실내공간정보에 대한 수요가 증가하고 있으나, 현재 오픈플랫폼은 실내와 실외의 공간정보 데이터가 상이한 형식과 저장구조로 구성되어 매끄럽게 연결된 서비스가 불가능한 상황이다. 또한 현재 서비스에 사용되는 3차원 데이터 포맷이 최근 서비스 환경의 변화와 신기술을 반영하지 못하고 있는 실정이다. 따라서 본 연구에서는 오픈플랫폼 3차원 데이터의 서비스 향상 및 상호운영성 확보를 위하여 서비스에 사용되는 3차원 데이터 포맷의 개선방안을 제시하였다. 제안한 포맷은 기존 포맷과 비교하여 경량화되었고 렌더링 속도가 개선되었다.

Topic: Innovation in Digital Healthcare Systems
Subfield: Health Information Management
Field: Health Professions
Domain: Health Sciences
Gaze Strategies in Skateboard Trick Jumps: Spatiotemporal Constraints in Complex Locomotion

This study underlines the functional adaptability of the visuomotor system to changing demands in highly dynamic situations. As a function of certain constraints, different gaze strategies were observed that can be considered as highly relevant for successfully performing skateboard jumps.

Topic: Winter Sports Injuries and Performance
Subfield: Pulmonary and Respiratory Medicine
Field: Medicine
Domain: Health Sciences
Charge radii and electromagnetic moments of Li and Be isotopes from the<i>ab initio</i>no-core shell model

Recently, charge radii and ground-state electromagnetic moments of Li and Be isotopes were measured precisely. We have performed large-scale ab initio no-core shell model calculations for these isotopes using high-precision nucleon-nucleon potentials. The isotopic trends of our computed charge radii and quadrupole and magnetic-dipole moments are in good agreement with experimental results with the exception of the 11Li charge radius. The magnetic moments are in particular well described, whereas the absolute magnitudes of the quadrupole moments are about 10% too small. The small magnitude of the 6Li quadrupole moment is reproduced, and with the CD-Bonn NN potential, also its correct sign.

Topic: Nuclear physics research studies
Subfield: Nuclear and High Energy Physics
Field: Physics and Astronomy
Domain: Physical Sciences
Low-loss chalcogenide waveguides on lithium niobate for the mid-infrared

We demonstrate low-loss chalcogenide (As(2)S(3)) waveguides on a LiNbO(3) substrate for the mid-IR wavelength (4.8 μm). Designed for single-mode propagation, they are fabricated through photolithography and dry-etching technology and characterized on a mid-IR measurement setup with a quantum cascade laser. For straight waveguides, propagation loss as low as 0.33 dB/cm is measured and low-loss bends on the order of 100 μm are simulated, with measurement results showing <3 dB for a 250 μm bend radius. The coupling efficiency is estimated to be 81%. In addition, the influences of variations in width and bend radius are also investigated.

Topic: Photonic and Optical Devices
Subfield: Electrical and Electronic Engineering
Field: Engineering
Domain: Physical Sciences
Le marché des ventes en ligne des Grands Crus Classés bordelais : quelles stratégies de développement adopter ? – Application à la Compagnie des Vins de Bordeaux et de la Gironde (CVBG)

The online wine trade has grown strongly since 2010. However, the Bordeaux Grands Crus Classés wines (GCC) have experienced several difficulties in gaining a foothold in this market. The CVBG, the 3rd largest Bordeaux merchant, duly removed the GCC for logistics reasons, from its online sales site. Yet other sites are getting a place on this market. The objective of this report is to evaluate the key results of the success of a sales site offering GCCs in Bordeaux and to establish recommendations to be considered for future developments of the CVBG site. To answer this issue, several marketing studies have been done, initially questioning GCC producers and sellers, potential customers and evaluating current market leaders. The results show that logistics represents the main obstacle to their online sales, but also that customers are not confident enough to buy these wines on the net. By studying in greater detail the potentialities of the CVBG and these results, it appears that certain shortcomings of the website could be filled by associating its activity with that of La Cave Dourthe. It would then be wise to place its management on the site of the Cave Dourthe in Saint-Émilion. A further study on the specific export markets of these wines should allow a better development of their website.

