bluuebunny/crossref_metadata_2025_split huggingface dataset:
Directed random geometric graphs: structural and spectral properties
Authors: Peralta-Martinez Kevin , Méndez-Bermúdez J A 
Published: December 2022

Abstract
In this work we analyze structural and spectral properties of a model of directed random geometric graphs: given n vertices uniformly and independently distributed on the unit square, a directed edge is set between two vertices if their distance is smaller than the connection radius

ℓ

, which is randomly drawn from a Pareto distribution. This Pareto distribution is characterized by the power-law decay α and the lower bound of its support

ℓ
0

; thus the graphs depend on three parameters

G
(
n
,
α
,

ℓ
0

)

. By increasing

ℓ
0

, for fixed

(
n
,
α
)

, the model transits from isolated vertices (

ℓ
0

≈
0

) to complete graphs (

ℓ
0

=

2

). We first propose a phenomenological expression for the average degree

⟨
k
(
G
)
⟩

which works well for α > 3, when k is a self-averaging quantity. Then we numerically demonstrate that

〈

V
x

(
G
)
〉
≈
n
[
1
−
exp
(
−
〈
k
〉
]

, for all α, where

V
x

(
G
)

is the number of nonisolated vertices of G. Finally, we explore the spectral properties of

G
(
n
,
α
,

ℓ
0

)

by the use of adjacency matrices represented by diluted random matrix ensembles; a non-Hermitian and a Hermitian one. We find that

⟨
k
⟩

is a good scaling parameter of spectral and eigenvector properties of G mainly for large α.
Discrimination and Sleep: Differential Effects by Type and Coping Strategy
Authors: Majeno Angelina , Molina Kristine M , Frisard Christine F , Lemon Stephenie C , Rosal Milagros C 
Published: December 2022

AbstractBackgroundDiscrimination has been posited as a contributor of sleep disparities for Latinxs. The strategy used to cope with discrimination may reduce or exacerbate its effects on sleep. This study examined whether different types of discrimination (everyday and major lifetime discrimination) were associated with sleep indices (quality, disturbances, efficiency) and whether coping strategy used moderated associations.MethodData of Latinx adults (N = 602; 51% women, 65% Dominican, Mage = 46.72 years) come from the Latino Health and Well-being Project, a community-based, cross-sectional study of Latinxs in Lawrence, MA. Multiple linear regressions were estimated separately for each sleep outcome.ResultsEveryday discrimination was significantly associated with poorer sleep quality and greater disturbances; major lifetime discrimination was significantly associated with worse sleep across the three sleep indices. Coping strategy moderated associations between discrimination and sleep. Compared with Latinxs who used passive coping, those who used passive–active coping strategies had poorer sleep quality the more they experienced everyday discrimination. Latinxs who used any active coping strategy, compared with passive coping, had greater sleep disturbances the more frequently they experienced major lifetime discrimination.ConclusionsFindings show that everyday discrimination and major lifetime discrimination are associated with different dimensions of sleep and suggest that coping with discrimination may require the use of different strategies depending on the type of discrimination experienced.
A generic parallel framework for inferring large-scale gene regulatory networks from expression profiles: application to Alzheimer’s disease network
Authors: Sebastian Softya , Roy Swarup , Kalita Jugal 
Published: December 2022

AbstractThe inference of large-scale gene regulatory networks is essential for understanding comprehensive interactions among genes. Most existing methods are limited to reconstructing networks with a few hundred nodes. Therefore, parallel computing paradigms must be leveraged to construct large networks. We propose a generic parallel framework that enables any existing method, without re-engineering, to infer large networks in parallel, guaranteeing quality output. The framework is tested on 15 inference methods (not limited to) employing in silico benchmarks and real-world large expression matrices, followed by qualitative and speedup assessment. The framework does not compromise the quality of the base serial inference method. We rank the candidate methods and use the top-performing method to infer an Alzheimer’s Disease (AD) affected network from large expression profiles of a triple transgenic mouse model consisting of 45,101 genes. The resultant network is further explored to obtain hub genes that emerge functionally related to the disease. We partition the network into 41 modules and conduct pathway enrichment analysis, revealing that a good number of participating genes are collectively responsible for several brain disorders, including AD. Finally, we extract the interactions of a few known AD genes and observe that they are periphery genes connected to the network's hub genes. Availability: The R implementation of the framework is downloadable from https://github.com/Netralab/GenericParallelFramework.
Brain volumes, thicknesses, and surface areas as mediators of genetic factors and childhood adversity on intelligence
Authors: Williams Camille M , Peyre Hugo , Ramus Franck 
Published: December 2022

