jimnoneill/paper-to-field-training huggingface dataset:
Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification

Field: Computer Science (Physical Sciences)

Abstract Motivation: The identification of peptides by tandem mass spectrometry (MS/MS) is a central method of proteomics research, but due to the complexity of MS/MS data and the large databases searched, the accuracy of peptide identification algorithms remains limited. To improve the accuracy of identification we applied a machine-learning approach using a hidden Markov model (HMM) to capture the complex and often subtle links between a peptide sequence and its MS/MS spectrum. Model: Our model, HMM_Score, represents ion types as HMM states and calculates the maximum joint probability for a peptide/spectrum pair using emission probabilities from three factors: the amino acids adjacent to each fragmentation site, the mass dependence of ion types and the intensity dependence of ion types. The Viterbi algorithm is used to calculate the most probable assignment between ion types in a spectrum and a peptide sequence, then a correction factor is added to account for the propensity of the model to favor longer peptides. An expectation value is calculated based on the model score to assess the significance of each peptide/spectrum match. Results: We trained and tested HMM_Score on three data sets generated by two different mass spectrometer types. For a reference data set recently reported in the literature and validated using seven identification algorithms, HMM_Score produced 43% more positive identification results at a 1% false positive rate than the best of two other commonly used algorithms, Mascot and X!Tandem. HMM_Score is a highly accurate platform for peptide identification that works well for a variety of mass spectrometer and biological sample types. Availability: The program is freely available on ProteomeCommons via an OpenSource license. See http://bioinfo.unc.edu/downloads/ for the download link. Contact: giddings@unc.edu, giddings@med.unc.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Determination of Initial Sr-Isotope Compositions of Dolostones from the Burlington-Keokuk Formations (Mississippian) of Iowa, Illinois, and Missouri: ABSTRACT

Field: Earth and Planetary Sciences (Physical Sciences)

Sr-isotope compositions, and Rb and Sr concentrations were measured on fine-grained, nearly pure dolostones, each consisting predominantly of one cathodoluminescent generation of dolomite. The results differ significantly, depending on the dissolution method used. For example, one sample gives replicate /sup 87/Sr//sup 86/Sr analyses by leaching with 1.25N HCl of 0.71032 and 0.71062. Adding HF to the leaching process gave a value of 0.71216, whereas complete dissolution with concentrated HF, HNO/sub 3/, and HCl yields a value of 0.71219. Using the time of dolomitization with Rb (12.4 ppm) and Sr (59.7 ppm) concentrations for the completely dissolved sample gives an initial /sup 87/Sr//sup 86/Sr ratio of 0.70943. Similar results for other samples indicate that most Rb and radiogenic Sr are associated with minor clay fractions (predominantly glauconite) in the samples, and that HCl leaches Rb and Sr from clays to a variable extent. Morphologic relationships between dolomite, calcite, and nonpelloidal glauconite suggest that some clay formed episodically during various stages of nonmarine diagenesis. Sr-isotopic exchange may have occurred between carbonate and clay during major influxes of diagenetic fluids. To obtain initial /sup 87/Sr//sup 86/Sr ratios on samples that are completely dissolved, the following corrections are needed: isotopic equilibration between carbonate andmore » clay, closure of the Rb-Sr system after diagenesis, and constraints on the timing of diagenesis. Such initial /sup 87/Sr//sup 86/Sr ratios give the isotopic composition of the carbonate phase at the time of its crystallization, whereas leaching with weak acid is not always carbonate selective and can produce ambiguous results.« less
Management of Alcohol Abusing Patients in Accident and Emergency Departments

Field: Health Professions (Health Sciences)

A pilot study was undertaken in the Accident & Emergency (A & E) departments of two central London teaching hospitals to determine if patients who were abusing alcohol and had not received any prior medical treatment or counselling for their drinking problem were amenable to offers of help. During the 24-month study period 104 patients were identified as having a previously untreated alcohol problem, and of these 46% attended an appointment to discuss their drinking habits. The group identified was much smaller than would be expected from the number attending the A & E departments during the study period and the reasons for this are discussed. However, the important observation from the study is that almost half the patients identified as having an alcohol problem returned to the department the following day to seek advice. This suggests that A & E departments are an appropriate place to offer patients initial help about their drinking habits.
Everglades Isotope Data

