bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimal Timing of Antiretroviral Therapy Initiation in Children and Adolescents With Human Immunodeficiency Virus-Associated Pulmonary Tuberculosis
Authors: Kay Alexander , Mendez-Reyes Jose , Devezin Tara , Bakaya Meenakshi , Steffy Teresa , Dlamini Sandile , Msekandiana Amos , Ness Tara , Bacha Jason , Amuge Pauline , Matshaba Mogomotsi , Chodota Moses , Nyasulu Phoebe , Thahane Lineo , Mwita Lumumbwa , Kekitiinwa Adeodata , DiNardo Andrew , Lukhele Bhekumusa , Kirchner H Lester , Mandalakas Anna 
Published: September 2022

Abstract

Background
There is insufficient evidence in children and adolescents with human immunodeficiency virus (CAHIV) to guide the timing of antiretroviral treatment (ART) initiation after starting treatment for pulmonary tuberculosis (pTB). To address this knowledge gap, we evaluated the risk of mortality associated with timing of ART initiation in ART-naive CAHIV treated for pTB.

Methods
Data were extracted from electronic medical records of ART-naive patients, aged 0–19 years, who were treated for HIV-associated pTB at Baylor Centers of Excellence in Botswana, Eswatini, Malawi, Lesotho, Tanzania, or Uganda between 2013 and 2020. Data were analyzed against a primary outcome of all-cause mortality with unadjusted Kaplan-Meier curves and Cox proportional hazard models.

Results
The study population included 774 CAHIV with variable intervals to ART initiation after starting TB treatment: &lt;2 weeks (n = 266), 2 weeks to 2 months (n = 398), &gt;2 months (n = 66), and no ART initiated (n = 44). Adjusted Cox proportional hazards models demonstrated increased mortality 1 year from TB treatment initiation in children never starting ART (adjusted HR [aHR]: 2.67; 95% CI: 1.03, 6.94) versus children initiating ART between 2 weeks and 2 months from TB treatment initiation. Mortality risk did not differ for the &lt;2-weeks group (aHR: 1.02; 95% CI: .55, 1.89) versus the group initiating ART between 2 weeks and 2 months.

Conclusions
This retrospective study demonstrated no increase in mortality among CAHIV initiating ART &lt;2 weeks from TB treatment initiation. Given the broad health benefits of ART, this evidence supports the recent WHO recommendation for CAHIV to initiate ART within 2 weeks of initiating TB treatment.
Practical Implementation of Encoding Range Top-2 Queries
Authors: Park Wooyoung , Jo Seungbum , Rao Satti Srinivasa 
Published: September 2022

Abstract
We design a practical variant of an encoding for range Top-2 query (RT2Q) and evaluate its performance. Given an array $A[1,n]$ of $n$ elements from a total order, the range Top-2 encoding problem is to construct a data structure that answers ${\textsf{RT2Q}}{}$, which returns the positions of the first and second largest elements within a given range of $A$, without accessing the array $A$ at query time. We design the following two implementations: (i) an implementation based on an alternative representation of Davoodi et al.’s [Phil. Trans. Royal Soc. A, 2016] data structure, which supports queries efficiently. Experimental results show that our implementation is efficient in practice and gives improved time-space trade-offs compared with the indexing data structures (which keep the original array $A$ as part of the data structure) for range maximum queries. (ii) Another implementation based on Jo et al.’s ${\textsf{RT2Q}}{}$ encoding on $2 \times n$ array [CPM, 2016], which can be constructed in $O(n)$ time. We compare our encoding with Gawrychowski and Nicholson’s optimal encoding [ICALP, 2015] and show that in most cases, our encoding shows faster construction time while using a competitive space in practice.
Shifting of Cognitive Assessments Between Face-to-Face and Telephone Administration: Measurement Considerations
Authors: Smith Jason R , Gibbons Laura E , Crane Paul K , Mungas Dan M , Glymour M Maria , Manly Jennifer J , Zahodne Laura B , Rose Mayeda Elizabeth , Jones Richard N , Gross Alden L 
Published: September 2022