Abstract
Although genetic and environmental factors influence general intelligence (g-factor), few studies examined the neuroanatomical measures mediating environmental and genetic effects on intelligence. Here, we investigate the brain volumes, cortical mean thicknesses, and cortical surface areas mediating the effects of the g-factor polygenic score (gPGS) and childhood adversity on the g-factor in the UK Biobank. We first examined the global and regional brain measures that contribute to the g-factor. Most regions contributed to the g-factor through global brain size. Parieto-frontal integration theory (P-FIT) regions were not more associated with the g-factor than non-PFIT regions. After adjusting for global brain size and regional associations, only a few regions predicted intelligence and were included in the mediation analyses. We conducted mediation analyses on global measures, regional volumes, mean thicknesses, and surface areas, separately. Total brain volume mediated 7.04% of the gPGS’ effect on the g-factor and 2.50% of childhood adversity’s effect on the g-factor. In comparison, the fraction of the gPGS and childhood adversity’s effects mediated by individual regional volumes, surfaces, and mean thicknesses was 10–15 times smaller. Therefore, genetic and environmental effects on intelligence may be mediated to a larger extent by other brain properties.
Heart–kidney transplant versus heart transplant in the obese: a propensity-matched analysis
Authors: Weingarten Noah , Iyengar Amit , Herbst David Alan , Helmers Mark , Rekhtman David , Song Cindy , Kim Samuel T , Atluri Pavan 
Published: December 2022

Abstract

OBJECTIVES
The decision to perform simultaneous heart–kidney transplant (HKT) rather than isolated heart transplant (IHT) for patients with advanced kidney disease is challenging. Limited data exist to guide this decision in obese patients. We sought to compare mortality after HKT and IHT in obese patients with non-dialysis-dependent kidney disease.

METHODS
The United Network for Organ Sharing was queried for data on adult heart transplant recipients from 2000 to 2022. Inclusion criteria were obesity, estimated glomerular filtration rate &lt;45 ml/min/1.73 m2 and no pretransplant dialysis. HKT and IHT recipients were propensity matched. Morbidity was compared using chi-squared, Fisher’s exact and McNemar’s tests. Survival was assessed with Kaplan–Meier estimation. Risk factors for mortality were examined with Cox regression.

RESULTS
A total of 289 HKT and 1920 IHT recipients met inclusion criteria. Heart–kidney recipients had higher baseline creatinine and rates of intensive care unit disposition than IHT recipients (both standardized mean differences &gt;0.10). Propensity matching resulted in 239 pairs of HKT and IHT recipients with minimal differences in baseline characteristics. Heart–kidney recipients had higher 5- and 10-year survival than IHT recipients on unmatched (77% vs 69%, P = 0.011 and 58% vs 48%, P = 0.008) and propensity matched analyses (77% vs 68%, P = 0.026 and 57% vs 39%, P = 0.007). Heart–kidney transplantation was protective against 10-year mortality on multivariable regression (hazard ratio 0.585, P = 0.002).

CONCLUSIONS
In obese patients with non-dialysis-dependent kidney disease, HKT may decrease long-term mortality relative to IHT and should be strongly considered as a preferred treatment.
Postoperative hypoxaemic acute respiratory failure after neoadjuvant treatment for lung cancer: radiologic findings and risk factors
Authors: Mammana Marco , Sella Nicolò , Giraudo Chiara , Verzeletti Vincenzo , Carere Anna , Bonis Alessandro , Silvestrin Stefano , Pacchiarini Giorgia , Pettenuzzo Tommaso , Monaco Eleonora , Lorenzoni Giulia , Navalesi Paolo , Rea Federico 
Published: December 2022

Abstract

OBJECTIVES
To investigate the rate of hypoxaemic acute respiratory failure (hARF) on patients undergoing surgery for non-small-cell lung cancer (NSCLC) after neoadjuvant chemotherapy, to describe clinical and radiological findings and to explore potential risk factors for this complication.

