bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interpretable delta-learning of GW quasiparticle energies from GGA-DFT
Authors: Fediai Artem , Reiser Patrick , Peña Jorge Enrique Olivares , Wenzel Wolfgang , Friederich Pascal 
Published: August 2023

Abstract
Accurate prediction of the ionization potential and electron affinity energies of small molecules are important for many applications. Density functional theory (DFT) is computationally inexpensive, but can be very inaccurate for frontier orbital energies or ionization energies. The GW method is sufficiently accurate for many relevant applications, but much more expensive than DFT. Here we study how we can learn to predict orbital energies with GW accuracy using machine learning (ML) on molecular graphs and fingerprints using an interpretable delta-learning approach. ML models presented here can be used to predict quasiparticle energies of small organic molecules even beyond the size of the molecules used for training. We furthermore analyze the learned DFT-to-GW corrections by mapping them to specific localized fragments of the molecules, in order to develop an intuitive interpretation of the learned corrections, and thus to better understand DFT errors.
Development and Validation of a Claims-Based Model to Predict Categories of Obesity
Authors: Suissa Karine , Wyss Richard , Lu Zhigang , Bessette Lily G , York Cassandra , Tsacogianis Theodore N , Lin Kueiyu Joshua 
Published: August 2023

Abstract
We developed and validated a claims-based algorithm that classifies patients into obesity categories. Using Medicare (2007–2017) and Medicaid (2000–2014) claims data linked to 2 electronic health record (EHR) systems in Boston, Massachusetts, we identified a cohort of patients with an EHR-based body mass index (BMI) measurement (calculated as weight (kg)/height (m)2). We used regularized regression to select from 137 variables and built generalized linear models to classify patients with BMIs of ≥25, ≥30, and ≥40. We developed the prediction model using EHR system 1 (training set) and validated it in EHR system 2 (validation set). The cohort contained 123,432 patients in the Medicare population and 40,736 patients in the Medicaid population. The model comprised 97 variables in the Medicare set and 95 in the Medicaid set, including BMI-related diagnosis codes, cardiovascular and antidiabetic drugs, and obesity-related comorbidities. The areas under the receiver-operating-characteristic curve in the validation set were 0.72, 0.75, and 0.83 (Medicare) and 0.66, 0.66, and 0.70 (Medicaid) for BMIs of ≥25, ≥30, and ≥40, respectively. The positive predictive values were 81.5%, 80.6%, and 64.7% (Medicare) and 81.6%, 77.5%, and 62.5% (Medicaid), for BMIs of ≥25, ≥30, and ≥40, respectively. The proposed model can identify obesity categories in claims databases when BMI measurements are missing and can be used for confounding adjustment, defining subgroups, or probabilistic bias analysis.
Life Expectancy Changes During the COVID-19 Pandemic, 2019–2021: Highly Racialized Deaths in Young and Middle Adulthood in the United States as Compared With Other High-Income Countries
Authors: Masters Ryan K , Aron Laudan Y , Woolf Steven H 
Published: August 2023

Abstract
We estimated changes in life expectancy between 2019 and 2021 in the United States (in the total population and separately for 5 racial/ethnic groups) and 20 high-income peer countries. For each country’s total population, we decomposed the 2019–2020 and 2020–2021 changes in life expectancy by age. For US populations, we also decomposed the life expectancy changes by age and number of coronavirus disease 2019 (COVID-19) deaths. Decreases in US life expectancy in 2020 (1.86 years) and 2021 (0.55 years) exceeded mean changes in peer countries (a 0.39-year decrease and a 0.23-year increase, respectively) and disproportionately involved COVID-19 deaths in midlife. In 2020, Native American, Hispanic, Black, and Asian-American populations experienced larger decreases in life expectancy and greater losses in midlife than did the White population. In 2021, the White population experienced the largest decrease in US life expectancy, although life expectancy in the Native American and Black populations remained much lower. US losses during the pandemic were more severe than in peer countries and disproportionately involved young and middle-aged adults, especially adults of this age in racialized populations. The mortality consequences of the COVID-19 pandemic deepened a US disadvantage in longevity that has been growing for decades and exacerbated long-standing racial inequities in US mortality.
Light intensity mediates phenotypic plasticity and leaf trait regionalization in a tank bromeliad
Authors: Lafont Rapnouil Tristan , Gallant Canguilhem Matthieu , Julien Frédéric , Céréghino Régis , Leroy Céline 
Published: August 2023