AbstractObjectivesTelephone-administered cognitive assessments are a cost-effective and sometimes necessary alternative to face-to-face assessments. There is limited information in large studies concerning mode effects, or differences in cognition attributable to the assessment method, as a potential measurement threat. We evaluated mode effects on cognitive scores using a population-based sample of community-living older adults.MethodsWe used data from participants aged 65–79 in the 2014 Health and Retirement Study for whom the interview mode was randomized (n = 6,825). We assessed mode differences in test means, whether mode modifies associations of cognition with criterion variables, and formal measurement invariance testing.ResultsRelative to face-to-face assessment, telephone assessment was associated with higher scores for memory and calculation (0.06 to 0.013 standard deviations [SD]) and lower scores for nonmemory items (−0.09 to −0.01 SD). Cognition was significantly differentially related to instrumental activities of daily living difficulty depending on assessment mode. Measurement invariance testing identified evidence of mode differences in certain tests as a function of mode: adjusting for underlying cognition, the largest mode differences in memory and attention: immediate noun recall, delayed word recall, and serial-7s scores were higher given telephone administration.DiscussionDifferences by mode of administration are apparent in cognitive measurement in older adults, albeit to a small degree in our study, and most pronounced for tests of memory and attention. The importance of accounting for mode differences ultimately depends on one’s research question and study sample: not all associations may be affected by mode differences, and such modification may only be apparent among those with lower cognitive functioning.
Spectral element method for 3-D controlled-source electromagnetic forward modelling using unstructured hexahedral meshes
Authors: Weiss M , Kalscheuer T , Ren Z 
Published: September 2022

SUMMARYFor forward modelling of realistic 3-D land-based controlled-source electromagnetic (EM) problems, we develop a parallel spectral element approach, blending the flexibility and versatility of the finite element method in using unstructured grids with the accuracy of the spectral method. Complex-shaped structures and topography are accommodated by using unstructured hexahedral meshes, in which the elements can have curved edges and non-planar faces. Our code is the first spectral element algorithm in EM geophysics that uses the total field formulation (here that of the electric field). Combining unstructured grids and a total field formulation provides advantages in dealing with topography, in particular, when the transmitter is located on rough surface topography. As a further improvement over existing spectral element methods, our approach does not only allow for arbitrary distributions of conductivity, but also of magnetic permeability and dielectric permittivity. The total electric field on the elements is expanded in terms of high-order Lagrangian interpolants, and element-wise integration in the weak form of the boundary value problem is accomplished by Gauss–Legendre–Lobatto quadrature. The resulting complex-valued linear system of equations is solved using the direct solver MUMPS, and, subsequently, the magnetic field is computed at the points of interest by Faraday’s law. Five numerical examples comprehensively study the benefits of this algorithm. Comparisons to semi-analytical and finite element results confirm accurate representation of the EM responses and indicate low dependency on mesh discretization for the spectral element method. A convergence study illuminates the relation between high order polynomial approximation and mesh size and their effects on accuracy and computational cost revealing that high-order approximation yields accurate modelling results for very coarse meshes but is accompanied by high computational cost. The presented numerical experiments give evidence that 2nd and 3rd degree polynomials in combination with moderately discretized meshes provide better trade-offs in terms of computational resources and accuracy than lowest and higher order spectral element methods. To our knowledge, our final example that includes pronounced surface topography and two geometrically complicated conductive anomalies represents the first successful attempt at using 2nd order hexahedral elements supporting curved edges and non-planar faces in controlled-source EM geophysics.
Pseudostable Hodge Integrals
Authors: Cavalieri Renzo , Gallegos Joel , Ross Dustin , Van Over Brandon , Wise Jonathan 
Published: September 2022

Abstract
This paper initiates a study of Hodge integrals on moduli spaces of pseudostable curves. We prove an explicit comparison formula that allows one to effectively compute any pseudostable Hodge integral in terms of intersection numbers on moduli spaces of stable curves, and we use this comparison to prove that pseudostable Hodge integrals are equal to their stable counterparts when they are linear in lambda classes, but not when they are nonlinear. This suggests that pseudostable Gromov–Witten invariants are equal to usual Gromov–Witten invariants for target curves, but not for higher-dimensional target varieties.
Low Prevalence of Interferon α Autoantibodies in People Experiencing Symptoms of Post–Coronavirus Disease 2019 (COVID-19) Conditions, or Long COVID
Authors: Peluso Michael J , Mitchell Anthea , Wang Chung Yu , Takahashi Saki , Hoh Rebecca , Tai Viva , Durstenfeld Matthew S , Hsue Priscilla Y , Kelly J Daniel , Martin Jeffrey N , Wilson Michael R , Greenhouse Bryan , Deeks Steven G , DeRisi Joseph L , Henrich Timothy J 
Published: September 2022

