bluuebunny/crossref_metadata_2025_split huggingface dataset:
Annotation and extraction of age and temporally-related events from clinical histories
Authors: Hong Judy , Davoudi Anahita , Yu Shun , Mowery Danielle L. 
Published: December 2020

Abstract
Background
Age and time information stored within the histories of clinical notes can provide valuable insights for assessing a patient’s disease risk, understanding disease progression, and studying therapeutic outcomes. However, details of age and temporally-specified clinical events are not well captured, consistently codified, and readily available to research databases for study.

Methods
We expanded upon existing annotation schemes to capture additional age and temporal information, conducted an annotation study to validate our expanded schema, and developed a prototypical, rule-based Named Entity Recognizer to extract our novel clinical named entities (NE). The annotation study was conducted on 138 discharge summaries from the pre-annotated 2014 ShARe/CLEF eHealth Challenge corpus. In addition to existing NE classes (TIMEX3, SUBJECT_CLASS, DISEASE_DISORDER), our schema proposes 3 additional NEs (AGE, PROCEDURE, OTHER_EVENTS). We also propose new attributes, e.g., “degree_relation” which captures the degree of biological relation for subjects annotated under SUBJECT_CLASS. As a proof of concept, we applied the schema to 49 H&P notes to encode pertinent history information for a lung cancer cohort study.

Results
An abundance of information was captured under the new OTHER_EVENTS, PROCEDURE and AGE classes, with 23%, 10% and 8% of all annotated NEs belonging to the above classes, respectively. We observed high inter-annotator agreement of >80% for AGE and TIMEX3; the automated NLP system achieved F1 scores of 86% (AGE) and 86% (TIMEX3). Age and temporally-specified mentions within past medical, family, surgical, and social histories were common in our lung cancer data set; annotation is ongoing to support this translational research study.

Conclusions
Our annotation schema and NLP system can encode historical events from clinical notes to support clinical and translational research studies.
Natural language processing (NLP) tools in extracting biomedical concepts from research articles: a case study on autism spectrum disorder
Authors: Peng Jacqueline , Zhao Mengge , Havrilla James , Liu Cong , Weng Chunhua , Guthrie Whitney , Schultz Robert , Wang Kai , Zhou Yunyun 
Published: December 2020

Abstract
Background
Natural language processing (NLP) tools can facilitate the extraction of biomedical concepts from unstructured free texts, such as research articles or clinical notes. The NLP software tools CLAMP, cTAKES, and MetaMap are among the most widely used tools to extract biomedical concept entities. However, their performance in extracting disease-specific terminology from literature has not been compared extensively, especially for complex neuropsychiatric disorders with a diverse set of phenotypic and clinical manifestations.

Methods
We comparatively evaluated these NLP tools using autism spectrum disorder (ASD) as a case study. We collected 827 ASD-related terms based on previous literature as the benchmark list for performance evaluation. Then, we applied CLAMP, cTAKES, and MetaMap on 544 full-text articles and 20,408 abstracts from PubMed to extract ASD-related terms. We evaluated the predictive performance using precision, recall, and F1 score.

Results
We found that CLAMP has the best performance in terms of F1 score followed by cTAKES and then MetaMap. Our results show that CLAMP has much higher precision than cTAKES and MetaMap, while cTAKES and MetaMap have higher recall than CLAMP.

Conclusion
The analysis protocols used in this study can be applied to other neuropsychiatric or neurodevelopmental disorders that lack well-defined terminology sets to describe their phenotypic presentations.
Impact of corticosteroids and immunosuppressive therapies on symptomatic SARS-CoV-2 infection in a large cohort of patients with chronic inflammatory arthritis
Authors: Favalli Ennio Giulio , Bugatti Serena , Klersy Catherine , Biggioggero Martina , Rossi Silvia , De Lucia Orazio , Bobbio-Pallavicini Francesca , Murgo Antonella , Balduzzi Silvia , Caporali Roberto , Montecucco Carlomaurizio 
Published: December 2020

