bluuebunny/crossref_metadata_2025_split huggingface dataset:
Infinite neural network quantum states: entanglement and training dynamics
Authors: Luo Di , Halverson James 
Published: June 2023

Abstract
We study infinite limits of neural network quantum states (

∞

-NNQS), which exhibit representation power through ensemble statistics, and also tractable gradient descent dynamics. Ensemble averages of entanglement entropies are expressed in terms of neural network correlators, and architectures that exhibit volume-law entanglement are presented. The analytic calculations of entanglement entropy bound are tractable because the ensemble statistics are simplified in the Gaussian process limit. A general framework is developed for studying the gradient descent dynamics of neural network quantum states (NNQS), using a quantum state neural tangent kernel (QS-NTK). For

∞

-NNQS the training dynamics is simplified, since the QS-NTK becomes deterministic and constant. An analytic solution is derived for quantum state supervised learning, which allows an

∞

-NNQS to recover any target wavefunction. Numerical experiments on finite and infinite NNQS in the transverse field Ising model and Fermi Hubbard model demonstrate excellent agreement with theory.

∞

-NNQS opens up new opportunities for studying entanglement and training dynamics in other physics applications, such as in finding ground states.
Multivariate spatiotemporal functional principal component analysis for modeling hospitalization and mortality rates in the dialysis population
Authors: Qian Qi , Nguyen Danh V , Telesca Donatello , Kurum Esra , Rhee Connie M , Banerjee Sudipto , Li Yihao , Senturk Damla 
Published: June 2023

Summary
Dialysis patients experience frequent hospitalizations and a higher mortality rate compared to other Medicare populations, in whom hospitalizations are a major contributor to morbidity, mortality, and healthcare costs. Patients also typically remain on dialysis for the duration of their lives or until kidney transplantation. Hence, there is growing interest in studying the spatiotemporal trends in the correlated outcomes of hospitalization and mortality among dialysis patients as a function of time starting from transition to dialysis across the United States Utilizing national data from the United States Renal Data System (USRDS), we propose a novel multivariate spatiotemporal functional principal component analysis model to study the joint spatiotemporal patterns of hospitalization and mortality rates among dialysis patients. The proposal is based on a multivariate Karhunen–Loéve expansion that describes leading directions of variation across time and induces spatial correlations among region-specific scores. An efficient estimation procedure is proposed using only univariate principal components decompositions and a Markov Chain Monte Carlo framework for targeting the spatial correlations. The finite sample performance of the proposed method is studied through simulations. Novel applications to the USRDS data highlight hot spots across the United States with higher hospitalization and/or mortality rates and time periods of elevated risk.
430 Comparison of effectiveness of topical treatments for atopic dermatitis
Authors: Uddin Sabiha , Upchurch Britton , Chandy Rithi J , Feldman Steven R 
Published: June 2023

Abstract
Atopic dermatitis (AD) is a chronic inflammatory condition that affects 15% of children and 7.3% of adults in the USA. While topical corticosteroids (TCs) and topical calcineurin inhibitors (TCIs) are considered the mainstay of topical treatments for AD management, long-term use is cautioned due to possible adverse effects (AEs). We present and review the efficacy and safety of new FDA-approved topical agents, topical agents currently in clinical trials, and TCs and TCIs that are currently available for AD management. We also present and compare the safety and efficacy of new and old FDA-approved topical agents, along with other topical treatments that are currently in clinical trials for AD management. An extensive review of the literature was performed using the PubMed, Cochrane, Scopus and ClinicalKey databases with year parameters set between 2014 and 2022. Search keywords included ‘atopic dermatitis’, ‘topical treatments’, ‘comparison’, ‘effectiveness’, ‘new topical treatments for AD’, ‘JAK inhibitors’, ‘PDE-4 inhibitors’, ‘delgocitinib’, ‘crisaborole’ and ‘tapinarof’. We identified four topical drug classes that are efficacious in treating AD: corticosteroids, calcineurin inhibitors, phosphodiesterase-4 (PDE-4) inhibitors and aryl hydrocarbon receptor agonists. Criteria for treatment success were an IGA score of 0 or 1 and improvement ≥2 grades from baseline. Treatment varied among studies from 2 to 24 weeks. Topical corticosteroids were the most effective after adjusting for vehicle (0.05% clobetasol propionate emulsion foam, 38%; 0.1% clocortolone pivalate, 31.6% IGA reduction), followed by tapinarof 1% cream with 29% of patients achieving treatment success, TCIs (0.03% tacrolimus ointment, 24.8%; 1% pimecrolimus cream, 32.1% vehicle-adjusted achieving IGA of ≤2) and PDE-4 inhibitors (2% crisaborole ointment, 10.4%). Tapinarof was the most efficacious in treating AD. There is a lack of head-to-head trials for topical treatments for AD. Due to the tremendous burden of AD on patients’ physical and mental health, there is a need for additional therapies.
435 Burden of disease and unmet needs in the diagnosis and management of atopic dermatitis in the Middle East
Authors: Mahmoud Omar , Attia Enas , Yosipovitch Gil 
Published: June 2023