Abstract
Interferon (IFN)–specific autoantibodies have been implicated in severe coronavirus disease 2019 (COVID-19) and have been proposed as a potential driver of the persistent symptoms characterizing “long COVID,” a type of postacute sequelae of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We report that only 2 of 215 participants with convalescent SARS-CoV-2 infection tested over 394 time points, including 121 people experiencing long COVID symptoms, had detectable IFN-α2 antibodies. Both had been hospitalized during the acute phase of the infection. These data suggest that persistent anti-IFN antibodies, although a potential driver of severe COVID-19, are unlikely to contribute to long COVID symptoms in the postacute phase of the infection.
Enhancing antimicrobial surveillance in hospitals in England: a RAND-modified Delphi
Authors: Patel Selina , Jhass Arnoupe , Hopkins Susan , Shallcross Laura 
Published: September 2022

Abstract

Background
Optimizing antimicrobial use (AMU) is key to reducing antimicrobial-resistant infections, but current AMU monitoring in hospital provides limited insights for quality improvement.

Objectives
To understand stakeholders’ priorities for developing national AMU surveillance in English hospitals to serve the needs of national policy makers and front-line practitioners.

Methods
Characteristics of existing AMU surveillance systems were identified from a previous systematic review and categorized by the Acceptability, Practicability, Effectiveness, Affordability, Side-effects and Equity (APEASE) criteria. Stakeholders prioritized characteristics using a two-round RAND-modified Delphi (rating round 1, telephone panel discussion, rating round 2). Findings informed the design of a framework used to assess the extent to which existing surveillance approaches meet stakeholders’ needs.

Results
Between 17/09/19 and 01/11/19, 24 stakeholders with national and local roles related to AMU prioritized 23 characteristics of AMU surveillance describing: resource for surveillance, data collection, data availability and pathways to translate information from surveillance into practice. No existing surveillance approaches demonstrated all prioritized characteristics. The most common limitation was failure to facilitate clinician engagement with AMU through delays in data access and/or limited availability of disaggregated metrics of prescribing.

Conclusions
Current surveillance delivers national public health priorities but improving stewardship demands patient-level data linked to clinical outcomes. This study offers a framework to develop current surveillance to meet the needs of local stakeholders in England. Increased investment in data infrastructure and training is essential to make information held within electronic systems available to front-line clinicians to facilitate quality improvement.
Toward informatics-enabled preparedness for natural hazards to minimize health impacts of climate change
Authors: Phuong Jimmy , Riches Naomi O , Calzoni Luca , Datta Gora , Duran Deborah , Lin Asiyah Yu , Singh Ramesh P , Solomonides Anthony E , Whysel Noreen Y , Kavuluru Ramakanth 
Published: September 2022

Abstract
Natural hazards (NHs) associated with climate change have been increasing in frequency and intensity. These acute events impact humans both directly and through their effects on social and environmental determinants of health. Rather than relying on a fully reactive incident response disposition, it is crucial to ramp up preparedness initiatives for worsening case scenarios. In this perspective, we review the landscape of NH effects for human health and explore the potential of health informatics to address associated challenges, specifically from a preparedness angle. We outline important components in a health informatics agenda for hazard preparedness involving hazard-disease associations, social determinants of health, and hazard forecasting models, and call for novel methods to integrate them toward projecting healthcare needs in the wake of a hazard. We describe potential gaps and barriers in implementing these components and propose some high-level ideas to address them.
Ractopamine and age alter oxygen use and nitrogen metabolism in tissues of beef steers
Authors: Eisemann Joan H , Nienaber John A , Huntington Gerald B 
Published: September 2022

