jimnoneill/paper-to-field-training huggingface dataset:
Real-time respiratory motion correction for simultaneous PET-MR using an MR-derived motion model

Field: Medicine (Health Sciences)

Respiratory motion during PET imaging causes the resulting PET images to become corrupted by artefacts. In this paper we describe a technique for motion-correction of PET data based on MR imaging that is suitable for use in a simultaneous PET-MR imaging system. The technique is based on the formation of a subject-specific respiratory motion model from near real-time dynamic MR images and is capable of making real-time motion estimates based on a one-dimensional MR navigator, allowing additional MR imaging to take place at the same time as PET imaging. The model estimates the complex freeform deformations present in the human thorax during respiration. We validate our motion compensation approach using PET simulations based on real MR data of the thorax acquired from a healthy volunteer. Qualitative results show a clear improvement in visualisation of the myocardium and three tumours that were artificially added to the emission/attenuation map of the volunteer close to the diaphragm. Quantitative analysis was based on computing DICE coefficients between true regions of interest (myocardium and the three artificial tumours) and regions manually segmented from a `no motion' PET image, an uncorrected PET image and a motion-corrected PET image. The DICE coefficients over all 4 regions were 0.8 ± 0.03 (`no motion'), 0.24 ± 0.11 (uncorrected) and 0.6 ± 0.08 (corrected), indicating that a significant improvement in PET resolution and quantification is achievable by applying our motion-correction technique.
Introduction to electrocardiogram interpretation: part 2

Field: Health Professions (Health Sciences)

Twelve-lead electrocardiograms (ECGs) record 12 different views of cardiac electrical activity, or leads. They therefore provide more information than bedside monitors, which usually record one or sometimes two leads. Many acutely ill patients have 12-lead ECGs recorded either on admission to hospital, before undergoing operations or when specific cardiac concerns have arisen. Traditionally, ECGs have aided clinical diagnoses and, by learning how to understand and interpret them, nurses will know when they need to summon expert help. This article describes what each of the 12 leads represents, outlines the main indications for recording 12-lead ECGs and identifies likely causes of error in interpreting them.
K-Mer Databases Of Plant Virus Sequences For Use With The Kodoja Workflow

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

Details This is a gzipped tar file that includes the plant virus database files required to run the Kodoja workflow (https://github.com/abaizan/kodoja)[1]. Kodoja is a workflow for the detection of plant virus sequences in RNA-seq data files that uses two previoulsy published tools Kraken[2] and Kaiju[3]. This file contains databases for Kraken [2] and Kaiju [3]. The file includes the kraken database files: database.idx, database.kdb, nodes.dmp, names.dmp and the kaiju database file kaij_library.fmi. These k-mer databases are based on virus sequences in RefSeq [4] (ttps://www.ncbi.nlm.nih.gov/refseq/) with plant hosts as defined in the Virus-Host Database [5] (https://www.genome.jp/virushostdb/). Version 1.0 kodojaDB_v1.0 is based on RefSeq v89 and the Virus-Host Database (accessed 03/09/2018 which is based on RefSeq 89 and Genbank 226.0). The viral partition of RefSeq v89 genome comprises 7946 viruses (ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/viral/assembly_summary.txt). kodojaDB_v1.0 was created using kodoja_retrieve.py which is part of the kodoja workflow (v0.05) (https://github.com/abaizan/kodoja). References [1] Baizan-Edge, A, Cock, P, MacFarlane, S, McGavin, W, Torrance, T, Jones, S. Kodoja: A workflow for virus detection in plants using k-mer analysis of RNA-sequencing data (under review Nucleic Acids Research). [2] Wood,D.E. and Salzberg,S.L. (2014) Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol., 15, R46 [3] Menzel,P., Ng,K.L. and Krogh,A. (2016) Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat. Commun., 7, 1–9. [4] O’Leary,N.A., Wright,M.W., Brister,J.R., Ciufo,S., Haddad,D., McVeigh,R., Rajput,B., Robbertse,B., Smith-White,B., Ako-Adjei,D., et al. (2016) Reference sequence (RefSeq) database at NCBI: Current status, taxonomic expansion, and functional annotation. Nucleic Acids Res., 44, D733–D745. [5] Mihara,T., Nishimura,Y., Shimizu,Y., Nishiyama,H., Yoshikawa,G., Uehara,H., Hingamp,P., Goto,S. and Ogata,H. (2016) Linking virus genomes with host taxonomy. Viruses, 8, 10–15
Impact of LHC probes of SUSY and recent measurement of $(g-2)_μ$ on $\mathbb{Z}_3$-NMSSM