METHODS
Retrospective review of medical records of all patients who underwent surgery for NSCLC after neoadjuvant chemotherapy at a single centre between 2014 and 2021. Computed tomography scans of patients who developed hARF were reviewed by an experienced radiologist to provide a quantitative assessment of radiologic alterations.

RESULTS
The final cohort consisted of 211 patients. Major morbidity was 13.3% (28/211) and hARF was the most common major complication (n = 11, 5.2%). Postoperative mortality was 1.9% (4/211) and occurred only in patients who experienced hARF. Most patients who experienced hARF underwent major procedures, including pneumonectomy (n = 3), lobectomy with chest wall resection (n = 3), bronchial or vascular reconstructions (n = 3) and extended or bilateral resections (n = 2). Analysis of computed tomography findings revealed that crazy paving and ground glass were the most common alterations and were more represented in the non-operated lung. Male gender, current smoking status, pathologic stage III–IV and operative time resulted significant risk factors for hARF at univariable analysis (P &lt; 0.05).

CONCLUSIONS
hARF is the main cause of major morbidity and mortality after neoadjuvant therapy and surgery for NSCLC and occurs more frequently after complex and lengthier surgical procedures. Overall, our findings suggest that operative time may represent the most important risk factor for hARF.
The logic of relative frustration revisited: theoretical revision of Boudon’s competition model and experimental evidence
Authors: Otten Kasper 
Published: December 2022

Abstract
It is commonly believed that improvements in social opportunities can paradoxically lead to a larger share of frustrated individuals. This paradox has been studied in the field of analytical sociology through a competition model proposed by Raymond Boudon. So far, analyses of the model suggest that the paradox indeed occurs, especially when opportunities improve from a low to medium level and acting on these opportunities carries relatively low costs. However, these analyses are based on the premise that actors care about their absolute payoffs and not their relative payoffs. We extend this premise such that actors care both about their absolute and relative payoffs, by incorporating a form of inequity aversion that we call relative deprivation aversion (RDA). Through game-theoretic analyses, we show that the paradoxical relationship is strongly attenuated when incorporating RDA. Using data from several experiments, we show also empirically that there is no significant increase in relative deprivation under improving opportunities. We conclude that the paradox is theoretically and empirically not likely in the situations captured in Boudon’s competition model. We discuss the implications this has for the paradox in general and provide suggestions for situations under which the paradox may be more likely.
Aiming at harmony. Comparing and contrasting International HFrEF Guidelines
Authors: Tomasoni Daniela , Adamo Marianna , Bozkurt Biykem , Heidenreich Paul , McDonagh Theresa , Rosano Giuseppe M C , Virani Sean A , Zieroth Shelley , Metra Marco 
Published: December 2022

Abstract
Large randomized controlled trials (RCTs) have led to major changes in the treatment of patients with heart failure and reduced left ventricular ejection fraction (HFrEF) and these advances are included in the recent European Society of Cardiology (ESC) and the American College of Cardiology/American Heart Association/Heart Failure Society of America (ACC/AHA/HFSA) guidelines issued in 2021 and 2022, respectively. According to both guidelines, treatment of patients with HFrEF is based on the administration of four classes of drugs that reduce the primary endpoint of cardiovascular death and HF hospitalizations in RCTs: angiotensin-converting enzyme or angiotensin receptor neprilysin inhibitors, beta-blockers, mineralocorticoid receptor antagonists, and sodium-glucose co-transporter 2 inhibitors. Specific sequences of treatment are not recommended but emphasis is given to reaching treatment with all four drugs as early as possible. Further treatments are considered in selected patients including ivabradine, hydralazine nitrates, digoxin, and the new agent vericiguat. Specific treatments, mostly new, for cardiovascular and non-cardiovascular comorbidities are also given. The aim of this article is to compare the two recent guidelines issued by the ESC and ACC/AHA/HFSA and show the few differences and the many consistent recommendations, now more numerous given the evidence available for many new treatments.
Crown Lifting of Low-Density Loblolly Pine (Pinus taeda) Plantations on Nonindustrial Private Forest Lands
Authors: Collins Darcey , Granger Joshua J , Dicke Stephen , Poudel Krishna P , Polinko Adam , Willis John L 
Published: December 2022

