bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ethnic, gender and other sociodemographic biases in genome-wide association studies for the most burdensome non-communicable diseases: 2005–2022
Authors: Fitipaldi Hugo , Franks Paul W 
Published: October 2022

Abstract
Introduction: Since 2005, disease-related human genetic diversity has been intensively characterized using genome-wide association studies (GWAS). Understanding how and by whom this work was performed may yield valuable insights into the generalizability of GWAS discoveries to global populations and how high-impact genetics research can be equitably sustained in the future. Materials and Methods: We mined the NHGRI-EBI GWAS Catalog (2005–2022) for the most burdensome non-communicable causes of death worldwide. We then compared (i) the geographic, ethnic and socioeconomic characteristics of study populations; (ii) the geographic and socioeconomic characteristics of the regions within which researchers were located and (iii) the extent to which male and female investigators undertook and led the research. Results: The research institutions leading the work are often US-based (37%), while the origin of samples is more diverse, with the Nordic countries having contributed as much data to GWAS as the United States (~17% of data). The majority of first (60%), senior (75%) and all (66%) authors are male; although proportions vary by disease and leadership level, male co-authors are the ubiquitous majority. The vast majority (91%) of complex trait GWAS has been performed in European ancestry populations, with cohorts and scientists predominantly located in medium-to-high socioeconomically ranked countries; apart from East Asians (~5%), other ethnicities rarely feature in published GWAS. See: https://hugofitipaldi.shinyapps.io/gwas_results/ to browse all results. Conclusion: Most GWAS cohorts are of European ancestry residing outside the United States, with a smaller yet meaningful proportion of East Asian ancestry. Papers describing GWAS research are predominantly authored by male scientists based in medium-to-high income countries.
Process mean selection and price differentiation in an imperfectly segmented market for a risk-averse firm
Authors: Asif Raza Syed , Madhumohan Govindaluri Srikrishna 
Published: October 2022

Abstract
In this paper, we propose an integrated model for optimizing the process mean, the price of products and the production quantity. This optimization is conducted considering the impact of price differentiation in an imperfectly segmented market where demand leakages are common. The products that are produced by the production process are assigned to two market segments using sampling inspection. For optimization of the process mean, pricing and production quantities, a multi-objective model is formulated that maximizes (i) The expected total risk-adjusted profit across segments for a risk-tolerant firm, (ii) The satisficing level, that is, the probability of exceeding a target set for total risk-adjusted expected profit and (iii) The two conflicting objectives, expected total risk-adjusted profit and satisficing level. Depending on the complexity of models, either derivative-based closed form solutions or heuristic solution procedures are developed. The problem finds applications in process industries. A detailed numerical simulation is performed to corroborate the models, and it shows that a higher risk aversion results in a lower total expected risk-adjusted profit but a higher probability of achieving the target profit.
Complexity of sparse polynomial solving 2: renormalization
Authors: Malajovich Gregorio 
Published: October 2022

Abstract
Renormalized homotopy continuation on toric varieties is introduced as a tool for solving sparse systems of polynomial equations or sparse systems of exponential sums. The cost of continuation depends on a renormalized condition length, defined as a line integral of the condition number along all the lifted renormalized paths. The theory developed in this paper leads to a continuation algorithm tracking all the solutions between two generic systems with the same structure. The algorithm is randomized, in the sense that it follows a random path between the two systems. The probability of success is one. In order to produce an expected cost bound, several invariants depending solely on the supports of the equations are introduced. For instance, the mixed area is a quermassintegral that generalizes surface area in the same way that mixed volume generalizes ordinary volume. The facet gap measures for each 1-cone in the fan and for each support polytope, how close is the supporting hyperplane to the nearest vertex. Once the supports are fixed, the expected cost depends on the input coefficients solely through two invariants: the renormalized toric condition number and the imbalance of the absolute values of the coefficients. This leads to a nonuniform polynomial complexity bound for polynomial solving in terms of those two invariants.
Telehealth care before and during COVID-19: trends and quality in a large health system
Authors: Luna Paulina , Lee Megan , Vergara Greeno Rebeca , DeLucia Nikki , London Yollanda , Hoffman Pamela , Burg Matthew , Harris Kristie , Spatz Erica S , Mena-Hurtado Carlos , Smolderen Kim G 
Published: October 2022

Abstract

Objective
COVID-19 accelerated telehealth use to ensure care delivery, but there is limited data on the patient perspective. This study aimed to examine telehealth visit uptake before and during COVID-19 and correlates of patient satisfaction and interest in future telehealth visits.

