bluuebunny/crossref_metadata_2025_split huggingface dataset:
Long-Term Mortality in Women With Pregnancy Loss and Modification by Race/Ethnicity
Authors: Grandi Sonia M , Hinkle Stefanie N , Mumford Sunni L , Sjaarda Lindsey A , Grantz Katherine L , Mendola Pauline , Mills James L , Pollack Anna Z , Yeung Edwina , Zhang Cuilin , Schisterman Enrique F 
Published: February 2022

Abstract
Pregnancy loss is a common reproductive complication, but its association with long-term mortality and whether this varies by maternal race/ethnicity is not well understood. Data from a racially diverse cohort of pregnant women enrolled in the Collaborative Perinatal Project (CPP) from 1959 to 1966 were used for this study. CPP records were linked to the National Death Index and the Social Security Death Master File to identify deaths and underlying cause (until 2016). Pregnancy loss comprised self-reported losses, including abortions, stillbirths, and ectopic pregnancies. Among 48,188 women (46.0% White, 45.8% Black, 8.2% other race/ethnicity), 25.6% reported at least 1 pregnancy loss and 39% died. Pregnancy loss was associated with a higher absolute risk of all-cause mortality (risk difference, 4.0 per 100 women, 95% confidence interval: 1.4, 6.5) and cardiovascular mortality (risk difference, 2.2 per 100 women, 95% confidence interval: 0.8, 3.5). Stratified by race/ethnicity, a higher risk of mortality persisted in White, but not Black, women. Women with recurrent losses are at increased risk of death, both overall and across all race/ethnicity groups. Pregnancy loss is associated with death; however, it does not confer an excess risk above the observed baseline risk in Black women. These findings support the need to assess reproductive history as part of routine screening in women.
Cuffless Blood Pressure Devices
Authors: Bradley Corey K , Shimbo Daichi , Colburn David Alexander , Pugliese Daniel N , Padwal Raj , Sia Samuel K , Anstey D Edmund 
Published: February 2022

Abstract
Hypertension is associated with more end-organ damage, cardiovascular events, and disability-adjusted life years lost in the United States compared with all other modifiable risk factors. Several guidelines and scientific statements now endorse the use of out-of-office blood pressure (BP) monitoring with ambulatory BP monitoring or home BP monitoring to confirm or exclude hypertension status based on office BP measurement. Current ambulatory or home BP monitoring devices have been reliant on the placement of a BP cuff, typically on the upper arm, to measure BP. There are numerous limitations to this approach. Cuff-based BP may not be well-tolerated for repeated measurements as is utilized with ambulatory BP monitoring. Furthermore, improper technique, including incorrect cuff placement or use of the wrong cuff size, may lead to erroneous readings, affecting diagnosis and management of hypertension. Compared with devices that utilize a cuff, cuffless BP devices may overcome challenges related to technique, tolerability, and overall utility in the outpatient setting. However, cuffless devices have several potential limitations that limit its routine use for the diagnosis and management of hypertension. The review discusses the different approaches for determining BP using various cuffless devices including engineering aspects of cuffless device technologies, validation protocols to test accuracy of cuffless devices, potential barriers to widespread implementation, and future areas of research. This review is intended for the clinicians who utilize out-of-office BP monitoring for the diagnosis and management of hypertension.
Bioabsorbable Polydioxanone Mesh for Soft Tissue Reinforcement in Revisional Breast Surgery
Authors: Turin Sergey Y , Gutowski Karol 
Published: February 2022

Abstract

Background
The need for revision procedures after breast implant surgery often arises from the failure of soft tissues to provide a stable implant pocket. Meshes or dermal matrices have been used to reinforce the implant’s soft tissue support. Durasorb (Surgical Innovation Associates, Chicago, IL) is a resorbable polydioxanone (PDO) mesh indicated for soft tissue reinforcement. Its monofilament, macroporous design allows for ease of handling and rapid tissue incorporation. The extended timeline of PDO bioabsorption provides support during the critical portions of soft tissue healing while avoiding long-term complications of permanent products.

Objectives
Evaluate the efficacy of Durasorb PDO mesh for soft tissue reinforcement in revision breast surgery.

Methods
This is a prospective case series of 17 patients (27 breasts) undergoing revision breast implant surgery with Durasorb PDO mesh.