Topic: Wine Industry and Tourism
Subfield: Tourism, Leisure and Hospitality Management
Field: Business, Management and Accounting
Domain: Social Sciences
Peroxynitrite-Induced Reactions of Synthetic Oligonucleotides Containing 8-Oxoguanine

8-Oxoguanine (8-oxo-G) is one of the most common DNA lesions present in normal tissues due to exposure to reactive oxygen species. Studies at this and other laboratories suggest that 8-oxo-G is highly susceptible to secondary oxidation, making it a likely target for endogenous oxidizing agents, such as peroxynitrite (ONOO-). Synthetic oligonucleotides containing 8-oxoguanine were treated with ONOO-, and the reaction products were analyzed by liquid chromatography/electrospray ionization mass spectrometry (LC/ESI--MS). CCACAACXCAAA, CCAAAGGXAGCAG, CCAAAXGGAGCAG, and TCCCGAGCGGCCAAAGGXAGCAG (X is 8-oxo-G) were found to readily react with peroxynitrite via the same transformations as those observed for free 8-oxo-2'-deoxyguanosine. The composition of the reaction mixtures was a function of ONOO- concentration and of the storage time after exposure. The oligonucleotide products isolated at low [ONOO-]/[DNA] ratios (<5) were tentatively assigned as containing 3a-hydroxy-5-imino-3,3a,4,5-tetrahydro-1H-imidazo[4, 5d]imidazol-2-one, 5-iminoimidazolidine-2,4-dione, and its hydrolytic product, oxaluric acid. At a [ONOO-]/[DNA] ratio of >10, 2,4,6-trioxo[1,3,5]triazinane-1-carboxamidine- and cyanuric acid-containing oligomers were the major products. The exact location of a modified base within a DNA sequence was determined using exonuclease digestion of oligonucleotide products followed by LC/ESI--MS analysis of the fragments. For all 8-oxo-G-containing oligomers, independent of the sequence, the reactions with ONOO- took place at the 8-oxo-G residues. These results suggest that 8-oxo-G, if present in DNA, is rapidly oxidized by peroxynitrite and that oxaluric acid is a likely secondary oxidation product of 8-oxo-G under physiological conditions.

Topic: DNA and Nucleic Acid Chemistry
Subfield: Molecular Biology
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
The Diagnostic Value of Combining 18F-FDG PET/CT with 3.0T MRI-DWI Imaging in Preoperative N stage of Rectal Cancer

1339 Objectives 18F-FDG PET/CT and MRI-DWI are useful in the the staging of rectal cancer, but data regarding their combined value in pre-surgical N stage is still lacking. The aim of this study is to evaluate the diagnostic value of combining PET/CT with 3.0T MRI-DWI imaging in preoperative staging of lymph nodes of rectal cancer. Methods We prospectively evaluated FDG PET/CT and 3.0T MRI-DWI studies obtained in patients with operable rectal cancer from February 2013 to February 2014. Staging of lymph nodes was conducted according to a standardized protocol, and findings were confirmed in all patients by surgical resection. Kappa consistency test was used to examine the relationship between diagnosis methods and pathological result and χ2 test was used to examine the differences between each data. A P-value inferior to 0.05 was considered statistically significant. Results Thirty-two patients with a median age of 60 (range 42～73) were included in this study. Twenty patients were verified with metastatic lymph nodes and 12 patients were verified with non-metastatic lymph nodes by histopathology. The sensitivities of PET/CT, MRI-DWI and the combination of PET/CT with MRI-DWI for lymph nodes staging of rectal cancer were 85%, 75%, and 90%, respectively; the specificities were 58.3%,66.7% and 66.7%, respectively; the accuracies were 75%,71.9% and 81.3%, , respectively; and the Kappa values were 0.448,0.410, and 0.586, respectively. The combination of 18F-FDG PET/CT with 3.0T MRI-DWI was superior to PET/CT or 3.0T MRI-DWI alone. But there were no statistically differences between PET/CT, MRI-DWI and the combination of PET/CT with MRI-DWI for preoperative staging of lymph nodes of rectal cancer. Conclusions The combination of 18F-FDG PET/CT with 3.0T MRI-DWI for preoperative staging of lymph nodes of rectal cancer may be superior to PET/CT or 3.0T MRI-DWI alone in sensitivity and accuracy. But more cases and further study are needed to find statistically differences. Research Support This study is funded by National Natural Science Foundation of China ((81170435,81471714)); China Postdoctoral Science Foundation (20100480545);The International Cooperationprojects ofShanghai Science and Technology Committee (10410708800).