Abstract
Atopic dermatitis (AD) affects diverse ethnic groups with significant disparities in prevalence, disease progression, clinical outcomes and access to care. There are limited data on AD in the Middle East, yet there is a substantial economic and psychosocial burden of AD in this region with a large unmet need with regards to disease management that is critical to address. There is a trend of increasing prevalence of AD in the Middle East; however, due to the large environmental, socioeconomic, and sociocultural heterogeneity of this region, prevalence varies greatly across and within countries. Similarly, clinical differences in disease presentations exist across the Middle East, although regional data ared limited. We will present clinical phenotypes of AD common in different regions of the Middle East, data on prevalence, genetic variations and challenges of treatment. Further studies exploring molecular biomarkers, genetic polymorphisms, immune factors and the microbiome of patients in the Middle East will help to elucidate the mechanism behind ethnic differences in AD in this population as well as to help understand treatment response and susceptibilities.
Physicochemical homeostasis in bacteria
Authors: Poolman Bert 
Published: June 2023

Abstract
In living cells, the biochemical processes such as energy provision, molecule synthesis, gene expression, and cell division take place in a confined space where the internal chemical and physical conditions are different from those in dilute solutions. The concentrations of specific molecules and the specific reactions and interactions vary for different types of cells, but a number of factors are universal and kept within limits, which we refer to as physicochemical homeostasis. For instance, the internal pH of many cell types is kept within the range of 7.0 to 7.5, the fraction of macromolecules occupies 15%–20% of the cell volume (also known as macromolecular crowding) and the ionic strength is kept within limits to prevent salting-in or salting-out effects. In this article we summarize the generic physicochemical properties of the cytoplasm of bacteria, how they are connected to the energy status of the cell, and how they affect biological processes (Fig. 1). We describe how the internal pH and proton motive force are regulated, how the internal ionic strength is kept within limits, what the impact of macromolecular crowding is on the function of enzymes and the interaction between molecules, how cells regulate their volume (and turgor), and how the cytoplasm is structured. Physicochemical homeostasis is best understood in Escherichia coli, but pioneering studies have also been performed in lactic acid bacteria.
The effect of climate on the occurrence and abundance of tree recruitment in the province of Quebec, Canada
Authors: Fortin Mathieu , Power Hugues , Van Couwenberghe Rosalinde , Eskelson Bianca N I 
Published: June 2023

AbstractTree recruitment is affected by numerous biotic and abiotic factors, including climate. However, the relative importance of climate variables in empirical models of tree recruitment remains to be evaluated. We fitted models of tree recruitment to 26 species in the province of Quebec, Canada. For a better understanding of the recruitment process, we used a two-part model to distinguish recruitment occurrence from abundance. The relative importance of the different variables was assessed using Akaike weights. Our main hypothesis was that climate is one of the major drivers of tree recruitment. Our results showed that growing degree-days counted among the major drivers of recruitment occurrence but not of recruitment abundance. Stand variables, such as the presence and abundance of adult trees of the species, and broadleaved and coniferous basal areas were found to be relatively more important than all the climate variables for both recruitment occurrence and abundance. Species occupancy within a 10-km radius also had a significant effect on recruitment occurrence for two-thirds of the species, but it was less important than growing degree-days and other stand variables. Climate change is expected to improve the suitability of habitats located at the northern edge of species distributions. However, our model predictions point to a low probability of colonization in newly suitable habitats in the short term.
Partial Harvest Effects on the Forest Floor at Four Northern Hardwood Sites in the Green Mountains of Vermont, USA
Authors: Ross Donald S , Knowles Meghan E 
Published: June 2023