AbstractBackgroundPrevalence and outcomes of coronavirus disease (COVID)-19 in relation to immunomodulatory medications are still unknown. The aim of the study is to investigate the impact of glucocorticoids and immunosuppressive agents on COVID-19 in a large cohort of patients with chronic immune-mediated inflammatory arthritis.MethodsThe study was conducted in the arthritis outpatient clinic at two large academic hospitals in the COVID-19 most endemic area of Northern Italy (Lombardy). We circulated a cross-sectional survey exploring the prevalence of severe acute respiratory syndrome-coronavirus-2 nasopharyngeal swab positivity and the occurrence of acute respiratory illness (fever and/or cough and/or dyspnea), administered face-to-face or by phone to consecutive patients from 25 February to 20 April 2020. COVID-19 cases were defined as confirmed or highly suspicious according to the World Health Organization criteria. The impact of medications on COVID-19 development was evaluated.ResultsThe study population included 2050 adults with chronic inflammatory arthritis receiving glucocorticoids, conventional-synthetic (cs), or targeted-synthetic/biological (ts/b) disease-modifying drugs (DMARDs). Laboratory-confirmed COVID-19 and highly suspicious infection were recorded in 1.1% and 1.4% of the population, respectively. Treatment with glucocorticoids was independently associated with increased risk of COVID-19 (adjusted OR [95% CI] ranging from 1.23 [1.04–1.44] to 3.20 [1.97–5.18] depending on the definition used). Conversely, patients treated with ts/bDMARDs were at reduced risk (adjusted OR ranging from 0.46 [0.18–1.21] to 0.47 [0.46–0.48]). No independent effects of csDMARDs, age, sex, and comorbidities were observed.ConclusionsDuring the COVID-19 outbreak, treatment with immunomodulatory medications appears safe. Conversely, glucocorticoids, even at low-dose, may confer increased risk of infection.Trial registrationRetrospectively registered. Not applicable.
Epidemiology of Blastocystis infection from 1990 to 2019 in China
Authors: Ning Chao-Qun , Hu Zhu-hua , Chen Jun-hu , Ai Lin , Tian Li-Guang 
Published: December 2020

Abstract
Background
Blastocystis is ubiquitous presence in animals and humans worldwide and has a high level genetic diversity. The aim of this study was to conduct a summary of Blastocystis prevalence, subtypes (STs) in humans and animals in China and depict their distribution.

Methods
We searched for the articles related to epidemiology of Blastocystis in humans and animals throughout China which published from January 1, 1990, to July 31, 2019 in the following databases: PubMed, China National Knowledge Infrastructure (CNKI) and Wanfang database. The keywords were Blastocystis and one of the following ones: STs, subtypes, distribution, epidemiology, prevalence, infection, molecular, geographic, intestinal parasites, genetic diversity and characterization.

Results
In recent years, various molecular epidemiological studies have been carried out in some provinces/regions of China to identify subtypes of Blastocystis. Infants and young children, school students, hospitalized diarrhea patients, HIV/AIDS patients, tuberculosis patients, and cancer patients as respondents had been included. ST1–ST7 and ST12 were the main subtypes in Chinese population. Moreover, surveys of Blastocystis infection in animal were also conducted in some provinces of China. A variety of animals were investigated including pigs, cattle, sheep, yak, giant panda, and crested ibis (Nipponia nippon) with the main subtypes of ST1–ST8, ST10, ST12–ST14.

Conclusions
In recent years, some provinces/regions in China have conducted various molecular epidemiological studies to identify the Blastocystis subtypes. It is important to focus on new subtypes and mixed subtypes of infection, while increasing data on ribosomal alleles. We encourage the scientific community to start research on humans and surrounding animals (including domestic and wild animals) to better understand the possibility of Blastocystis transmission between humans and animals. We call for action among researchers studying intestinal parasitic diseases (Blastocystis), start drawing the subtype of Blastocystis and increase the subtype related to its clinical symptoms.
RAD50 deficiency is a predictor of platinum sensitivity in sporadic epithelial ovarian cancers
Authors: Alblihy Adel , Alabdullah Muslim L. , Toss Michael S. , Algethami Mashael , Mongan Nigel P. , Rakha Emad A. , Madhusudan Srinivasan 
Published: December 2020