Topic: Radiomics and Machine Learning in Medical Imaging
Subfield: Radiology, Nuclear Medicine and Imaging
Field: Medicine
Domain: Health Sciences
LHD nb3pwr_PortThrough #173581.1 (analyzed)

Neutral beam injector (NBI) power-PortThrough of beam line 3 (BL3). The effective power that actually reaches the plasma after the negative ion-based neutral particle beam emitted from the NBI system passes through BL3.

Topic: Total Knee Arthroplasty Outcomes
Subfield: Surgery
Field: Medicine
Domain: Health Sciences
Riboflavin Biosynthesis by<i>Candida robusta</i>

Journal Article Riboflavin Biosynthesis by Candida robusta: Part III. Effect of Metal Ion and Necessity of CaCO3 Get access Shoichi Takao Shoichi Takao Laboratory of Applied Microbiology, Faculty of Agriculture, Hokkaido University, Sapporo Search for other works by this author on: Oxford Academic Google Scholar Agricultural and Biological Chemistry, Volume 28, Issue 11, 1 November 1964, Pages 765–769, https://doi.org/10.1080/00021369.1964.10858305 Published: 01 November 1964 Article history Received: 13 May 1964 Published: 01 November 1964

Topic: Microbial Metabolites in Food Biotechnology
Subfield: Nutrition and Dietetics
Field: Nursing
Domain: Health Sciences
A branch-and-bound approach to scheduling of data-parallel tasks on multi-core architectures

This paper studies a task scheduling problem which schedules a set of data-parallel tasks on multiple cores. Unlike most of previous literature where each task is assumed to run on a single core, this work allows individual tasks to run on multiple cores in a data-parallel fashion. Since the scheduling problem is NP-hard, a couple of heuristic algorithms which find near-optimal schedules in a short time were proposed so far. In some cases, however, exactly-optimal schedules are desired, for example, in order to evaluate heuristic algorithms. This paper proposes an exact algorithm to find optimal schedules. The proposed algorithm is based on depth-first branch-and-bound search. In our experiments with up to 100 tasks, the proposed algorithm could successfully find optimal schedules for 135 test cases out of 160 within 12 hours. Even in cases where optimal schedules were not found within 12 hours, our algorithm found better schedules than state-of-the-art heuristic algorithms.

Topic: Parallel Computing and Optimization Techniques
Subfield: Hardware and Architecture
Field: Computer Science
Domain: Physical Sciences
[Acute infantile bilateral striatal necrosis].

This paper describes the clinical case of a nine year old child clinical features of tetraparesis and acute encephalopathy after an infectious disease. The brain magnetic resonance imaging was compatible with a symmetrical bilateral necrosis of the brain nucleus which, associated with the clinical evolution, led to the diagnosis of acute bilateral infant striatal necrosis.

Topic: Infectious Encephalopathies and Encephalitis
Subfield: Infectious Diseases
Field: Medicine
Domain: Health Sciences
Identity Transformations of Women Who Left Abusive Military Marriages: A Narrative Study

This research reports first person accounts of the identity transformations of eight former military wives after leaving their abusive marriages, and gives voice to the isolation they experienced within the military culture while enduring verbal and physical violence perpetuated by their husbands. Narrative methodology was used to honor their stories and to capture a rich perspective of these women’s experiences during and after their marriages. Two primary themes: identity loss and identity reform, and their several subthemes emerged from their narratives. Implications for clinical practice, advocacy, and future research are discussed.

Topic: Gender, Security, and Conflict
Subfield: Gender Studies
Field: Social Sciences
Domain: Social Sciences
Gene therapy in primary immunodeficiencies

Primary immunodeficiencies are a group of disorders that are highly amenable to gene therapy due to their defined molecular biology and pathophysiology. The development of this new therapeutic modality has been driven by the established morbidity and mortality associated with conventional allogeneic stem cell transplantation, particularly in the human leukocyte antigen-mismatched setting. Recently, several clinical studies have demonstrated that conventional gene transfer technology can produce major beneficial therapeutic effects, but as for all cellular and pharmacologic treatment approaches, with a finite potential for toxicity. New strategies to overcome these issues are likely to establish gene therapy as an efficacious strategy for many forms of primary immunodeficiencies.

Topic: Virus-based gene therapy research
Subfield: Genetics
Field: Biochemistry, Genetics and Molecular Biology
Domain: Life Sciences
Internal quality control of hormone determinations by RIA. Detection of clinically significant analytical errors of serum thyroxine determination.