Field: Physics and Astronomy (Physical Sciences)

It is well known that excessively heavy supersymmetric particles (sparticles) are disfavored to explain the $(g-2)_μ$ anomaly, but some people overlook that moderately light sparticles are also disfavored by the LHC probes of supersymmetry. We take the Next-to-Minimal Supersymmetric Standard Model as an example to emphasize the latter point. It is found that, if the theory is required to explain the anomaly at $2σ$ level and meanwhile keep consistent with the LHC results, the following lower bounds may be set: $\tan β\gtrsim 20$, $|M_1| \gtrsim 275~{\rm GeV}$, $M_2 \gtrsim 300~{\rm GeV}$, $μ\gtrsim 460~{\rm GeV}$, $m_{\tildeμ_L} \gtrsim 310~{\rm GeV}$, and $m_{\tildeμ_R} \gtrsim 350~{\rm GeV}$, where $M_1$ and $M_2$ denote gaugino masses, $μ$ represents the Higgsino mass, and $m_{\tildeμ_L}$ and $m_{\tildeμ_R}$ are the mass of Smuons with $L$ and $R$ denoting their dominant chiral component. This observation has significant impacts on dark matter (DM) physics, e.g., the popular $Z$- and Higgs-funnel regions have been excluded, and the Bino-dominated neutralino DM has to co-annihilate with the Wino-dominated electroweakinos (in most cases) and/or Smuons (in few cases) to obtain the correct density. It is also inferred that these conclusions should apply to the Minimal Supersymmetric Standard Model since the underlying physics for the bounds are the same.
IoT-Based Electronic System for Real-Time Soil Nutrient Detection in Precision Agriculture

Field: Agricultural and Biological Sciences (Life Sciences)

In crop development, the presence of soil nutrients plays a very remarkable role due to their capability to determine the productivity of the planted crops. There is a traditional method for determining the level of nutrients in the soil, but it is laborious and ineffective. In addition, it is often not a profitable method due to its labour-intensive nature. In recent years, the emergence of contemporary electronic-based technologies for measuring the level of nutrients in the soil has been embraced. The technique has enhanced soil nutrient management, leading to higher crop yields. In the context of a modern smart agricultural farm, the application of programmable Internet of Things (IoTs) with integrated artificial intelligence (AI) technology for the easy identification of soil nutritional deficiencies. Therefore, the focal objective of this study is the design, implementation and testing of an IoT-based soil nutrient detection device utilizing intelligence techniques. The unfamiliarity of the farmers with the level of soil nutrient composition and the environmental conditions might limit the productivity of the soil for the farmer. Therefore, the performance of the instrument designed and developed was tested experimentally on two different farmlands. Measurements were conducted for soil temperature, moisture content, pH value and humidity. It was found in farmland 1 that the corresponding average values of the soil temperature, moisture content, pH value and humidity are 32.12oC, 29.66%, 5.58 and 72.06% while the values obtained from the farmland were 32.28oC, 30.16%, 6.00 and 72.96% with satisfactory outcomes based on small error margins.
Neural Network Model of Dynamical Grouping Process in the Human Visual System.

Field: Neuroscience (Life Sciences)

The mechanism underlying perceptual grouping of visual stimuli is not static, but dynamic. In this paper, the dynamical grouping process is implemented with a neural network model consisting of an array of (hyper) columns suggested by Hubel & Wiesel, where intracolumnar inhibition and intercolumnar facilitation are incorporated. The model was applied successfully to figures consisting of a.set of points yielding either of two ways of groupings from time to time due to neural fatigue. Then the model was extended to introduce dependency on fixation points as well as neural fatigue and then applied to the Necker Cube. The model output either of two ways of 3D interpretations depending on the fixation points.
[Russian society and patients with rheumatic diseases].