Results
Five patients (5 breasts) presented for revision after implant placement for breast reconstruction, with the remaining 22 presenting for revision after implant placement for cosmetic indications. Average patient age was 47.9 years, and average BMI 24.3. Indications for surgery were implant malposition (37%), capsular contracture (30%), poor cosmesis/asymmetry (26%), and recurrent soft tissue ptosis (7%). Follow up averaged 355 days (range 174 to 799 days, SD=155). One patient experienced a seroma 2 weeks post-operatively, which resolved after a single aspiration. No infections, wound healing problems, or recurrences of implant malposition/capsular contracture were encountered.

Conclusions
Durasorb PDO mesh appears to be efficacious as a breast implant pocket reinforcement in the reoperative setting with a low complication rate and durable results.

Level of Evidence: 4
Performance optimization in DNA short-read alignment
Authors: Wilton Richard , Szalay Alexander S 
Published: February 2022

AbstractSummaryOver the past decade, short-read sequence alignment has become a mature technology. Optimized algorithms, careful software engineering and high-speed hardware have contributed to greatly increased throughput and accuracy. With these improvements, many opportunities for performance optimization have emerged. In this review, we examine three general-purpose short-read alignment tools—BWA-MEM, Bowtie 2 and Arioc—with a focus on performance optimization. We analyze the performance-related behavior of the algorithms and heuristics each tool implements, with the goal of arriving at practical methods of improving processing speed and accuracy. We indicate where an aligner's default behavior may result in suboptimal performance, explore the effects of computational constraints such as end-to-end mapping and alignment scoring threshold, and discuss sources of imprecision in the computation of alignment scores and mapping quality. With this perspective, we describe an approach to tuning short-read aligner performance to meet specific data-analysis and throughput requirements while avoiding potential inaccuracies in subsequent analysis of alignment results. Finally, we illustrate how this approach avoids easily overlooked pitfalls and leads to verifiable improvements in alignment speed and accuracy.Contactrichard.wilton@jhu.eduSupplementary informationAppendices referenced in this article are available at Bioinformatics online.
A reinforcement learning framework for pooled oligonucleotide design
Authors: David Benjamin M , Wyllie Ryan M , Harouaka Ramdane , Jensen Paul A 
Published: February 2022

Abstract

Motivation
The goal of oligonucleotide (oligo) design is to select oligos that optimize a set of design criteria. Oligo design problems are combinatorial in nature and require computationally intensive models to evaluate design criteria. Even relatively small problems can be intractable for brute-force approaches that test every possible combination of oligos, so heuristic approaches must be used to find near-optimal solutions.

Results
We present a general reinforcement learning (RL) framework, called OligoRL, to solve oligo design problems with complex constraints. OligoRL allows ‘black-box’ design criteria and can be adapted to solve many oligo design problems. We highlight the flexibility of OligoRL by building tools to solve three distinct design problems: (i) finding pools of random DNA barcodes that lack restriction enzyme recognition sequences (CutFreeRL); (ii) compressing large, non-degenerate oligo pools into smaller degenerate ones (OligoCompressor) and (iii) finding Not-So-Random hexamer primer pools that avoid rRNA and other unwanted transcripts during RNA-seq library preparation (NSR-RL). OligoRL demonstrates how RL offers a general solution for complex oligo design problems.

Availability and implementation
OligoRL and all simulation codes are available as a Julia package at http://jensenlab.net/tools and archived at https://archive.softwareheritage.org/browse/origin/directory/?origin_url=https://github.com/bmdavid2/OligoRL.

Supplementary information
Supplementary data are available at Bioinformatics online.
Metabolomic profiling in small vessel disease identifies multiple associations with disease severity
Authors: Harshfield Eric L , Sands Caroline J , Tuladhar Anil M , de Leeuw Frank Erik , Lewis Matthew R , Markus Hugh S 
Published: February 2022