An internal quality control system by which clinically significant analytical errors can be detected with high probability was developed for serum thyroxine (T4) determination by RIA. The mean concentration of the quality control samples (C1, C2, and C3) were 40.0, 101.8, and 156.7 nmol/l, and their total standard deviations (st) 2.5, 4.1, and 7.1 nmol/l, respectively, in stable analytical performance of the T4 assay. From the clinical point of view it was accepted that the results of C1 varied from 30 to 50 nmol/l at the most. When expressed in standard deviations, the same size of error was accepted for C2 and C3. It followed that the quality control system had to detect a systematic shift of 2.43st (delta SEc) and a 2.08 times increase in random error (delta REc) in order that the quality goals could be reached. With three control samples the combination of rules, 1: 3s/CS1: (1.0s; 2.7s), which was chosen for manual quality control, detected the delta SEc with about an 80% probability and the delta REc with about a 30% probability. The probability of false rejections was less than 1%. The probability of detecting the delta SEc was considered acceptable, but to detect the delta REc with a higher probability, the within-assay variation of each run was calculated from the results of duplicate patient samples. Although the whole run was not rejected because of systematic and/or random errors, individual samples were reanalysed if the results of their duplicate determinations differed from the criteria stated.(ABSTRACT TRUNCATED AT 250 WORDS)

Topic: Pharmacogenetics and Drug Metabolism
Subfield: Pharmacology
Field: Pharmacology, Toxicology and Pharmaceutics
Domain: Life Sciences
ChemInform Abstract: An Oxygen Sensor Using a Process of High‐Temperature Oxidation of Metal.

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.

Topic: Analytical Chemistry and Sensors
Subfield: Bioengineering
Field: Chemical Engineering
Domain: Physical Sciences
ベラ科魚2種Iniistius trivittatusとLeptojulis lambdastigmaのタイとマレーシアからの初記録

The razorfish Iniistius trivittatus (Randall and Cornish, 2000), previously recorded only from Taiwan, Hong Kong and Vietnam, and the wrasse Leptojulis lambdastigma Randall and Ferraris, 1981, previously from Taiwan and the Philippines, are redescribed on the basis of four and six specimens, respectively, collected from Thailand and Malaysian waters. The range extensions of the two species both indicate wide South China Sea distributions.

Topic: Ichthyology and Marine Biology
Subfield: Nature and Landscape Conservation
Field: Environmental Science
Domain: Physical Sciences
Konsep Prajurit Allah Berdasarkan Efesus 6:10-20 dan Implementasinya Dalam Kehidupan Orang Percaya

A soldier of God will always be identical to his armor. God's armor itself is a picture used by the Apostle Paul in his letter to the congregation at Ephesus. Paul ended this letter to the congregation by giving a description of the weapons used by the Roman army at that time. The weapons themselves are belts, armor, shoes, shields, helmets and swords. Paul gives this picture so that his readers in Ephesus can understand that it is actually one of the Roman provinces. This weapon of God does not only apply to the Ephesians, but can also be drawn into the lives of believers, namely that the war of believers against the powers of Satan must be equipped with truth, justice, willingness, faith, the word of God, and prayer.&#x0D; Seorang prajurit Allah akan selalu identik dengan perlengkapan senjatanya. Perlengkapan senjata Allah sendiri merupakan suatu gambaran yang dipakai oleh Rasul Paulus dalam suratnya kepada jemaaat di Efesus. Paulus mengakhiri suratnya ini kepada jemaat disana dengan memberikan gambaran perlengkapan senjata yang dipakai oleh tentara Romawi pada saat itu. Perlengkapan senjata itu sendiri ialah ikat pinggang, baju zirah, kasut kaki, perisai, ketopong, dan pedang. Paulus memberikan gambaran ini agar dapat dimengerti oleh pembacanya di Efesus yang notabene adalah salah satu propinsi Romawi. Perlengkapan senjata Allah ini tidak hanya berlaku bagi jemaat di Efesus saja, tetapi juga dapat ditarik ke dalam kehidupan orang percaya yaitu bahwa peperangan orang percaya melawan kuasa-kuasa Iblis harus dilengkapi dengan kebenaran, keadilan, kerelaan, iman, firman Allah, dan doa.

Topic: Contemporary Christian Leadership and Education
Subfield: Religious studies
Field: Arts and Humanities
Domain: Social Sciences