AbstractIntrinsic or acquired resistance seriously limits the use of platinating agents in advanced epithelial ovarian cancers. Increased DNA repair capacity is a key route to platinum resistance. RAD50 is a critical component of the MRN complex, a ‘first responder’ to DNA damage and essential for the repair of DSBs and stalled replication forks. We hypothesised a role for RAD50 in ovarian cancer pathogenesis and therapeutics. Clinicopathological significance of RAD50 expression was evaluated in clinical cohorts of ovarian cancer at the protein level (n = 331) and at the transcriptomic level (n = 1259). Sub-cellular localization of RAD50 at baseline and following cisplatin therapy was tested in platinum resistant (A2780cis, PEO4) and sensitive (A2780, PEO1) ovarian cancer cells. RAD50 was depleted and cisplatin sensitivity was investigated in A2780cis and PEO4 cells. RAD50 deficiency was associated with better progression free survival (PFS) at the protein (p = 0.006) and transcriptomic level (p < 0.001). Basal level of RAD50 was higher in platinum resistant cells. Following cisplatin treatment, increased nuclear localization of RAD50 was evident in A2780cis and PEO4 compared to A2780 and PEO1 cells. RAD50 depletion using siRNAs in A2780cis and PEO4 cells increased cisplatin cytotoxicity, which was associated with accumulation of DSBs, S-phase cell cycle arrest and increased apoptosis. We provide evidence that RAD50 deficiency is a predictor of platinum sensitivity. RAD50 expression-based stratification and personalization could be viable clinical strategy in ovarian cancers.
Investigation of bipartite entanglement across the magnetization process of a highly frustrated spin-1/2 Heisenberg octahedral chain as a new paradigm of the localized-magnon approach
Authors: Strečka J. , Krupnitska O. , Richter J. 
Published: December 2020

Abstract
The bipartite entanglement across the magnetization process of a highly frustrated spin-1/2 Heisenberg octahedral chain is examined within the concept of localized magnons, which enables a simple calculation of the concurrence measuring a strength of the pairwise entanglement between nearest-neighbor and next-nearest-neighbor spins from square plaquettes. A full exact diagonalization of the finite-size Heisenberg octahedral chain with up to 4 unit cells (20 spins) evidences an extraordinary high precision of the localized-magnon theory in predicting measures of the bipartite entanglement at sufficiently low temperatures. While the monomer-tetramer phase emergent at low enough magnetic fields exhibits presence (absence) of the bipartite entanglement between the nearest-neighbor (next-nearest-neighbor) spins, the magnon-crystal phase emergent below the saturation field contrarily displays identical bipartite entanglement between the nearest-neighbor and next-nearest-neighbor spins. The presented results verify a new paradigm of the localized-magnon approach concerned with a simple calculation of entanglement measures.
Quantum correlations in neutrino oscillation: Coherence and entanglement
Authors: Ettefaghi M. M. , Tabatabaei Lotfi Z. S. , Ramezani Arani R. 
Published: December 2020

Abstract
In this paper, we consider the quantum correlations, coherence and entanglement, in neutrino oscillation. We find that the l
1-norm as a coherence measure is equal to the sum of the three possible concurrences for measuring the entanglement among different flavor modes which were calculated in the paper by Blasone M. et al., EPL, 112 (2015) 20007. Our result shows that the origin of the flavor entanglement in neutrino oscillation is the same as that of quantum coherence. Furthermore, in the wave packet framework, the variation of the l
1-norm is investigated by varying the wave packet width

. As expected, the amount of coherence increases by

due to the increase in overlapping of the mass eigenstates.
On the importance of np-pairs in the isovector pairing model
Authors: Pan Feng , Qi Chong , Dai Lianrong , Sargsyan Grigor , Launey Kristina D. , Draayer Jerry P. 
Published: December 2020