Abstract
Cerebral small vessel disease is a major cause of vascular cognitive impairment and dementia. There are few treatments, largely reflecting limited understanding of the underlying pathophysiology. Metabolomics can be used to identify novel risk factors to better understand pathogenesis and to predict disease progression and severity.
We analysed data from 624 patients with symptomatic cerebral small vessel disease from two prospective cohort studies. Serum samples were collected at baseline and patients underwent MRI scans and cognitive testing at regular intervals with up to 14 years of follow-up. Using ultra-performance liquid chromatography–mass spectrometry and nuclear magnetic resonance spectroscopy, we obtained metabolic and lipidomic profiles from 369 annotated metabolites and 54 764 unannotated features and examined their association with respect to disease severity, assessed using MRI small vessel disease markers, cognition and future risk of all-cause dementia.
Our analysis identified 28 metabolites that were significantly associated with small vessel disease imaging markers and cognition. Decreased levels of multiple glycerophospholipids and sphingolipids were associated with increased small vessel disease load as evidenced by higher white matter hyperintensity volume, lower mean diffusivity normalized peak height, greater brain atrophy and impaired cognition. Higher levels of creatine, FA(18:2(OH)) and SM(d18:2/24:1) were associated with increased lacune count, higher white matter hyperintensity volume and impaired cognition. Lower baseline levels of carnitines and creatinine were associated with higher annualized change in peak width of skeletonized mean diffusivity, and 25 metabolites, including lipoprotein subclasses, amino acids and xenobiotics, were associated with future dementia incidence.
Our results show multiple distinct metabolic signatures that are associated with imaging markers of small vessel disease, cognition and conversion to dementia. Further research should assess causality and the use of metabolomic screening to improve the ability to predict future disease severity and dementia risk in small vessel disease. The metabolomic profiles may also provide novel insights into disease pathogenesis and help identify novel treatment approaches.
Influence of NAT2 Genotype and Maturation on Isoniazid Exposure in Low-Birth-Weight and Preterm Infants With or Without Human Immunodeficiency Virus (HIV) Exposure
Authors: Béranger Agathe , Bekker Adrie , Solans Belén P , Cotton Mark F , Mirochnick Mark , Violari Avy , Wang Jiajia , Cababasay Mae , Wiesner Lubbe , Browning Renee , Moye Jack , Capparelli Edmund V , Savic Radojka M 
Published: February 2022

Abstract

Background
Isoniazid (INH) metabolism depends on the N-acetyl transferase 2 (NAT2) enzyme, whose maturation process remains unknown in low birth weight (LBW) and preterm infants. We aimed to assess INH exposure and safety in infants receiving oral tuberculosis prevention.

Methods
This population pharmacokinetics (PK) analysis used INH and N-acetyl-isoniazid (ACL) concentrations in infants (BW ≤ 4 kg), including preterm, with follow-up for 6 months. PK parameters were described using nonlinear mixed effects modeling. Simulations were performed to assess INH exposure and optimal dosing regimens, using 2 targets: Cmax at 3–6 mg/L and area under the curve (AUC) ≥ 10.52 mg h/L.

Results
We included 57 infants (79% preterm, 84% LBW) in the PK analysis, with a median (range) gestational age of 34 (28.7–39.4) weeks. At the time of sampling, postnatal age was 2.3 (0.2–7.3) months and weight (WT) was 3.7 (0.9–9.3) kg. NAT2 genotype was available in 43 (75.4%) patients (10 slow, 26 intermediate, and 7 fast metabolizers). Ninety percent of NAT2 maturation was attained by 4.4 post-natal months. WT, postmenstrual age, and NAT2 genotype significantly influenced INH exposure, with a 5-fold difference in AUC between slow and fast metabolizers for the same dose. INH appeared safe across the broad range of exposure for 61 infants included in the safety analysis.

Conclusions
In LBW/preterm infants, INH dosing needs frequent adjustment to account for growth and maturation. Pharmacogenetics-based dosing regimens is the most powerful approach to deliver safe and equalized exposures for all infants, because NAT2 genotype highly impacts INH pharmacokinetic variability.
Exploring the Natural Origins of SARS-CoV-2 in the Light of Recombination
Authors: Lytras Spyros , Hughes Joseph , Martin Darren , Swanepoel Phillip , de Klerk Arné , Lourens Rentia , Kosakovsky Pond Sergei L , Xia Wei , Jiang Xiaowei , Robertson David L 
Published: February 2022