Field: Environmental Science (Physical Sciences)

Data are available for the following sites: Cell 4, ENR-OUT, L7, Cell 3, LOX, North Holeyland, E0, F1, U3/Glory Hole, L35B, 2BS, L67, 3A-15, 3A-TH, Lostmans Creek, North Prong Creek, TS-7, and TS-9 for the plants and animals found at each site.
on An Argument On Behalf of Classical Negation

Field: Arts and Humanities (Social Sciences)

Journal Article on An Argument On Behalf of Classical Negation Get access CRISPIN WRIGHT CRISPIN WRIGHT Universities of St. Andrews and MichiganAnn Arbor Search for other works by this author on: Oxford Academic Google Scholar Mind, Volume 102, Issue 405, January 1993, Pages 123–131, https://doi.org/10.1093/mind/102.405.123 Published: 01 January 1993
Reactions of Japanese industrial managers to government incentives to innovation — An empirical study

Field: Business, Management and Accounting (Social Sciences)

The set of studies employed a nine-stage model of the process indicating the potential influence of federal actions on the perceptions, attitudes, decisions, and innovation outputs of industrial firms and the further impact of the firms' innovations on the economy. This study focused on four of these stages: awareness of the Government Incentive Programmes (GIP), attitudes toward them, general behavior affected by them, and specific decisions related to them. In the Japanese firms, it was found that once a firm is in the `attitude' stage (implying awareness) it will very likely also be in the action stages (general and specific decisions related to the application of the GIPs by the firm). Acceptance of the GIPs (measured by the stage score) by the firms is positively related to the attractiveness of the GIP (measured by a scoring method), and has low correlation with the age of the GIP.
Quantum chemical study of thiazole derivative cyclobutyl molecule C18H18N2O3S

Field: Chemistry (Physical Sciences)

In ongoing research geometry optimisation of cyclobutyl molecule C18H18N2O3S has been done by using a combination of DFT/6–311++G(d,p) methods. The calculated optimised bond geometry is well-matched with experimental geometry. The nonbonding interactions in the title molecule are analysed by QTAIM analysis. The vibration analysis of the molecule has been done with the assignments. The calculated hyperpolarizability of the molecule shows that the molecule can be used as a better NLO agent in the future. NBO analysis shows that moment of π electrons from donor to acceptor is more dominant than other interactions.
White House summit tackles opioid abuse

Field: Health Professions (Health Sciences)

Two public health problems in the United States—prescription drug abuse and heroin use—are inextricably linked, and solutions will require comprehensive efforts, said participants in a June 19 White House policy summit. “It is impossible to understand our nation’s heroin challenge without also understanding our prescription drug abuse challenge,” said Michael Boticelli, acting director of the Office of National Drug Control Policy. The half-day summit was closed to the public but broadcast live via a web-cast. Participants included U.S. Attorney General Eric Holder, state and local officials, and professionals in fields related to addiction treatment, education, and prevention. About 110 Americans died of a drug overdose every day during 2011—more than died from traffic accidents, according to federal data. Boticelli said that prescription opioids were a factor in nearly 17,000 overdose deaths in 2011, and heroin use contributed to more than 4,000 deaths. Some recent research suggests that people who became addicted to heroin were first hooked on prescription opioids. And policymakers and others have speculated that efforts to restrict the illicit use of prescription opioids may be prompting those who are addicted to switch to heroin.
Cloning of DNA segments of phage 2C, which allows autonomous plasmid replication in Bacillus subtilis