Abstract

Background and Aims
Phenotypic plasticity allows plants to cope with environmental variability. Plastic responses to the environment have mostly been investigated at the level of individuals (plants) but can also occur within leaves. Yet the latter have been underexplored, as leaves are often treated as functional units with no spatial structure. We investigated the effect of a strong light gradient on plant and leaf traits and examined whether different portions of a leaf show similar or differential responses to light intensity.

Methods
We measured variation in 27 morpho-anatomical and physiological traits of the rosette and leaf portions (i.e. base and apex) of the tank bromeliad Aechmea aquilega (Bromeliaceae) when naturally exposed to a marked gradient of light intensity.

Key Results
The light intensity received by A. aquilega had a strong effect on the structural, biochemical and physiological traits of the entire rosette. Plants exposed to high light intensity were smaller and had wider, shorter, more rigid and more vertical leaves. They also had lower photosynthetic performance and nutrient levels. We found significant differences between the apex and basal portions of the leaf under low-light conditions, and the differences declined or disappeared for most of the traits as light intensity increased (i.e. leaf thickness, adaxial trichome density, abaxial and adaxial trichome surface, and vascular bundle surface and density).

Conclusions
Our results reveal a strong phenotypic plasticity in A. aquilega, particularly in the form of a steep functional gradient within the leaf under low-light conditions. Under high-light conditions, trait values were relatively uniform along the leaf. This study sheds interesting new light on the functional complexity of tank bromeliad leaves, and on the effect of environmental conditions on leaf trait regionalization.
XIV—Hegel and Fichte: Two Early Critiques of Capitalism
Authors: Honneth Axel 
Published: August 2023

Abstract
In what follows, I attempt to reconstruct Fichte’s and Hegel’s reasons for developing at almost the same time two very different conceptions of a rational economic order. Whereas Hegel, on the basis of his objective notion of reason, would recommend that a rational state, founded on the notion of right, should include a strictly confined, socially embedded market economy, Fichte, on the basis of his subjective notion of reason, thought instead that the very same state must adopt an economic order that might well be described as a ‘planned economy’. Throughout the article I discuss whether it is the stark differences in their methodological premisses or their very different ideas about the individual freedom to be institutionalized in the economic sphere that helps us understand their respective notions of a rational economy.
DBPMod: a supervised learning model for computational recognition of DNA-binding proteins in model organisms
Authors: Pradhan Upendra K , Meher Prabina K , Naha Sanchita , Sharma Nitesh K , Agarwal Aarushi , Gupta Ajit , Parsad Rajender 
Published: August 2023

AbstractDNA-binding proteins (DBPs) play critical roles in many biological processes, including gene expression, DNA replication, recombination and repair. Understanding the molecular mechanisms underlying these processes depends on the precise identification of DBPs. In recent times, several computational methods have been developed to identify DBPs. However, because of the generic nature of the models, these models are unable to identify species-specific DBPs with higher accuracy. Therefore, a species-specific computational model is needed to predict species-specific DBPs. In this paper, we introduce the computational DBPMod method, which makes use of a machine learning approach to identify species-specific DBPs. For prediction, both shallow learning algorithms and deep learning models were used, with shallow learning models achieving higher accuracy. Additionally, the evolutionary features outperformed sequence-derived features in terms of accuracy. Five model organisms, including Caenorhabditis elegans, Drosophila melanogaster, Escherichia coli, Homo sapiens and Mus musculus, were used to assess the performance of DBPMod. Five-fold cross-validation and independent test set analyses were used to evaluate the prediction accuracy in terms of area under receiver operating characteristic curve (auROC) and area under precision-recall curve (auPRC), which was found to be ~89–92% and ~89–95%, respectively. The comparative results demonstrate that the DBPMod outperforms 12 current state-of-the-art computational approaches in identifying the DBPs for all five model organisms. We further developed the web server of DBPMod to make it easier for researchers to detect DBPs and is publicly available at https://iasri-sg.icar.gov.in/dbpmod/. DBPMod is expected to be an invaluable tool for discovering DBPs, supplementing the current experimental and computational methods.
More efficient exact group invariance testing: using a representative subgroup
Authors: Koning N W , Hemerik J 
Published: August 2023