Field: Medicine (Health Sciences)

The morbidity, primary morbidity, temporary incapacity for work and disablement due to rheumatoid diseases registered among Russia's population in the recent 3 years are described on the basis of an analysis of Russian statistics. Issues related with mortality, caused by rheumatic diseases, the related expenses and influence on patients' life quality are under discussion. A conclusion is made on a high social-and-medical importance of the above category of diseases as viewed from the standpoint of society (state), patient and his or her family.
THE IRREDUCIBLE ROLE OF DERIVED MARGINAL UTILITY IN DYNAMIC STOCHASTIC PROGRAMMING

Field: Decision Sciences (Social Sciences)

Abstract. Using the important case of multi‐period investing between a safe asset with a low mean return and an equity basket with a higher total return but a riskier one, this analysis demonstrates that the relevant stochastic programming involves irreducibly recursive variational relations. The “direct” Lagrange‐Chow procedure is related to the derivatives of the Bellman “indirect”’algorithms and shown to require essentially the same computations save only for standard integrations or taking of first derivatives. To demonstrate that the comparison is unchanged when a vector of control variables must be optimized in a many‐period stochastic scenario, the problem is solved for a rentier to both decide how much to save in each period and how much to put of each period's investment into risky securities.
On the taxonomic identity of five Senecio species (Compositae) described by Candolle on material collected by Haenke during the Malaspina Expedition

Field: Agricultural and Biological Sciences (Life Sciences)

Calvo, Joel, Granda, Arturo (2022): On the taxonomic identity of five Senecio species (Compositae) described by Candolle on material collected by Haenke during the Malaspina Expedition. Candollea 77 (2): 145-158, DOI: 10.15553/c2022v772a2, URL: http://dx.doi.org/10.15553/c2022v772a2
Effect of adsorbates on surface phonon modes: H on Pd(001) and Pd(110)

Field: Physics and Astronomy (Physical Sciences)

We investigate the effect of adsorbates on surface vibrations by calculating the phonon spectra of clean and hydrogen-covered (001) and (110) surfaces of Pd. The dynamical matrix of these systems is determined using a model many-body alloy Hamiltonian based on ab initio density-functional results for these systems, with no adjustable parameters for surface properties. The most pronounced effect of hydrogen is a strong softening of the Rayleigh wave on Pd(001) and a hardening of surface modes on Pd(001) and Pd(110) with vibration amplitudes confined to the surface layer.
Oral Health Activities of Early Head Start and Migrant and Seasonal Head Start Programs

Field: Health Professions (Health Sciences)

Guidelines recommend that Migrant and Seasonal Head Start programs (MSHS) address the dental needs of children of migrant and seasonal farmworkers. This study describes parent- and child-oriented oral health activities of North Carolina’s MSHS programs and compares them with non-migrant Early Head Start (EHS) programs using data collected from a questionnaire completed by teachers and family services staff. Migrant and Seasonal Head Start staff reported engaging in more oral health activities than EHS staff, which was confirmed by results of logit and ordered logit regression models. Despite promising findings about the engagement of MSHS staff, participation in oral health activities is lower than recommended. Differences between EHS and MSHS programs might be due to differing needs of enrolled children and families or to different approaches to meeting the needs of families.
A Trustworthy Network Fault Diagnosis Approach

Field: Computer Science (Physical Sciences)

Trustworthy network fault diagnosis approach is one critical management item to enhance network trustworthiness. Aiming at gaining highly trustworthy of fault diagnosis in Internet, we present a trustworthy fault diagnosis approach based on integration of Artificial Neural Network and Rule-based Reasoning. Supported by the topology of hierarchical and distributed in multi-domains, reasoning rule matrix and its operation are studied to acquire parallel reasoning capability. Moreover, the quantitative trustworthy degree is defined and information entropy is applied to define threshold function marked on arcs and nodes in the Artificial Neural Network. Our approach possesses higher parallel capability guaranteeing by matrix operation and trustworthiness by trustworthy degree definition and calculation using Artificial Neural Network. Further, it is general so that it can be transplanted into various application fields.
Inhibition Mechanism of Ketamine‐Apatinib by CYP2C9 and 3A4: A Prediction of Possible Drug‐Drug Interaction