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

The chromosome of Bacillus subtilis phage 2C is a 100-MDa double-stranded DNA molecule, containing hydroxymethyluracil in place of thymine and carrying redundant ends each encompassing 10% of the genome. 2C DNA was cleaved with EcoRI and HindIII, and cloned in the shuttle plasmids pSC 540 and pCP 115, both containing segments originating from B. subtilis and Escherichia coli plasmids. These chimaerical plasmids, carrying the chloramphenicol resistance gene, were unable to replicate in B. subtilis; this ability was restored, however, after the insertion of viral DNA segments. Physical maps of the recombinant plasmids were made; a large deletion of the E. coli-derived segment of pSC 540 was observed (which paralleled a loss of replication in this host), whereas addition of 2C DNA segments in pCP 115 was not accompanied by deletion (replication in E. coli was conserved in this case). Cloned viral segments mapped mostly, but not exclusively, within the redundant ends of 2C DNA. It is suggested that the thirteen recombinant clones carried the replication origin region of phage 2C DNA, and that these sequences originated within or close to the redundant extremities of the viral chromosome.
Bezier Curve Based Programmed Trajectory for Coordinated Motion of Two Robots in Cartesian Space

Field: Engineering (Physical Sciences)

Coordinated motion of two robots in Cartesian space is considered in the paper. The goal is to generate trajectories for which change of distance between points on trajectories during motion is minimal. To minimize relative position errors along trajectories an idea of corrective motion is introduced. Trajectory coordinates are calculated as the sum of programmed and corrective motions. To calculate the speed vector of the programmed motion at the current position, the speed at the closest point on the programmed trajectory is used. The closest point is defined as the one to which the distance from the current position is minimal or the programmed position at given time. In order to attract the generated trajectory to the programmed one a modification of the programmed speed vector is proposed. The described approach is verified in simulation. For simulation experiments programmed trajectories defined by Bezier curve segments are used. Simulations for different shapes of programmed trajectories and different programmed velocity rates are presented.
Recommendation of Points-of-Interest Using Graph Embeddings

Field: Computer Science (Physical Sciences)

The rapid growth of Location-based Social Networks (LBSNs) has lead to the generation of massive datasets which are collected in an exponential rate. The collected information may be used to facilitate users' needs with recommendations related to their past preferences. Many recommendation models were introduced in the literature, which learn by the history of users and provide recommendations for Points-of-Interest. Unfortunately, most of them ignore the relation existing among the temporal properties, the spatial attributes and the periodicity of the check-ins. In this work, we present a novel methodology, named JLGE, that combines all aforementioned factors into one unified approach which facilitates POI recommendations. In particular, the model jointly learns the embeddings of six informational graphs i.e., two unipartite (user-user and POIPOI) and four bipartite (user-location, user-time, location-user, and location-time) into the same latent space and personalize the recommendations based on these embeddings. We have experimentally evaluated the accuracy of our model using two real-world datasets in terms of the top-n POIs recommendations. The performance evaluation results indicate a significant improvement in accuracy, in comparison to another state-of-theart graph-based approach.
Organisational learning in small learning organisations: an empirical overview

Field: Business, Management and Accounting (Social Sciences)

Much has been written, in recent years, on the subject of learning organisations and knowledge‐based businesses. Most research in this area, however, focuses upon large businesses. In this type of firm, it appears the concepts of “organisational learning” and “learning organisation” can be, and often are, used interchangeably to describe learning‐based individual and collective development. Until recently, issues relating to organisational learning in small businesses were mostly ignored or marginalised. This paper sets out to redress the balance. It reports a study of organisational learning in the small business sector of the UK economy. Research data, collected over the 1996‐1998 period, through telephone surveys, in‐depth interviews and case studies, were analysed through quantitative and qualitative methods. The results indicate that although learning can occur in the majority of small businesses in the sample, only a minority of these manage new knowledge strategically to sustain and advance their competitive advantage.
Implications of endoplasmic reticulum stress and autophagy in aging and cardiovascular diseases

Field: Medicine (Health Sciences)