Abstract
It is shown that the isovector np-pair number operator can be realized in the O(5) quasi-spin

basis. The computation of the isovector np-pair number is demonstrated for even-even and odd-odd ds-shell nuclei described by the charge-independent mean field plus isovector pairing model restricted within the O(5) seniority-zero subspace, thereby binding energies and low-lying

excited states of these ds-shell nuclei are fit, along with estimates for the isovector neutron-proton pairing contributions. For reasonable neutron-proton pairing strengths the isovector np-pairing energy contribution to the total binding energy in odd-odd N = Z nuclei is systematically larger than that in the even-even nuclei. In sum, the results suggest that the isovector np-pairing mode is favored in odd-odd N = Z nuclei; and additionally, a decrease in the double binding-energy difference for odd-odd nuclei is primarily due to the symmetry and Wigner energy contributions to the binding energy.
Hall effect for Dirac electrons in graphene exposed to an Abrikosov flux lattice
Authors: Schirmer Jonathan , Kumar Ravi , Bagwe Vivas , Raychaudhuri Pratap , Taniguchi Takashi , Watanabe Kenji , Liu C.-X. , Das Anindya , Jain J. K. 
Published: December 2020

Abstract
The proposals for realizing exotic particles through coupling of quantum Hall effect to superconductivity involve spatially non-uniform magnetic fields. As a step toward that goal, we study, both theoretically and experimentally, a system of Dirac electrons exposed to an Abrikosov flux lattice. We theoretically find that the non-uniform magnetic field causes a carrier-density–dependent reduction of the Hall conductivity. Our studies show that this reduction originates from a rather subtle effect: a levitation of the Berry curvature within Landau levels broadened by the non-uniform magnetic field. Experimentally, we measure the magneto-transport in a monolayer graphene-hexagonal boron nitride-niobium diselenide (NbSe2) heterostructure, and find a density-dependent reduction of the Hall resistivity of graphene as the temperature is lowered from above the superconducting critical temperature of NbSe2, when the magnetic field is uniform, to below, where the magnetic field bunches into an Abrikosov flux lattice.
Understanding the temperature- and pressure-dependent electronic properties of FeSi: DFT + DMFT study
Authors: Dutta Paromita , Pandey Sudhir K. 
Published: December 2020

Abstract
Electronic structures of FeSi and Fe1.02Si0.98 under pressure (achieved through volume compression) have been investigated by using DFT+DMFT and KKR-CPA methods, respectively. The widening of band gap with increasing pressure suggests that the experimentally observed insulator-to-metal transition temperature should shift towards the higher temperature for FeSi. KKR-CPA calculations have shown the presence of impurity states in the gapped region which predicts the half-metallic nature. The closure of the gap (in one spin channel) with pressure increment appears to be responsible for the experimentally observed semiconductor-to-metal transition in Fe excess samples at a temperature below 50 K. Magnetic moments at Fe excess sites are found to be decreasing with increasing pressure from

per Fe atom (

) to

per Fe atom (

). Moreover, for FeSi the calculated local spin susceptibility has shown decreasing behavior with pressure rise similar to experimental result.
Behavior inertia of individuals promotes cooperation in spatial prisoner's dilemma game
Authors: He Jialu , Wang Jianwei , Yu Fengyuan 
Published: December 2020

AbstractCooperation is ubiquitous in real world, even in a fierce competitive environment, which is in contrast with natural selection theory. To address this contradiction, many scholars pay more attention to researching the emergence and maintenance of cooperation. In recent decades, lots of mechanisms about individual behavior are put forward to promote cooperation in spatial prisoner's dilemma game. However, fewer studies focus on the effects of behavior inertia on cooperation. For example, insistence is the key to habit formation, and every extra day you insist, the more motivation you have to keep going, the bigger the inertia of the same behavior is, and the weaker the intention you have to make a change. In other words, it is easier to insist than to change. To this end, we propose a new mechanism, called inertia mechanism of individual behavior to explore the evolution of cooperation, in which each player's behavior inertia relies on the persistence of his/her current strategy: the longer the strategy duration is, the bigger his/her behavior inertia is, and, as a result, the weaker the willingness he/she has to update strategy. Moreover, a reinforcement parameter,α, which characterizes the degree of the impact of the strategy persistence on the behavior inertia, is introduced. The results of numerical simulation show that our inertia mechanism can promote cooperation effectively, compared with the traditional model, and the mechanism performs better with the decrease ofα.
Conformal inflation in the metric-affine geometry
Authors: Mikura Y. , Tada Y. , Yokoyama S. 
Published: December 2020