Summary
We consider testing invariance of a distribution under an algebraic group of transformations, such as permutations or sign flips. As such groups are typically huge, tests based on the full group are often computationally infeasible. Hence, it is standard practice to use a random subset of transformations. We improve upon this by replacing the random subset with a strategically chosen, fixed subgroup of transformations. In a generalized location model, we show that the resulting tests are often consistent for lower signal-to-noise ratios. Moreover, we establish an analogy between the power improvement and switching from a t-test to a Z-test under normality. Importantly, in permutation-based multiple testing, the efficiency gain with our approach can be huge, since we attain the same power with many fewer permutations.
Characterization of sperm and implications for male fertility in the last of the Rhynchocephalians
Authors: Lamar Sarah K , Nelson Nicola J , Ormsby Diane K 
Published: August 2023

Abstract
Managing a species of conservation concern can be best achieved when there is information on the reproductive physiology of both sexes available; however, many species lack this critical, baseline information. One such species, the tuatara (Sphenodon punctatus), is the last surviving member of one of the four reptile orders (Rhynchocephalia) and is the only reptile known to lack a male intromittent organ. Culturally and evolutionarily significant, the conservation of this species is a global priority for the maintenance of biodiversity. In light of this, we characterized the morphology, viability and swim speed of mature tuatara sperm for the first time. We found that tuatara sperm are filiform and bear the remarkably conserved three-part sperm structure seen across the animal kingdom. Tuatara sperm are long (mean total length 166 μm), with an approximate head:midpiece:tail ratio of 15:1:17. While tuatara sperm are capable of high levels of within-mating viability (94.53%), the mean viability across all samples was 58.80%. Finally, tuatara sperm had a mean curvilinear velocity swim speed (μ × s − 1) of 82.28. At the population level, there were no differences in viability or mean swim speed between sperm collected from a male’s first mating of a season and repeat matings; however, the maximum sperm swim speed increased in observed repeated matings relative to first matings. Interestingly, faster sperm samples had shorter midpieces, but had greater viability and longer head and tail sections. This work expands our understanding of male reproductive characteristics and their variation to a new order, provides wild references for the assessment of captive individuals, lays the groundwork for potential assisted reproductive techniques and highlights variation in male reproductive potential as an important factor for consideration in future conservation programs for this unique species.
Childhood and spatial hermeneutics in tertiary education: pathways to place-based learning
Authors: Barratt-Peacock Ruth 
Published: August 2023

Abstract
Spatial hermeneutics is a key topic in Australian literary studies. This article asserts that the same attention should be paid to space in Australian children’s literature in tertiary education. Because the discursive nature of childhood and postmodern geography are challenging and highly abstract concepts for undergraduates, this article details two place-based approaches for tertiary teaching on children’s literature and childhood with a particular focus on the Australian children’s texts May Gibb’s 1914 classic GumnutBabies,1 Mem Fox’s Possum Magic (1983),2 and the more recent Tales from Outer Suburbia by Shaun Tan (2008).3
Effects of weight loss in heart failure patients with overweight and obesity: a systematic review and meta-analysis
Authors: Chi Meixuan , Nie Yangfan , Su Yue , Wang Naijuan , Li Anan , Ma Tianyu , Hou Yunying 
Published: August 2023

Abstract

Aims
To perform a systematic review and meta-analysis to evaluate the impact of weight loss (WL) on the prognosis of overweight and obese patients with heart failure (HF).