The average lifespan of humans has been increasing, resulting in a rapidly rising percentage of older individuals and high morbidity of aging-associated diseases, especially cardiovascular diseases (CVDs). Diverse intracellular and extracellular factors that interrupt homeostatic functions in the endoplasmic reticulum (ER) induce ER stress. Cells employ a dynamic signaling pathway of unfolded protein response (UPR) to buffer ER stress. Recent studies have demonstrated that ER stress triggers various cellular processes associated with aging and many aging-associated diseases, including CVDs. Autophagy is a conserved process involving lysosomal degradation and recycling of cytoplasmic components, proteins, organelles, and pathogens that invade the cytoplasm. Autophagy is vital for combating the adverse influence of aging on the heart. The present report summarizes recent studies on the mechanism of ER stress and autophagy and their overlap in aging and on CVD pathogenesis in the context of aging. It also discusses possible therapeutic interventions targeting ER stress and autophagy that might delay aging and prevent or treat CVDs.
Online Dating: Market or Bazaar? The Marriage Partner Search Process on an Orthodox Dating Site

Field: Social Sciences (Social Sciences)

Э лектронный журнал «Экономическая социология» издаётся с 2000 г.Учредителями являются Национальный исследовательский университет «Высшая школа экономики» (с 2007 г.) и Вадим Валерьевич Радаев (главный редактор).Цель журнала -утверждать международные стандарты экономико-социологических исследований в России, представлять современные работы российских и зарубежных авторов в области экономической социологии, информировать профессиональное сообщество о новых актуальных публикациях и исследовательских проектах, а также вовлекать в профессиональное сообщество молодых коллег.Журнал представляет собой специализированное академическое издание.В нём публикуются материалы, отражающие современное состояние экономической социологии и способствующие развитию данной области в её современном понимании.В числе приоритетных тем: теоретические направления экономической социологии, социологические исследования рынков и организаций, социально-экономические стратегии индивидов и домашних хозяйств, неформальная экономика.Также публикуются тексты из смежных дисциплин -неоинституциональной экономической теории, антропологии, экономической психологии и других областей, которые могут представлять интерес для экономсоциологов
Characterization of a FOXG1:TLE1 transcriptional network in glioblastoma‐initiating cells

Field: Biochemistry, Genetics and Molecular Biology (Life Sciences)

Glioblastoma ( GBM ) is the most common and deadly malignant brain cancer of glial cell origin, with a median patient survival of less than 20 months. Transcription factors FOXG 1 and TLE 1 promote GBM propagation by supporting maintenance of brain tumour‐initiating cells (BTICs) with stem‐like properties. Here, we characterize FOXG 1 and TLE 1 target genes in GBM patient‐derived BTICs using Ch IP ‐Seq and RNA ‐Seq approaches. These studies identify 150 direct FOXG 1 targets, several of which are also TLE 1 targets, involved in cell proliferation, differentiation, survival, chemotaxis and angiogenesis. Negative regulators of NOTCH signalling, including CHAC 1 , are among the transcriptional repression targets of FOXG 1: TLE 1 complexes, suggesting a crosstalk between FOXG 1: TLE 1 and NOTCH ‐mediated pathways in GBM . These results provide previously unavailable insight into the transcriptional programs underlying the tumour‐promoting functions of FOXG 1: TLE 1 in GBM .
Cage Compound

Field: Chemistry (Physical Sciences)

This Glossary contains definitions, explanatory notes, and sources for terms used in physical organic chemistry. Its aim is to provide guidance on the terminology of physical organic chemistry, with a view to achieving a consensus on the meaning and applicability of useful terms and the abandonment of unsatisfactory ones. Owing to the substantial progress in the field, this 2021 revision of the Glossary is much expanded relative to the previous edition, and it includes terms from cognate fields.
$L^2$ Serre Duality on Domains in Complex Manifolds and Applications

Field: Mathematics (Physical Sciences)

An $L^2$ version of the Serre duality on domains in complex manifolds involving duality of Hilbert space realizations of the $\bar{\partial}$-operator is established. This duality is used to study the solution of the $\bar{\partial}$-equation with prescribed support. Applications are given to $\bar{\partial}$-closed extension of forms, as well to Bochner-Hartogs type extension of CR functions.
Determinants of return intention of visitors: An investigative study in Phu Quoc islands, Vietnam

Field: Social Sciences (Social Sciences)