Abstract
Systematic understanding for classes of inflationary models is investigated from the viewpoint of the local conformal symmetry and the slightly broken global symmetry in the framework of the metric-affine geometry. In the metric-affine geometry, which is a generalisation of the Riemannian one adopted in the ordinary General Relativity, the affine connection is an independent variable of the metric rather than being given, e.g., by the Levi-Civita connection as its function. Thanks to this independency, the metric-affine geometry can preserve the local conformal symmetry in each term of the Lagrangian contrary to the Riemannian geometry, and then the local conformal invariance can be compatible with much more kinds of global symmetries. As simple examples, we consider the two-scalar models with the broken SO(1, 1) or O(2), leading to the well-known α-attractor or natural inflation, respectively. The inflaton, can be understood as their pseudo–Nambu-Goldstone boson.
Defect dynamics for self-propelled rods in a doublet of circular confinement
Authors: Wang Zhengjia , Hao Junhua , Xu Jihua , Qin Feng , Yang Bin 
Published: December 2020

Abstract
Rod-shaped active micro/nano-particles, such as bacterial and bipolar metallic micro/ nano-motors, exhibit emergent collective phenomena far from equilibrium state compared to passive particles. We apply a simulation approach —dissipative particle dynamics (DPD)— to explore the collectively ordered states of self-propelled rods (SPRs) which rely on the defect dynamics in the rod cluster. The SPRs are confined in a doublet of circular confinement and repel each other when two rods touch each other. When the rod flow in the connecting passage of the circles is suppressed, namely the small passage width, the steady vortex pattern is obtained in the two circles for weak activity. In binary-passage system, long single-passage system, and short single-passage system, ferromagnetic vortices (FMV), uncorrelated vortices (UV), and anti-ferromagnetic vortices (AFMV) can be obtained, respectively. For intermediate activity, a regular periodic oscillation of the rod number n

r
in one circle can be seen clearly. For strong activity, mixing of high- and low-frequency oscillation is observed. The amplitude of the rod current in the passage I

p
follows the relation

, where F

a
denotes the self-propelled force.
IGF-I/IGFBP3/ALS Deficiency in Sarcopenia: Low GHBP Suggests GH Resistance in a Subgroup of Geriatric Patients
Authors: Ferrari Uta , Schmidmaier Ralf , Jung Theresa , Reincke Martin , Martini Sebastian , Schoser Benedikt , Bidlingmaier Martin , Drey Michael 
Published: December 2020

Abstract

Context
Definition of etiological subgroups of sarcopenia may help to develop targeted treatments. insulin like growth factor-I (IGF-I), Insulinlike growth factor binding protein 3 (IGFBP3), and acid labile subunit (ALS) build a ternary complex that mediates growth hormone (GH) effects on peripheral organs, such as muscle. Low GH binding protein (GHBP) as a marker of GH receptor number would hint toward GH resistance.

Objective
We aimed to analyze the association of IGF-I, IGFBP3, and ALS with sarcopenia.

Study Participants and Setting
A total of 131 consecutively recruited patients of a geriatric ward were included in a single-center cross-sectional analysis; the nonsarcopenic patients served as controls.

Methods
Measures included sarcopenia status by hand-grip strength measurement and Skeletal Muscle Index (SMI); IGF-I, IGFBP3, ALS, GH, GHBP; body mass index (BMI); Activity of Daily Living (ADL); Mini–Mental State Examination (MMSE); routine laboratory parameters; and statistical regression modeling.

Results
Compared with controls, sarcopenic patients did not differ regarding age, sex, ADL, MMSE, C-reactive protein, glomerular filtration rate, and albumin serum concentrations. However, sarcopenic patients had significantly lower IGF-I, IGFBP3, and ALS. IGF-I and ALS associated significantly with sarcopenia and low hand-grip strength, even after adjustment for age, sex, BMI, and albumin, but not with low SMI. GHBP serum was low in sarcopenic patients, but normal in geriatric patients without sarcopenia. Over 60% of patients with IGF-I/ALS deficiency patients showed GH resistance.

Conclusions
Our data suggest that in geriatric patients, low IGF-I/IGFBP3/ALS could be evaluated for causative connection of the sarcopenia spectrum. Low GHBP points toward potential GH resistance as one possible explanation of this deficiency.