Abstract
The lack of an identifiable intermediate host species for the proximal animal ancestor of SARS-CoV-2, and the large geographical distance between Wuhan and where the closest evolutionary related coronaviruses circulating in horseshoe bats (members of the Sarbecovirus subgenus) have been identified, is fueling speculation on the natural origins of SARS-CoV-2. We performed a comprehensive phylogenetic study on SARS-CoV-2 and all the related bat and pangolin sarbecoviruses sampled so far. Determining the likely recombination events reveals a highly reticulate evolutionary history within this group of coronaviruses. Distribution of the inferred recombination events is nonrandom with evidence that Spike, the main target for humoral immunity, is beside a recombination hotspot likely driving antigenic shift events in the ancestry of bat sarbecoviruses. Coupled with the geographic ranges of their hosts and the sampling locations, across southern China, and into Southeast Asia, we confirm that horseshoe bats, Rhinolophus, are the likely reservoir species for the SARS-CoV-2 progenitor. By tracing the recombinant sequence patterns, we conclude that there has been relatively recent geographic movement and cocirculation of these viruses’ ancestors, extending across their bat host ranges in China and Southeast Asia over the last 100 years. We confirm that a direct proximal ancestor to SARS-CoV-2 has not yet been sampled, since the closest known relatives collected in Yunnan shared a common ancestor with SARS-CoV-2 approximately 40 years ago. Our analysis highlights the need for dramatically more wildlife sampling to: 1) pinpoint the exact origins of SARS-CoV-2’s animal progenitor, 2) the intermediate species that facilitated transmission from bats to humans (if there is one), and 3) survey the extent of the diversity in the related sarbecoviruses’ phylogeny that present high risk for future spillovers.
Pulmonary Function in Midlife as a Predictor of Later-Life Cognition: The Coronary Artery Risk Development in Adults (CARDIA) Study
Authors: Joyce Brian T , Chen Xuefen , Yaffe Kristine , Henkle Benjamin E , Gao Tao , Zheng Yinan , Kalhan Ravi , Washko George , Kunisaki Ken M , Thyagarajan Bharat , Gross Myron , Jacobs David R , Lloyd-Jones Donald , Liu Kiang , Sidney Stephen , Hou Lifang 
Published: February 2022

Abstract

Background
Studies found associations between pulmonary function (PF) and cognition, but these are limited by mostly cross-sectional design and a single measure of PF (typically forced expiratory volume in 1 second [FEV1]). Our objective was to prospectively analyze the association of repeatedly measured PF with cognition.

Methods
We studied 3 499 participants in the Coronary Artery Risk Development in Young Adults cohort with cognition measured at year 25 (Y25) and Y30, and PF (FEV1 and forced vital capacity [FVC], reflecting better PF) measured up to 6 times from Y0 to Y20. Cognition was measured via Stroop test, Rey-Auditory Verbal Learning Test [RAVLT], and digit symbol substitution test [DSST], which capture executive function, verbal learning and memory, and attention and psychomotor speed, respectively; lower Stroop, and higher RAVLT and DSST scores indicate better cognition. We modeled linear, cross-sectional associations between cognition and PF at Y30 (mean age 55), and mixed models to examine associations between cognition at Y25–Y30 and longitudinal PF (both annual rate of change, and cumulative PF from Y0 to Y20).

Results
At Y30, FEV1 and FVC were cross-sectionally associated with all 3 measures of cognition (β = 0.08–0.12, p &lt; .01–.02). Annual change from peak FEV1/FVC ratio was associated with Stroop and DSST (β = 18.06, 95% CI = 7.71–28.40; β = 10.30, 95% CI = 0.26–20.34, respectively), but not RAVLT. Cumulative FEV1 and FVC were associated with Stroop and DSST (β = 0.07–0.12, p &lt; .01–.02), but only cumulative FEV1 was associated with RAVLT (β = 0.07, 95% CI = 0.00–0.14).

Conclusions
We identified prospective associations between measures of PF and cognition even at middle ages, adding evidence of a prospective association between reduced PF and cognitive decline.
A GNSS velocity field for crustal deformation studies: The influence of glacial isostatic adjustment on plate motion models
Authors: Vardić Katarina , Clarke Peter J , Whitehouse Pippa L 
Published: February 2022