AbstractPruning or the physical removal of lower branches, in combination with wider tree spacing, offers an alternative management scheme for small nonindustrial private forest landowners in areas lacking markets for small diameter wood. A 5-year-old loblolly pine (Pinus taeda) plantation was thinned to 495 trees/ha (200 trees/ac). Four crown-lifting treatments of 35%, 40%, 45%, and 50% live crown ratio (LCR) were then implemented. An additional unmanaged plot was established in an unthinned, unpruned area. Two replications were established for all pruning treatments. The target LCR was maintained throughout the study with the additional crown-lifting activities in 2003, 2004, and 2008. At age 8, the average diameter of the unmanaged plot was 13.5 cm (5.3 in), and the diameter of the 50% LCR treatment, which had the greatest diameter growth of all the treatments, was 20.8 cm (8.2 in). The highest mortality rate (22%) was observed in the unmanaged plot, but it was not significantly greater than the other treatments. Low density plantings maintained with pruning could allow small nonindustrial private landowners to obtain a high value sawtimber product while eliminating the need for thinning practices commonly used in traditional pine plantation management.
Transcriptome-wide analysis of pseudouridylation in Drosophila melanogaster
Authors: Song Wan , Podicheti Ram , Rusch Douglas B , Tracey William Daniel 
Published: December 2022

Abstract
Pseudouridine (Psi) is one of the most frequent post-transcriptional modification of RNA. Enzymatic Psi modification occurs on rRNA, snRNA, snoRNA, tRNA, and non-coding RNA and has recently been discovered on mRNA. Transcriptome-wide detection of Psi (Psi-seq) has yet to be performed for the widely studied model organism Drosophila melanogaster. Here, we optimized Psi-seq analysis for this species and have identified thousands of Psi modifications throughout the female fly head transcriptome. We find that Psi is widespread on both cellular and mitochondrial rRNAs. In addition, more than a thousand Psi sites were found on mRNAs. When pseudouridylated, mRNAs frequently had many Psi sites. Many mRNA Psi sites are present in genes encoding for ribosomal proteins, and many are found in mitochondrial encoded RNAs, further implicating the importance of pseudouridylation for ribosome and mitochondrial function. The 7SLRNA of the signal recognition particle is the non-coding RNA most enriched for Psi. The 3 mRNAs most enriched for Psi encode highly expressed yolk proteins (Yp1, Yp2, and Yp3). By comparing the pseudouridine profiles in the RluA-2 mutant and the w1118 control genotype, we identified Psi sites that were missing in the mutant RNA as potential RluA-2 targets. Finally, differential gene expression analysis of the mutant transcriptome indicates a major impact of loss of RluA-2 on the ribosome and translational machinery.
Mega-scale Bayesian regression methods for genome-wide prediction and association studies with thousands of traits
Authors: Qu Jiayi , Runcie Daniel , Cheng Hao 
Published: December 2022

Abstract
Large-scale phenotype data are expected to increase the accuracy of genome-wide prediction and the power of genome-wide association analyses. However, genomic analyses of high-dimensional, highly correlated traits are challenging. We developed a method for implementing high-dimensional Bayesian multivariate regression to simultaneously analyze genetic variants underlying thousands of traits. As a demonstration, we implemented the BayesC prior in the R package MegaLMM. Applied to Genomic Prediction, MegaBayesC effectively integrated hyperspectral reflectance data from 620 hyperspectral wavelengths to improve the accuracy of genetic value prediction on grain yield in a wheat dataset. Applied to Genome-Wide Association Studies, we used simulations to show that MegaBayesC can accurately estimate the effect sizes of QTL across a range of genetic architectures and causes of correlations among traits. To apply MegaBayesC to a realistic scenario involving whole-genome marker data, we developed a 2-stage procedure involving a preliminary step of candidate marker selection prior to multivariate regression. We then used MegaBayesC to identify genetic associations with flowering time in Arabidopsis thaliana, leveraging expression data from 20,843 genes. MegaBayesC selected 15 single nucleotide polymorphisms as important for flowering time, with 13 located within 100 kb of known flowering-time related genes, a higher validation rate than achieved by a single-stage analysis using only the flowering time data itself. These results demonstrate that MegaBayesC can efficiently and effectively leverage high-dimensional phenotypes in genetic analyses.
Quantifying the impact of COVID-19 on essential health services: a comparison of interrupted time series analysis using Prophet and Poisson regression models
Authors: Ogallo William , Wanyana Irene , Tadesse Girmaw Abebe , Wanjiru Catherine , Akinwande Victor , Kabwama Steven , Remy Sekou Lionel , Wachira Charles , Okwako Sharon , Kizito Susan , Wanyenze Rhoda , Kiwanuka Suzanne , Walcott-Bryant Aisha 
Published: December 2022