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

ABSTRACT Most cancer patients experience severe pain, and apatinib, a vascular endothelial growth factor receptor 2 (VEGFR2) inhibitor, demonstrates therapeutic efficacy against gastric cancer. Ketamine, a psychotropic drug used for cancer pain relief, exhibits potential in inhibiting gastric cancer progression but is associated with dose‐dependent adverse effects including neurological toxicity and dependency. Thus, clarifying whether apatinib influences ketamine therapy when co‐administered is critical. In this study, we investigated apatinib's inhibitory effects on ketamine metabolism using CYP2C9 and CYP3A4 isoform assays. Results showed that apatinib exerted inhibition of ketamine metabolism, acted as a noncompetitive inhibitor of CYP2C9*1, CYP2C9*16, and rat liver microsomes (RLM), a competitive inhibitor of CYP2C9*3 and CYP2C9*13, and a mixed‐model inhibitor of four CYP3A4 alleles (*1, *4, *18, and *23). Molecular docking revealed apatinib's stronger binding affinity (−10.6 kcal/mol) to CYP3A4*1 than ketamine (−6.9 kcal/mol). Consequently, co‐administration may increase adverse risk in poor metabolizers (PMs), warranting in vivo validation of their therapeutic interaction.
A Receiver-Driven Transport Protocol With High Link Utilization Using Anti-ECN Marking in Data Center Networks

Field: Computer Science (Physical Sciences)

Existing reactive or proactive congestion control protocols are hard to simultaneously achieve ultra-low latency and high link utilization across all workloads ranging from delay-sensitive flows to bandwidth-hungry ones in datacenter networks. We present an Anti-ECN (Explicit Congestion Notification) Marking Receiver-driven Transport protocol called AMRT, which achieves both near-zero queueing delay and full link utilization by reasonably increasing sending rate in the case of under-utilization. Specifically, switches mark the ECN bit of data packets once detecting spare bandwidth. When receiving the anti-ECN marked packet, the receiver generates the corresponding marked grant to trigger more data packets. The testbed and simulation experiments show that AMRT effectively reduces the average flow completion time (AFCT) by up to 42% and improves the link utilization by up to 38% over the state-of-the-art receiver-driven transmission schemes.
Aberration Correction with Low-Frequency Transmission for Medical Acoustic Imaging

Field: Medicine (Health Sciences)

Phase aberration is one of the major causes of deterioration in the quality of medical acoustic imaging. To suppress the effect of aberration, we employ a focused transmit beam with a low center frequency for the calculation of an aberration correction value set. The aberration correction value set is applied to an imaging process utilizing high-frequency transmission. To evaluate the focus quality under severe aberration conditions, we introduce an evaluation criterion for beam patterns using the second moment of the acoustic field. The result implies that in severe aberration conditions without aberration correction, a low-frequency transmission acquires a better beam pattern, and the aberration correction value set for a high-frequency transmission should be calculated using a low-frequency transmission.
Rates of de novo fatty acid synthesis in liver, muscle and adipose tissue in non-pregnant and pregnant rats in vivo.

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

Fatty acid de novo synthesis was measured quantitatively in liver, muscle and adipose tissue of non-pregnant and 21-day pregnant Uje: WIST rats in vivo. By means of 3H2O incorporation experiments the following rates of fatty acid synthesis, expressed as mumol palmitate-equivalents/animal.min, were calculated in non-pregnant and pregnant animals: liver 0.20 +/- 0.06 and 0.24 +/- 0.06; muscle 0.21 +/- 0.06 and 0.24 +/- 0.08; adipose tissue, 0.36 +/- 0.10 and 0.28 +/- 0.09, respectively. Thus, liver, muscle and adipose tissue contribute at approximately equal amounts to the summarized rate of fatty acid synthesis, which is similar in both pregnant and non-pregnant rats.
The Idea of Woman in Fundamentalist Islam

Field: Arts and Humanities (Social Sciences)