SUMMARYThe two main causes of global-scale secular deformation of the Earth are tectonic plate motion and glacial isostatic adjustment (GIA). We create a bespoke global 3D GNSS surface velocity field ‘NCL20’ to investigate tectonic plate motion and the effect of GIA on plate motion models (PMMs), drawing on a set of 1D and 3D GIA model predictions. The main motivation for creating NCL20 is to include a larger number of GNSS sites in the most GIA-affected areas of investigation, namely North America, Europe, and Antarctica. We do this using the IGS repro2 data and other similarly processed GNSS data sets. Our final GNSS velocity field has horizontal uncertainties mostly within ±0.5 mm yr–1 and vertical uncertainties mostly within ±1 mm yr–1 (at 95 per cent confidence), which make it suitable for testing GIA models. We generate a suite of 117 global GIA model predictions by combining three different ice history models (ICE-5G, ICE-6G and W12) with a range of 1D and 3D Earth models. By subtracting this ensemble from the GNSS velocity field, we identify and compare a range of PMMs which are expected to be unaffected by GIA. Our method allows us to include GNSS sites that are typically excluded from PMM estimations due to their location in GIA-affected regions. We demonstrate that significant GIA-related horizontal motion outside of the rapidly uplifting regions may bias PMMs if left uncorrected. Based on their ability to explain the observed surface velocity field, a group of best-performing GIA models is selected for three regions of interest: North America, Europe and Antarctica. The range of GIA predictions in each best-performing group is assumed to represent the uncertainty in regional GIA modelling insofar as it can be constrained by present-day geodetic velocities. In the horizontal component, we note that 3D GIA models show more variation in the direction of predicted velocities than 1D GIA models, confirming that horizontal velocities are strongly sensitive to lateral variations in Earth structure. Furthermore, for Antarctica the variation in predicted GIA vertical velocities suggests that the total GIA contribution to annual gravimetric mass change ranges from –3 to 22 Gt yr–1 depending on which of the best-performing GIA models is used.
‘I shall paint my nails with the blood of those that covet me’: Kashmir’s Women’s Militia and Independence-era Nationalism
Authors: Whitehead Andrew 
Published: February 2022

Abstract
Towards the close of 1947, amid increasing turbulence and conflict in Kashmir, women activists established their own militia and were trained to use rifles – a rare initiative in South Asia even amid the turmoil of Partition and independence. The women were aligned with radical Kashmiri nationalism. Their militia was a self-defence force as well as a demonstration of support for Indian rule in Kashmir and for a democratic dispensation to replace the autocratic maharaja. Although the militia was short-lived and never saw active service, the sight of women drilling in the Kashmiri capital with rifles on their shoulders was a powerful demonstration of a change of regime. The testimony of former members of the women's militia emphasizes the sense of empowerment they gained – though the subsequent trajectory of the unresolved Kashmir conflict has clouded over this episode of women's political activism.
Total arch replacement using frozen elephant trunk technique with Frozenix for distal aortic arch aneurysms
Authors: Tokunaga Chiho , Kumagai Yu , Chubachi Fumiya , Hori Yuto , Takazawa Akitoshi , Hayashi Jun , Asakura Toshihisa , Ishii Ryota , Nakajima Hiroyuki , Yoshitake Akihiro 
Published: February 2022

Abstract

OBJECTIVES
Total arch replacement (TAR) using an endovascular approach has been initially introduced as the frozen elephant trunk technique (FET). In our institute, TAR using the FET with Frozenix has been used as the first-line treatment for distal aortic arch aneurysms since 2014. This study aimed to evaluate the early and long-term outcomes and demonstrate the efficacy of this procedure.

METHODS
Between 2014 and 2021, 121 consecutive patients were treated with TAR using the FET with Frozenix for distal aortic arch aneurysms. Early and long-term outcomes were retrospectively analysed.

RESULTS
The 30-day mortality rate was 2.5% (3/121). Of postoperative complications, paraplegia due to spinal cord injury occurred in 2 (1.7%) patients, stroke in 12 (9.9%) and acute renal failure in 10 (8.3%). At follow-up, 23 secondary aortic interventions were required and 8 (6.6%) patients underwent intended secondary thoracic endovascular aortic repair for residual descending aortic aneurysm. Late and aortic-related deaths occurred in 16 (13.2%) and 4 (3.3%) patients, respectively. The overall long-term survival rates at 1, 3 and 5 years were 87.6%, 83.1% and 65.4%, respectively, while the rates of freedom from aortic-related death at 1, 3 and 5 years were 95.7%, 95.7% and 84.8%, respectively.

CONCLUSIONS
TAR using the FET with Frozenix for distal aortic arch aneurysms has acceptable early mortality and morbidity. Spinal cord injury and paraplegia occur less frequently than previously reported. The technique has satisfactory long-term survival and freedom from aortic-related death.