Materials and Methods
This was a cross-sectional observational study between October 2019 and April 2020. Participants included patients who completed satisfaction surveys following telehealth visits.

Results
A total of 8930 patients completed the satisfaction survey using 4-point Likert Scales. Multivariable, hierarchical, cumulative logit models were constructed to examine correlates of satisfaction with quality of care and interest in future telehealth visits. Most patients were satisfied with the patient portal, video quality, and instructions (92.7%–96.8%). Almost half reported saving 1–2 h (46.9%). Correlates positively associated with quality of care and interest in future telehealth visits were ease of patient portal (odds ratio [OR], 1.43, 95% confidence interval [CI], 1.30–1.58; OR, 1.56, 95% CI, 1.41–1.73, respectively), video quality (OR, 1.62, 95% CI, 1.50–1.75; OR, 1.26, 95% CI, 1.16–1.37, respectively), instructions (OR, 5.62, 95% CI, 5.05–6.26; OR, 1.80, 95% CI, 1.62–2.01, respectively), and time saved (&gt;4 h: OR, 1.69, 95%,CI, 1.22–2.34; OR, 3.49, 95% CI, 2.47–4.93, respectively). Being seen after the COVID-19 surge in telehealth (OR, 0.76, 95% CI, 0.63–0.93) or by providers with higher visit volume (OR, 0.71, 95% CI, 0.60–0.85) was associated with lower interest in future telehealth visits.

Conclusions
Patients expressed relatively high satisfaction levels with telehealth. Better technical quality, quality of instructions, and greater time saved were associated with higher satisfaction ratings. To maintain interest in future telehealth use and improve the patient experience, we must enhance the quality of telehealth delivery platforms and instructions provided to patients.
Use of Real Time Specimen Radiography to Evaluate the Number of Stereotactic Core Biopsy Specimens Containing Calcifications Required for Diagnosis
Authors: Kwait Dylan C , Chikarmane Sona A , Semine-Misbach Laura , Agoston Agoston , Lester Susan , Giess Catherine S 
Published: October 2022

Abstract

Objective
To determine the minimum number of stereotactic biopsy specimens containing calcifications sufficient for pathologic diagnosis and the minimum number of specimens containing calcifications sufficient for immunohistochemistry (IHC) in cases of malignancy.

Methods
In this IRB-exempt quality assurance initiative, individual specimens from 126 patients with 129 calcified targets retrieved using a stereotactic system with real time specimen imaging were prospectively analyzed. Pathology was reported independently for each specimen containing calcifications. In every case, the pathologist reported which specimen containing calcifications was sufficient for diagnosis and, in cases of malignancy, which calcified specimen was sufficient for diagnosis and IHC.

Results
A diagnosis was made from the first calcified specimen in 74% of cases (95/129), from the first two calcified specimens in 92% (119/129) of cases, and from the first three calcified specimens in 100% of cases. Pathology was benign in 66% (85/129) of cases, with the diagnosis made from the first calcified specimen in 78% (66/85) of cases. High-risk lesions were the primary pathology in 8% (11/129) of cases, with 55% (6/11) diagnosed from the first calcified specimen. Pathology was malignant in 26% (33/129) of cases. The first calcified specimen was sufficient for diagnosis and IHC in 73% (24/33) of malignancies and the first three calcified specimens were sufficient for diagnosis and IHC in all cases of malignancy.