Abstract
The objective was to quantify the effects of age and ractopamine (RAC) on whole body oxygen consumption and Leu flux, and oxygen flux and metabolism of nitrogenous compounds by the portal-drained viscera (PDV), liver, and hindquarters (HQ) of steers. Multicatheterized steers were fed a high energy diet every 2 h in 12 equal portions. Five younger steers (body weight, [BW] = 223 ± 10.1 kg) were 6 mo old and five older steers (BW = 464 ± 16.3 kg) were 14 mo old. Treatments were control (Cont) or 80 mg RAC per kg diet in a crossover design. Nitrogen (N) balance was measured on day 9 to 13. Whole body oxygen consumption and net flux were measured on day 11 and day 13, and net flux of N variables, Phe and Leu kinetics were measured on day 13. Whole body oxygen consumption increased (P &lt; 0.05) in response to RAC in older but not younger steers. Retained N was greater (P = 0.009) for younger than older steers and increased (P = 0.010) with RAC in both ages of steers. Nitrogen retained as a percentage of N apparently absorbed increased (P &lt; 0.05) in the older steers but not the younger steers in response to RAC. Oxygen uptake was greater (P &lt; 0.05) in PDV, liver, and total splanchnic tissues in the younger steers and there was no response to RAC. In contrast, oxygen uptake in HQ increased (P &lt; 0.05) with RAC in the older but not the younger steers. Concentration and net PDV release of α-amino N (AAN) were not affected by age or RAC. Uptake of AAN by liver decreased with RAC (P = 0.001). Splanchnic release of AAN was greater in younger steers (P = 0.020) and increased (P = 0.024) in response to RAC. For HQ tissues, uptake (P = 0.005) and extraction (P = 0.005) of AAN were lesser in older than younger steers and both increased (P = 0.001) in response to RAC. Based on Phe kinetics in HQ, RAC increased (P &lt; 0.05) protein synthesis in older steers but not in younger steers. In contrast, protein breakdown decreased (P &lt; 0.05) in response to RAC in younger steers. In response to RAC, protein degradation was less (P &lt; 0.05) in younger than older steers. Based on Leu kinetics, whole body protein synthesis was greater in the younger steers (P = 0.022) but not altered in response to RAC. Ractopamine enhanced lean tissue growth by increasing supply of AAN to peripheral tissues and altering protein metabolism in HQ. These metabolic responses are consistent with established responses to RAC in production situations.
The mechanisms of S-wave attenuation in grainstones
Authors: Li Guangquan , Zhao Hai , Wang Qianhe , Wang Zhenwei , Luo Haitao 
Published: September 2022

Abstract
The dominant mechanism of P-wave attenuation in fluid-saturated rock is well known to be the pore-scale squirt. However, the S-wave does not change the average fluid pressure in a pore and the pore volume stays unchanged. As such, the S-wave has a mechanism of attenuation distinctively different from the P-wave. This paper attempts to resolve the mechanisms of S-wave attenuation in fluid-saturated grainstones. The first mechanism is the viscous boundary layer in a fracture, the second is fluid acceleration plus a real-number permeability and the third mechanism is fluid acceleration plus a complex-number permeability (which arises from the viscous boundary layer). D'Euville limestone and Berea sandstone are used as illustrative examples. Ultrasonic velocity and the quality factor due to pore fluid (Qs) are compared between the three models and measurement. The results indicate that fluid acceleration plus the viscous boundary layer is the mechanism of S-wave attenuation in the water-saturated grainstones. In addition, the third model reveals a novel convex in the curve of Qs in the frequency range of 107–108 Hz.
A reference genome assembly of the declining tricolored blackbird,Agelaius tricolor
Authors: Ballare Kimberly M , Escalona Merly , Barr Kelly , Seligmann William , Sacco Samuel , Sahasrabudhe Ruta Madhusudan , Nguyen Oanh , Wyckoff Christy , Smith Thomas B , Shapiro Beth 
Published: September 2022