Abstract
Harvesting activities are known to decrease forest floor carbon pools, but the response varies with harvest intensity. We examined partial harvesting (33–55% of basal area removed) effects on the forest floor at four northern hardwood sites in Vermont, USA. Six baseline quantitative samples were taken at each site and 9–36 new locations were sampled 1.5–2.6 years after harvesting. Forest soil disturbance was estimated, and basal area was tallied pre- and post-harvest. The forest floor consisted primarily of Oi and Oe horizons. The pre-harvest site means in carbon stock ranged from 6.8 to 12.3 Mg ha-1 and were not significantly different after harvesting. The pre-harvest site means in depth ranged from 2.8 to 4.5 cm and, post-harvest, there was significantly decreased thickness at one site and significantly greater density at two sites postharvest. This compaction was also visually observed in the field. Partial harvesting, which included single-tree and group selection, created highly variable conditions that challenged our experimental design. However, the two sites with the higher number of resampling locations (35–36) had relatively low variability in forest floor metrics and showed significant responses in thickness and density. Continued monitoring is needed to determine long-term trends.
Sex estimation from virtual models: exploring the potential of stereolithic 3D crania models for morphoscopic trait scoring
Authors: Robles Madeline , Carew Rachael M , Rando Carolyn , Nakhaeizadeh Sherry , Morgan Ruth M 
Published: June 2023

Abstract

Modern computed tomography (CT) databases are becoming an accepted resource for the practice and development of identification methods in forensic anthropology. However, the utility of 3D models created using free and open-source visualization software such as 3D Slicer has not yet been thoroughly assessed for morphoscopic biological profiling methods where virtual methods of analysis are becoming more common. This paper presents a study that builds on the initial findings from Robles et al. (2020) to determine the feasibility of estimating sex on stereolithic (STL) 3D cranial models produced from CT scans from a modern, living UK population (n = 80) using equation 2 from the Walker’s (2008) morphoscopic method. Kendall’s coefficients of concordance (KCC) indicated substantial agreement using cranial features scores in an inter-observer test and a video-inter-observer test. Fleiss’ Kappa scores showed moderate agreement (0.50) overall between inter-observer sex estimations, and for observer sex estimations in comparison to recorded sexes (0.56). It was found that novice users could virtually employ morphoscopic sex estimation methods effectively on STL 3D cranial models from modern individuals. This study also highlights the potential that digital databases of modern living populations can offer forensic anthropology.

Key points
Chromosome-scale genome assembly of the rusty patched bumble bee, Bombus affinis (Cresson) (Hymenoptera: Apidae), an endangered North American pollinator
Authors: Koch Jonathan Berenguer Uhuad , Sim Sheina B , Scheffler Brian , Geib Scott M , Smith Tamara A 
Published: June 2023

Abstract
The rusty patched bumble bee, Bombus affinis, is an important pollinator in North America and a federally listed endangered species. Due to habitat loss and large declines in population size, B. affinis is facing imminent extinction unless human intervention and recovery efforts are implemented. To better understand B. affinis biology and population genetic and genomic landscapes, we sequenced and assembled the B. affinis genome from a single haploid male. Whole genome HiFi sequencing on PacBio coupled with HiC sequencing resulted in a complete and highly contiguous contig assembly that was scaffolded into a chromosomal context, resolving 18 chromosomes distributed across the 365.1 Mb assembly. All material for both HiFi and HiC sequencing was derived from a single abdominal tissue segment from the single male. These assembly results, coupled with the minimal amount of tissue destructively sampled, demonstrate methods for generating contiguous and complete genomic resources for a rare and endangered species with limited material available and highlight the importance of sample preservation. Precise methods and applications of these methods are presented for potential applications in other species with similar limitations in specimen availability and curation considerations.
Transcriptomic approach to uncover dynamic events in the development of mid-season sunburn in apple fruit
Authors: Waite Jessica M , Kelly Elizabeth A , Zhang Huiting , Hargarten Heidi L , Waliullah Sumyya , Altman Naomi S , dePamphilis Claude W , Honaas Loren A , Kalcsits Lee 
Published: June 2023