Conclusion
Three cores verified to contain calcifications on real time specimen imaging were sufficient to make a diagnosis in all cases and to make a diagnosis and obtain IHC in nearly all cases of malignancy.
Learning by Doing: Lessons from the Graduate Students in the Boston Human Rights City Pilot Project
Authors: Mnisi Weeks Sindiso , MacNaughton Gillian , Annunziato Matthew , Kamau Esther , Sajadi Shahrzad , Tarimo Prisca 
Published: October 2022

AbstractThis article describes the experience and lessons learned by graduate students and supervising faculty in piloting an action-research project aimed at realizing positive economic and social change by advancing the vision of Boston as a human rights city that was articulated in a city council resolution adopted in 2011. It details the efforts led by the graduate students in their roles as paid outreach coordinators and research assistants to resuscitate the latent social movement that had resulted in the adoption of the Boston Human Rights City resolution. Against the backdrop of the Boston Human Rights City pilot project’s success at inspiring the re-establishment of the long-defunct city-level human rights commission, each of the graduate student leaders shares their reflections on and analysis of their experience of ‘learning by doing’. They detail the challenges they confronted and what key lessons were yielded by their trial and error. The article concludes with a summary of insights that readers (including the human rights commissioners) might find helpful with respect to both transdisciplinary human rights pedagogy in higher education, especially at the graduate level, and development of social movements, particularly in the advancement of the Human Rights Cities movement. The article therefore contributes to ongoing elucidation in the Journal of Human Rights Practice of what makes for effective human rights education—both in academic environments and in society more generally—outside of the prevalent disciplinary focus on law. Through the lens of the authors’ example of the direct, hands-on experience provided to students by the project, the article invites deeper engagement with transdisciplinary experiential learning as human rights education praxis that aims to reach members of local communities outside the classroom by creating a city-level culture of valuing, protecting and promoting economic and social rights.
Evaluation of Oxidative Stress by Dynamic Thiol/Disulfide Homeostasis and Ischemia-Modified Albumin Levels in Children with β-Thalassemia Major
Authors: Güler Kazancı Elif , Korkmaz Muhammet Furkan , Eren Funda , Erel Özcan 
Published: October 2022

AbstractObjectiveβ-thalassemia major (β-TM) is a hemoglobinopathy characterized by reduced or absent β-globin production. A balance remains between the production of free radicals and suppression of increased levels of reactive oxygen species by the antioxidant system. This study aimed to examine thiol/disulfide homeostasis (TDH) and serum ischemia-modified albumin (IMA) levels to evaluate the oxidant/antioxidant balance in healthy children and persons with β-TM receiving and not receiving chelation therapy.MethodsThis prospective study was carried out from January to June 2021 among 46 individuals with β-TM and 35 healthy controls. A spectrophotometric method was used to analyze TDH and IMA concentrations.ResultsWe found that, compared to controls, native thiol (NT) (P = .048) and total thiol (TT) (P = .027) values were lower in the patient group, whereas disulfide (P &lt; .001), disulfide/native thiol (D/NT) (P = .004), disulfide/total thiol (D/TT) (P = .005), native thiol/total thiol (NT/TT) (P = .004) and IMA (P = .045) values were higher. NT and TT levels were significantly lower in the chelation− group compared to the chelation+ and control groups (P = .002, P = .001). D/NT, D/TT, and NT/TT levels were higher in the chelation+ group than the control group (P = .007), and IMA levels were significantly higher in the chelation+ and chelation− groups compared to the control group (P = .002). The receiver operating characteristic analysis demonstrated that IMA levels were significantly higher in the children with β-TM not taking regular chelation therapy.ConclusionThiol/disulfide homeostasis was observed to be weakened in children with β-TM in our study. Our findings show that when children with β-TM do not receive regular chelation therapy, their oxidant imbalance worsens.
Simulations of black hole fueling in isolated and merging galaxies with an explicit, multiphase ISM
Authors: Sivasankaran Aneesh , Blecha Laura , Torrey Paul , Kelley Luke Zoltan , Bhowmick Aklant , Vogelsberger Mark , Losacco Rachel , Weinberger Rainer , Hernquist Lars , Marinacci Federico , Sales Laura V , Qi Jia 
Published: October 2022