Lamia Rustum Shehadeh’s timely book, The Idea of Woman inFundamentalist Islam, begins with a brief biography of influential “fundamentalists.” She examines the context in which they formulated their theoriesand the extent to which they influenced each other, a process thatallows us to see their ideas as a response to the historical, political, andsocial environments in which they lived. For example, the MuslimBrotherhood, founded by Hasan al-Banna in 1928, not only helped formulateand consolidate Islamic revivalism in Egypt, but also helped provide ablueprint for a sociopolitical organization that promoted the political Islamor Islamism influencing chapters in Syria, Lebanon, Iraq, and Palestine.The ideas promoted by the Brotherhood also spread to Sudan, where theycontinue to guide the current regime’s policies. In some cases, as in Iran andSudan, pronouncements of these ideologues influence state law and publicpolicy. At other times they challenge the state, as in Tunisia.Al-Banna promotes the view that Muslim countries became impoverishedand fell under European control because they have deviated fromIslam. He suggests that Muslims see Islam as the solution to their problems.However, al-Banna and other Islamists believe that Islam’s historicaltraditions are irrelevant for modern times. Instead, they propose areturn to what they believe to be the traditions of the Prophet’s time andthat of the first four caliphs. Moreover, they advocate the use of ijtihad(independent judgment), a practice that allows them to interpret seventhcenturytraditions in light of modern needs. Islamist ideologues reservethis practice for themselves, and thus largely marginalize its alternativeuses by feminists and other progressive groups to advance women’s rightsor minority rights ...
Cardiolipin

Field: Pharmacology, Toxicology and Pharmaceutics (Life Sciences)

The primary objective of this “Glossary of Terms Used in Immunotoxicology” is to give clear definitions for those who contribute to studies relevant to immunotoxicology but are not themselves immunologists. This applies especially to chemists who need to understand the literature of immunology without recourse to a multiplicity of other glossaries or dictionaries. The glossary includes terms related to basic and clinical immunology insofar as they are necessary for a self-contained document, and particularly terms related to diagnosing, measuring, and understanding effects of substances on the immune system. The glossary consists of about 1200 terms as primary alphabetical entries, and Annexes of common abbreviations, examples of chemicals with known effects on the immune system, autoantibodies in autoimmune disease, and therapeutic agents used in autoimmune disease and cancer. The authors hope that among the groups who will find this glossary helpful, in addition to chemists, are toxicologists, pharmacologists, medical practitioners, risk assessors, and regulatory authorities. In particular, it should facilitate the worldwide use of chemistry in relation to occupational and environmental risk assessment.
Best Practices: Implementation of a Glucose Screening Program Based on Diffusion of Innovation Theory Methods

Field: Health Professions (Health Sciences)

There is public health interest in the identification and treatment of modifiable cardiometabolic risk factors among patients treated with antipsychotic medications. However, best-practice screening recommendations endorsed by multiple medical organizations have not translated into real-world clinical practice. Quality improvement strategies may help to address the gap between policy and implementation. This column describes the successful implementation of a best-practice glucose screening program in a large network of community mental health centers that was based on Six Sigma and diffusion of innovation theory. (Psychiatric Services 62:12–14, 2011)
Impact of human papillomavirus on the tumor microenvironment in oropharyngeal squamous cell carcinoma

Field: Medicine (Health Sciences)

Abstract Increasing evidence has elucidated the clinicopathological significance of tumor microenvironment (TME) cells. However, TME differences associated with human papillomavirus (HPV) infection in oropharyngeal squamous cell carcinoma (OPSCC) have not been well characterized. In our study, we comprehensively determined the TME infiltration patterns in 315 OPSCC patients, and systematically correlated the TME phenotypes with genomic characteristics and clinical features of OPSCCs. In this way, we observed the enrichment of high endothelial cells and adaptive immune cells in HPV‐positive (HPV+) OPSCCs, in contrast to the enrichment of fibroblasts and capillary endothelial cells in HPV− negative (HPV−) OPSCCs. By focusing on immune checkpoint genes, we constructed a coexpression network using genes that were differentially expressed between HPV+ and HPV− OPSCCs. Functional analysis of the network indicated that HPV+ OPSCCs had elevated immune activities by promoting adaptive immune response and suppressing activities related to extracellular matrix organization. Subsequently, clinical analysis showed that identified TME‐relevant genes were closely associated with the prognosis and therapy response in OPSCC. Importantly, results from the TME analysis were further validated using an independent OPSCC cohort.
Pathogenic role of cardiac mast cell activation/degranulation,TNF-alpha, and cell death in acute drug-related fatalities.

Field: Medicine (Health Sciences)

Mast cells are recruited and activated in the heart of drug-associated deaths and the myocytes are the main source of TNF-alpha with the ability of different production patterns. The high degree of MC degranulation and the elevated levels of tryptase together with the pathological changes in heart of drug-related victims resemble that of the anaphylactic deaths as demonstrated in our previous study.