AbstractThe tricolored blackbird, Agelaius tricolor, is a gregarious species that forms enormous breeding and foraging colonies in wetland and agricultural habitats, primarily in California, USA. Once extremely abundant, species numbers have declined dramatically in the past century, largely due to losses of breeding and foraging habitats. Tricolored blackbirds are currently listed as Endangered by the IUCN, and Threatened under the California Endangered Species Act. Increased genetic information is needed to detail the evolutionary consequences of a species-wide bottleneck and inform conservation management. Here, we present a contiguous tricolored blackbird reference genome, assembled with PacBio HiFi long reads and Dovetail Omni-C data to generate a scaffold-level assembly containing multiple chromosome-length scaffolds. This genome adds a valuable resource for important evolutionary and conservation research on tricolored blackbirds and related species.
Phytochemistry and biological activity of Lansium domesticum Corr. species: a review
Authors: Mayanti Tri , Sinaga Siska Elisahbet , Supratman Unang 
Published: September 2022

Abstract

Objectives
This study aims to review and describe the ethnobotanical, phytochemical and biological activity of various extracts and compounds isolated from Lansium domesticum Corr. from 1967 to 2022 and to study the opportunities that can be developed in the future in the pharmaceutical and pharmacology fields. The related articles, followed by the classification of L. domesticum Corr. according to ethnobotanical, biological and phytochemical properties, were collected from SciFinder, Google Scholar and PubMed.

Key findings
More than 80 compounds have been isolated and identified from L. domesticum Corr., including terpenoids and their glycosides. Furthermore, the pharmacological activity of the extracts and pure compounds of L. domesticum Corr. tested in vitro and in vivo were mainly confirmed to include antifeedant, antimalarial, antimicrobial, antibacterial, and radical scavenging activity, antimutagenic, and anticancer.

Summary
In conclusion, based on this review, all data on the phytochemical and biological activity of L. domesticum Corr. can be used to support scientists in further research aim to determine the reaction mechanism of the extracts or compounds and need to be further validated using in vivo models together with toxicological analysis to establish their maximum tolerated dose.
The double round-robin population unravels the genetic architecture of grain size in barley
Authors: Shrestha Asis , Cosenza Francesco , van Inghelandt Delphine , Wu Po-Ya , Li Jinquan , Casale Federico A , Weisweiler Marius , Stich Benjamin 
Published: September 2022

Abstract
Grain number, size and weight primarily determine the yield of barley. Although the genes regulating grain number are well studied in barley, the genetic loci and the causal gene for sink capacity are poorly understood. Therefore, the primary objective of our work was to dissect the genetic architecture of grain size and weight in barley. We used a multi-parent population developed from a genetic cross between 23 diverse barley inbreds in a double round-robin design. Seed size-related parameters such as grain length, grain width, grain area and thousand-grain weight were evaluated in the HvDRR population comprising 45 recombinant inbred line sub-populations. We found significant genotypic variation for all seed size characteristics, and observed 84% or higher heritability across four environments. The quantitative trait locus (QTL) detection results indicate that the genetic architecture of grain size is more complex than previously reported. In addition, both cultivars and landraces contributed positive alleles at grain size QTLs. Candidate genes identified using genome-wide variant calling data for all parental inbred lines indicated overlapping and potential novel regulators of grain size in cereals. Furthermore, our results indicated that sink capacity was the primary determinant of grain weight in barley.
MLL1:EZH2 Ratio in Uterine Secretions and Endometrial Receptivity in Patients with Endometriosis
Authors: Zou Kehan , Du Qing , Chen Xin , Tang Pingfang , Liang Huizhen 
Published: September 2022

ABSTRACT

Objective
To establish a novel approach for diagnosing endometriosis (EM) in patients with impaired endometrial receptivity.

Method
Mixed lineage leukemia 1 (MLL1) and enhancer of zeste homolog 2 (EZH2) levels were analyzed. The MLL1:EZH2 ratio in identifying impaired endometrial receptivity has been established and validated.

Results
In normal endometrial tissue, the MLL1:EZH2 ratio increased significantly in the midsecretory phase, compared with that in the proliferative phase. In the midsecretory phase, the MLL1:EZH2 ratio in endometrial tissues and uterine secretions accurately identifies patients with EM who have impaired endometrial receptivity. In the validation group, the sensitivity and specificity of the MLL1:EZH2 ratio in the uterine secretions of the midsecretory phase, in diagnosing patients EM who have impaired endometrial receptivity, were 100% and 96.55%, respectively.

Conclusions
The MLL1:EZH2 ratio in uterine secretions of the midsecretory phase may serve as a marker to diagnose EM in patients with impaired endometrial receptivity.