ABSTRACT
We study gas inflows on to supermassive black holes using hydrodynamics simulations of isolated galaxies and idealized galaxy mergers with an explicit, multiphase interstellar medium (ISM). Our simulations use the recently developed ISM and stellar evolution model called Stars and MUltiphase Gas in GaLaxiEs (SMUGGLE). We implement a novel super-Lagrangian refinement scheme that increases the gas mass resolution in the immediate neighbourhood of the black holes (BHs) to accurately resolve gas accretion. We do not include black hole feedback in our simulations. We find that the complex and turbulent nature of the SMUGGLE ISM leads to highly variable BH accretion. BH growth in SMUGGLE converges at gas mass resolutions ≲3 × 103 M⊙. We show that the low resolution simulations combined with the super-Lagrangian refinement scheme are able to produce central gas dynamics and BH accretion rates very similar to that of the uniform high resolution simulations. We further explore BH fueling by simulating galaxy mergers. The interaction between the galaxies causes an inflow of gas towards the galactic centres and results in elevated and bursty star formation. The peak gas densities near the BHs increase by orders of magnitude resulting in enhanced accretion. Our results support the idea that galaxy mergers can trigger AGN activity, although the instantaneous accretion rate depends strongly on the local ISM. We also show that the level of merger-induced enhancement of BH fueling predicted by the SMUGGLE model is much smaller compared to the predictions by simulations using an effective equation of state model of the ISM.
The Three Hundred project: galaxy groups do not survive cluster infall
Authors: Haggar Roan , Kuchner Ulrike , Gray Meghan E , Pearce Frazer R , Knebe Alexander , Yepes Gustavo , Cui Weiguang 
Published: October 2022

ABSTRACT
Galaxy clusters grow by accreting galaxies as individual objects, or as members of a galaxy group. These groups can strongly impact galaxy evolution, stripping the gas from galaxies, and enhancing the rate of galaxy mergers. However, it is not clear how the dynamics and structure of groups are affected when they interact with a large cluster, or whether all group members necessarily experience the same evolutionary processes. Using data from The Three Hundred project, a suite of 324 hydrodynamical resimulations of large galaxy clusters, we study the properties of 1340 groups passing through a cluster. We find that half of group galaxies become gravitationally unbound from the group by the first pericentre, typically just 0.5–1 Gyr after cluster entry. Most groups quickly mix with the cluster satellite population; only $8{{\ \rm per\ cent}}$ of infalling group haloes later leave the cluster, although for nearly half of these, all of their galaxies have become unbound, tidally disrupted or merged into the central by this stage. The position of galaxies in group-centric phase space is also important – only galaxies near the centre of a group (r ≲ 0.7R200) remain bound once a group is inside a cluster, and slow-moving galaxies in the group centre are likely to be tidally disrupted, or merge with another galaxy. This work will help future observational studies to constrain the environmental histories of group galaxies. For example, groups observed inside or nearby to clusters have likely approached very recently, meaning that their galaxies will not have experienced a cluster environment before.
Asymptotic Green’s function solutions of the general relativistic thin disc equations
Authors: Mummery Andrew 
Published: October 2022

ABSTRACT
The leading order Green’s function solutions of the general relativistic thin disc equations are computed, using a pseudo-Newtonian potential and asymptotic Laplace mode matching techniques. This solution, valid for a vanishing innermost stable circular orbit (ISCO) stress, is constructed by ensuring that it reproduces the leading order asymptotic behaviour of the near-ISCO, Newtonian, and global Wentzel–Kramers–Brillouin limits. Despite the simplifications used in constructing this solution, it is typically accurate, for all values of the Kerr spin parameter a and at all radii, to less than a per cent of the full numerically calculated solutions of the general relativistic disc equations. These solutions will be of use in studying time-dependent accretion discs surrounding Kerr black holes.
Clinical characteristics of rheumatoid arthritis patients complicated with pulmonary nontuberculous mycobacterial disease: A cross-sectional case series study
Authors: Nakayama Yoichi , Tanaka Eisaku , Ueyama Masakuni , Terada Satoru , Inao Takashi , Kaji Yusuke , Yasuda Takehiro , Hashimoto Seishu , Hajiro Takashi , Hatta Kazuhiro , Noma Satoshi , Taguchi Yoshio 
Published: October 2022

ABSTRACT

Objectives
Pulmonary nontuberculous mycobacterial disease (pNTM) is a common pulmonary complication of rheumatoid arthritis (RA), but their association has rarely been researched. We aimed to reveal the clinical characteristics of RA with pNTM.