Methods and results
We reviewed the literature up to 1 February 2023 from PubMed, Web of Science, Embase, Cochrane Library, and Chinese databases for cohort studies, and randomized controlled trials (RCTs). Data from eligible studies were extracted, and statistical analyses were performed using Review Manager 5.3. A total of 19 studies (involving 449 882 patients) were included in the systematic review and meta-analyses. The results showed that WL did not reduce the mortality and rehospitalization rates in overweight and obese HF patients, but could improve the quality of life (P = 0.002), cardiac function (P = 0.0001), and exercise capacity (P = 0.03). The subgroup analysis showed that WL from bariatric surgery (BS) reduced the risk of death (P &lt; 0.00001), WL from medication or exercise was not significantly associated with the risk of death (P = 0.18), and WL was associated with a higher mortality in the subgroup with unspecified WL modality or unintentional WL (P &lt; 0.00001). In addition, it did not reduce the risk of short-term rehospitalization (P = 0.11), but reduced the rehospitalization rates over the long-term (P = 0.03).

Conclusion
WL improves the long-term rehospitalization (&gt;3 months), quality of life, cardiac function, and exercise capacity in overweight and obese HF patients. Although overall WL is not proven effective, subgroup analysis shows that BS can reduce mortality.
Impact of COVID-19 epidemic on temporal pattern of new HIV diagnoses in Italy, 2021 database
Authors: Dorrucci Maria , Regine Vincenza , Pugliese Lucia , Suligoi Barbara 
Published: August 2023

Abstract

Background
New HIV diagnoses in Italy decreased drastically in 2020 due to COVID-19 related effects: 50% fewer diagnoses were reported by the National HIV Surveillance System. COVID-19 pandemic impact on HIV surveillance is unclear. We estimated the expected number of new HIV diagnoses in 2020 in order to isolate the impact of the COVID-19 pandemic.

Methods
We analyzed 29 697 new HIV infections diagnosed from 2012 to 2020, reported to the National HIV Surveillance System. We assessed temporal trends of new HIV diagnoses applying negative binomial mixed effects models. We estimated the COVID-19 impact as the difference between the model-estimated slopes from 2012 to 2019 and the change reported in the diagnoses. The expected number of new HIV diagnoses in 2020 was also estimated and compared with the reported count.

Results
Based on the historical trend, we expected a 15% (95% CI: 5–25%) decline of new HIV diagnoses in 2020. We reported, however, a 49% decrease, yielding to a 34% net decrease in the number of new diagnoses. The strongest impact was estimated in northern regions (−40%) and MSM (−38%). We estimated 761 (95% prediction interval: 350–1277) missed diagnoses during 2020, the majority of them occurring in the North (465 cases), among MSM (416) and heterosexual males (217).

Conclusions
In 2020, when excluding 15% decrease of new diagnoses attributable to the expected reduction, an additional 34% decrease was observed, representing a large decline in new HIV diagnoses associated with the COVID-19 pandemic.
Apilactobacillus kunkeei releases RNA-associated membrane vesicles and proteinaceous nanoparticles
Authors: Seeger Christian , Dyrhage Karl , Näslund Kristina , Andersson Siv G E 
Published: August 2023