The Vietnamese tourism sector was fastly growing in several years, this sector also has played an important role in support the social development in Vietnam. Our paper tries to analysis the factors affect return intention of visitors with the data sample are collected from a survey including 230 visitors in Phu Quoc islands, which is the most well known and beautiful one in Vietnam. The research model has one dependent variable which is Return intention and eight independence variables including Destination Image, Natural and Cultural Environment, Perceived Price, Infrastructure, Accessibility, Local Cuisine, Leisure and Entertainment, and Attitude of the local people. The results show that all independent variables also have the positive effects on the Return intention of visitors at the statistical significance at 5% level. Finally, our paper provides some suggestions which are useful for managers in the tourist service sector and academics in the service economics field.
Effects of Treatments and Fermentation Time on Phenolic Compounds, Glycoalkaloid Contents, and Antioxidant Capacity of Industrial Potato Waste

Field: Agricultural and Biological Sciences (Life Sciences)

Potato processing plants generate waste in the form of peels, pulp, and rejects, which is estimated to be around 12–20 % of their total production volume. Potato peels, pulp, and unmarketable potatoes can be processed and incorporated into animal feed formulations. However, there is a limited information on phenolic compounds from industrial potato waste (IPW) phenolic compounds subjected to short-term solid-state fermentation. Bioactive compounds could be improved via solid-state fermentation. Lactiplantibacillus plantarum (MW296876), Saccharomyces cerevisiae (MW296931), and Aspergillus oryzae (MW297015) were purposely selected to ferment IPW at 0, 24, 48, and 72 hr in a two-factor factorial design (treatment × fermentation time). The fermented products were analysed for phytochemical compounds such as total phenolic content (TPC), total flavonoid content (TFC), glycoalkaloid (GLA) content, and antioxidant capacity. The results revealed that the bioactive compounds, except phytic acid, had a significant interaction between treatment and fermentation time. Alpha solanine significantly (p<0.05) decreased while α chaconine increased (p<0.05) with fermentation time across all the treatments except in the control and L. plantarum treatment groups. IPW inoculated with L. plantarum significantly influenced the solubility of GLA compared to other treatment groups. Antioxidant capacity increased (p<0.05) across the fermentation time; at 48 hr of fermentation, L. plantarum had the highest (p<0.05) antioxidant capacity than S. cerevisiae and A. oryzae. Among the three inocula, L. plantarum (MW296876) consistently increased TPC, antioxidant activity, and solubility of both GLA and tannin.
Biaxial surface order dynamics in calamitic nematics

Field: Physics and Astronomy (Physical Sciences)

Thermotropic nematic materials relax strong distortions by lowering the nematic order: the uniaxial symmetry is broken and is locally replaced by biaxial domains. We investigated the dynamics of the nematic order near a boundary surface of an asymmetric π-cell submitted to an external electric field, close to the electric order reconstruction threshold. An unexpected phenomenon is observed close, but below the threshold: the biaxial order spreads on the surface inducing a consequent bulk topological behaviour equivalent to the splay-bend fast transition allowed by order reconstruction at higher voltage.
Improved lossless compression of color palette images by re-indexing with particle swarm optimization

Field: Computer Science (Physical Sciences)

This work builds on previous work in the area of one dimensional lossless color compression. The previous work applied a cross entropy (CE) solution to traveling salesman problem (TSP) for color re-indexing with a Burrows-Wheeler transformation and inversion ranks. The proposed technique replaces the cross entropy based TSP algorithm with a particle swarm optimization (PSO) for the task of color re-indexing. The proposed method yields improvement over the previous work regardless of the number of colors in the image.
Kirkjubømúrurin: KV007

Field: Arts and Humanities (Social Sciences)

Sligin basalt steinur úr Kirkjubømúrinum, partur av steinasavninum hjá Tjóðsavninum. *English:* Carved basalt stone from Kirkjubømúrinum (The Saint Magnus Cathedral), in storage at Tjóðsavnið. Dimension: 21 x 41 x 11.5 cm. Created by Petur Hansen, using Artec space spider scanner and Artec Studio 15. Source: Objaverse 1.0 / Sketchfab