Methods
Among all the RA patients who visited Tenri hospital from April 2017 to March 2018, we enrolled those fulfilling the 2007 ATS/IDSA diagnostic criteria of pNTM, and sex- and age- matched control group at a ratio of 1:5. Demographic characteristics were compared between the two groups.

Results
Among 865 RA patients, 35 (4.0%) patients were complicated with pNTM. RA patients with pNTM had significantly lower BMI and higher rheumatoid factor (RF) and anti-citrullinated protein antibody (ACPA) positivity. Bronchiectasis was the most frequent lesion, followed by clusters of small nodules, patchy consolidation and cavity. Multivariable logistic regression analysis revealed bronchiectasis as a strong independent associated factor of pNTM. Treatment for pNTM was needed in 14 of the 35 (40%) RA patients with pNTM and sputum negative conversion was accomplished in 11 of the 14 cases (78.6%).

Conclusions
RA patients with lower BMI, RF/ACPA positivity, and bronchiectasis were associated with pNTM. Treatment for pNTM may attain sputum negative conversion and radiological improvement in patients with RA.
microbioTA: an atlas of the microbiome in multiple disease tissues of Homo sapiens and Mus musculus
Authors: Wang Ping , Zhang Sainan , He Guoyou , Du Meiyu , Qi Changlu , Liu Ruyue , Zhang Siyuan , Cheng Liang , Shi Lei , Zhang Xue 
Published: October 2022

Abstract
microbioTA (http://bio-annotation.cn/microbiota) was constructed to provide a comprehensive, user-friendly resource for the application of microbiome data from diseased tissues, helping users improve their general knowledge and deep understanding of tissue-derived microbes. Various microbes have been found to colonize cancer tissues and play important roles in cancer diagnoses and outcomes, with many studies focusing on developing better cancer-related microbiome data. However, there are currently no independent, comprehensive open resources cataloguing cancer-related microbiome data, which limits the exploration of the relationship between these microbes and cancer progression. Given this, we propose a new strategy to re-align the existing next-generation sequencing data to facilitate the mining of hidden sequence data describing the microbiome to maximize available resources. To this end, we collected 417 publicly available datasets from 25 human and 14 mouse tissues from the Gene Expression Omnibus database and use these to develop a novel pipeline to re-align microbiome sequences facilitating in-depth analyses designed to reveal the microbial profile of various cancer tissues and their healthy controls. microbioTA is a user-friendly online platform which allows users to browse, search, visualize, and download microbial abundance data from various tissues along with corresponding analysis results, aimimg at providing a reference for cancer-related microbiome research.
EURISCO update 2023: the European Search Catalogue for Plant Genetic Resources, a pillar for documentation of genebank material
Authors: Kotni Pragna , van Hintum Theo , Maggioni Lorenzo , Oppermann Markus , Weise Stephan 
Published: October 2022

Abstract
The European Search Catalogue for Plant Genetic Resources (EURISCO) is a central entry point for information on crop plant germplasm accessions from institutions in Europe and beyond. In total, it provides data on more than two million accessions, making an important contribution to unlocking the vast genetic diversity that lies deposited in &gt;400 germplasm collections in 43 countries. EURISCO serves as the reference system for the Plant Genetic Resources Strategy for Europe and represents a significant approach for documenting and making available the world’s agrobiological diversity. EURISCO is well established as a resource in this field and forms the basis for a wide range of research projects. In this paper, we present current developments of EURISCO, which is accessible at http://eurisco.ecpgr.org.