Abstract
Extracellularly released particles, including membrane vesicles, have increasingly been recognized as important for bacterial community functions and host-interaction processes, but their compositions and functional roles differ between species and also between strains of the same species. In this study, we have determined the composition of membrane vesicles and protein particles identified in the cell-free pellets of two strains of Apilactobacillus kunkeei, a defensive symbiont of honeybees. The membrane vesicles were separated from the extracellular particles using density gradient ultracentrifugation. The peaks of the RNA and protein distributions were separated from each other and the highest concentration of RNA was observed in the fractions that contained the membrane vesicles while the highest protein concentration coincided with the fractions that contained extracellular particles. A comparative proteomics analysis by LC-MS/MS showed that 37 proteins with type-I signal peptides were consistently identified across the fractionated samples obtained from the cell-free pellets, of which 29 were orthologs detected in both strains. Functional predictions of the extracellular proteins revealed the presence of glycoside hydrolases, glycosyltransferases, giant proteins and peptidases. The extracellular transcriptomes mapped to a broad set of genes with a similar functional profile as the whole cell transcriptome. This study provides insights into the composition of membrane vesicles and extracellular proteins of a bee-associated symbiont.
A Quantitative, Genome-Wide Analysis in Drosophila Reveals Transposable Elements’ Influence on Gene Expression Is Species-Specific
Authors: Fablet Marie , Salces-Ortiz Judit , Jacquet Angelo , Menezes Bianca F , Dechaud Corentin , Veber Philippe , Rebollo Rita , Vieira Cristina 
Published: August 2023

Abstract
Transposable elements (TEs) are parasite DNA sequences that are able to move and multiply along the chromosomes of all genomes. They can be controlled by the host through the targeting of silencing epigenetic marks, which may affect the chromatin structure of neighboring sequences, including genes. In this study, we used transcriptomic and epigenomic high-throughput data produced from ovarian samples of several Drosophila melanogaster and Drosophila simulans wild-type strains, in order to finely quantify the influence of TE insertions on gene RNA levels and histone marks (H3K9me3 and H3K4me3). Our results reveal a stronger epigenetic effect of TEs on ortholog genes in D. simulans compared with D. melanogaster. At the same time, we uncover a larger contribution of TEs to gene H3K9me3 variance within genomes in D. melanogaster, which is evidenced by a stronger correlation of TE numbers around genes with the levels of this chromatin mark in D. melanogaster. Overall, this work contributes to the understanding of species-specific influence of TEs within genomes. It provides a new light on the considerable natural variability provided by TEs, which may be associated with contrasted adaptive and evolutionary potentials.
Prevalence Estimates of Arthritis and Activity-Limiting Pain Among Family Caregivers to Older Adults
Authors: Turner Shelbie G , Robinson Jamaica R M , Pillemer Karl A , Reid M Carrington 
Published: August 2023

Abstract

Background and Objectives
Little is known about the prevalence of physical pain among family caregivers to older adults. We used national survey data to assess the relative prevalence of caregivers’ arthritis and activity-limiting bothersome pain by caregiver and care-recipient characteristics to identify which caregivers may be at a higher risk for physical pain.

Research Design and Methods
We analyzed data collected from 1,930 caregivers who participated in the National Study on Caregiving (2017). We utilized modified Poisson models to estimate adjusted associations of caregiver and care-recipient characteristics with the relative prevalence of arthritis and bothersome pain.

Results
Forty percent of caregivers had a lifetime diagnosis of arthritis. Seventy-five percent of caregivers with arthritis reported bothersome pain, nearly 30% of whom endorsed bothersome pain that limited their activities on most or every day of the previous month (i.e., activity-limiting bothersome pain). Regardless of whether they had arthritis, 51% of the sample reported bothersome pain in the previous month, 24% of whom indicated activity-limiting bothersome pain. Caregivers who were older or more highly educated had a higher prevalence of arthritis. Black caregivers had a lower prevalence of arthritis and activity-limiting bothersome pain compared to White caregivers. Caregivers with physical difficulty providing care had a higher prevalence of arthritis and activity-limiting bothersome pain than caregivers without physical difficulty providing care.

Discussion and Implications
Arthritis and activity-limiting bothersome pain are highly prevalent among caregivers. Given increased prevalence of pain among certain caregivers, it may be efficient to target these groups for pain management interventions.