AbstractBackgroundCoronavirus disease 2019 (COVID-19) altered healthcare utilization patterns. However, there is a dearth of literature comparing methods for quantifying the extent to which the pandemic disrupted healthcare service provision in sub-Saharan African countries.ObjectiveTo compare interrupted time series analysis using Prophet and Poisson regression models in evaluating the impact of COVID-19 on essential health services.MethodsWe used reported data from Uganda’s Health Management Information System from February 2018 to December 2020. We compared Prophet and Poisson models in evaluating the impact of COVID-19 on new clinic visits, diabetes clinic visits, and in-hospital deliveries between March 2020 to December 2020 and across the Central, Eastern, Northern, and Western regions of Uganda.ResultsThe models generated similar estimates of the impact of COVID-19 in 10 of the 12 outcome-region pairs evaluated. Both models estimated declines in new clinic visits in the Central, Northern, and Western regions, and an increase in the Eastern Region. Both models estimated declines in diabetes clinic visits in the Central and Western regions, with no significant changes in the Eastern and Northern regions. For in-hospital deliveries, the models estimated a decline in the Western Region, no changes in the Central Region, and had different estimates in the Eastern and Northern regions.ConclusionsThe Prophet and Poisson models are useful in quantifying the impact of interruptions on essential health services during pandemics but may result in different measures of effect. Rigor and multimethod triangulation are necessary to study the true effect of pandemics on essential health services.
Dose optimization during drug development: whether and when to optimize
Authors: Korn Edward L , Moscow Jeffrey A , Freidlin Boris 
Published: December 2022

Abstract
The goal of dose optimization during drug development is to identify a dose that preserves clinical benefit with optimal tolerability. Traditionally, the maximum tolerated dose in a small phase I dose escalation study is used in the phase II trial assessing clinical activity of the agent. Although it is possible that this dose level could be altered in the phase II trial if an unexpected level of toxicity is seen, no formal dose optimization has routinely been incorporated into later stages of drug development. Recently it has been suggested that formal dose optimization (involving randomly assigning patients between 2 or more dose levels) be routinely performed early in drug development, even before it is known that the experimental therapy has any clinical activity at any dose level. We consider the relative merits of performing dose optimization earlier vs later in the drug development process and demonstrate that a considerable number of patients may be exposed to ineffective therapies unless dose optimization is delayed until after clinical activity or benefit of the new agent has been established. We conclude that patient and public health interests may be better served by conducting dose optimization after (or during) phase III evaluation, with some exceptions when dose optimization should be performed after activity shown in phase II evaluation.
Likelihood calculations for reconstructed lacunae and Papyrus 46’s text of Ephesians 6:19
Authors: McCollum Joey 
Published: December 2022

AbstractThis article presents an approach to quantify the likelihood of a given reconstruction of lacunose text in a manuscript using statistics on line lengths (in letters), information about the line-breaking conventions and scribal habits of the scribe who copied the manuscript, and the well-known computational technique of dynamic programming. The approach and its value are illustrated with an application to a textual contest between the readings τὸ μυστήριον τοῦ εὐαγγελίου and τὸ μυστήριον in Ephesians 6:19, where the early papyrus witness P. Chester Beatty II/P. Mich. Inv. 6238 (Gregory–Aland P46) is lacunose. The study shows that under reasonable assumptions, P46 is over fifty times more likely to have read τὸ μυστήριον.