Abstract
Apples grown in high heat, high light, and low humidity environments are at risk for sun injury disorders like sunburn and associated crop losses. Understanding the physiological and molecular mechanisms underlying sunburn will support improvement of mitigation strategies and breeding for more resilient varieties. Numerous studies have highlighted key biochemical processes involved in sun injury, such as the phenylpropanoid and reactive oxygen species (ROS) pathways, demonstrating both enzyme activities and expression of related genes in response to sunburn conditions. Most previous studies have focused on at-harvest activity of a small number of genes in response to heat stress. Thus, it remains unclear how stress events earlier in the season affect physiology and gene expression. Here, we applied heat stress to mid-season apples in the field and collected tissue along a time course—24, 48, and 72 h following a heat stimulus—to investigate dynamic gene expression changes using a transcriptomic lens. We found a relatively small number of differentially expressed genes (DEGs) and enriched functional terms in response to heat treatments. Only a few of these belonged to pathways previously described to be involved in sunburn, such as the AsA–GSH pathway, while most DEGs had not yet been implicated in sunburn or heat stress in pome fruit.
Clonal reproduction of Moniliophthora roreri and the emergence of unique lineages with distinct genomes during range expansion
Authors: Minio Andrea , Figueroa-Balderas Rosa , Cohen Stephen P , Ali Shahin S , Carriel Denny , Britto Dahyana , Stack Conrad , Baruah Indrani K , Marelli Jean-Philippe , Cantu Dario , Bailey Bryan A 
Published: June 2023

Abstract
The basidiomycete Moniliophthora roreri causes frosty pod rot of cacao (Theobroma cacao) in the western hemisphere. Moniliophthora roreri is considered asexual and haploid throughout its hemibiotrophic life cycle. To understand the processes driving genome modification, using long-read sequencing technology, we sequenced and assembled 5 high-quality M. roreri genomes out of a collection of 99 isolates collected throughout the pathogen's range. We obtained chromosome-scale assemblies composed of 11 scaffolds. We used short-read technology to sequence the genomes of 22 similarly chosen isolates. Alignments among the 5 reference assemblies revealed inversions, translocations, and duplications between and within scaffolds. Isolates at the front of the pathogens' expanding range tend to share lineage-specific structural variants, as confirmed by short-read sequencing. We identified, for the first time, 3 new mating type A locus alleles (5 in total) and 1 new potential mating type B locus allele (3 in total). Currently, only 2 mating type combinations, A1B1 and A2B2, are known to exist outside of Colombia. A systematic survey of the M. roreri transcriptome across 2 isolates identified an expanded candidate effector pool and provided evidence that effector candidate genes unique to the Moniliophthoras are preferentially expressed during the biotrophic phase of disease. Notably, M. roreri isolates in Costa Rica carry a chromosome segment duplication that has doubled the associated gene complement and includes secreted proteins and candidate effectors. Clonal reproduction of the haploid M. roreri genome has allowed lineages with unique genome structures and compositions to dominate as it expands its range, displaying a significant founder effect.
Exploring regression dilution bias using repeat measurements of 2858 variables in ≤49 000 UK Biobank participants
Authors: Rutter Charlotte E , Millard Louise A C , Borges Maria Carolina , Lawlor Deborah A 
Published: June 2023

Abstract

Background
Measurement error in exposures and confounders can bias exposure–outcome associations but is rarely considered. We aimed to assess random measurement error of all continuous variables in UK Biobank and explore approaches to mitigate its impact on exposure–outcome associations.

Methods
Random measurement error was assessed using intraclass correlation coefficients (ICCs) for all continuous variables with repeat measures. Regression calibration was used to correct for random error in exposures and confounders, using the associations of red blood cell distribution width (RDW), C-reactive protein (CRP) and 25-hydroxyvitamin D [25(OH)D] with mortality as illustrative examples.

Results
The 2858 continuous variables with repeat measures varied in sample size from 109 to 49 121. They fell into three groups: (i) baseline visit [529 variables; median (interquartile range) ICC = 0.64 (0.57, 0.83)]; (ii) online diet by 24-h recall [22 variables; 0.35 (0.30, 0.40)] and (iii) imaging measures [2307 variables; 0.85 (0.73, 0.94)]. Highest ICCs were for anthropometric and medical history measures, and lowest for dietary and heart magnetic resonance imaging.
The ICCs (95% confidence interval) for RDW, CRP and 25(OH)D were 0.52 (0.51, 0.53), 0.29 (0.27, 0.30) and 0.55 (0.54, 0.56), respectively. Higher RDW and levels of CRP were associated with higher risk of all-cause mortality, and higher concentration of 25(OH)D with lower risk. After correction for random measurement error in the main exposure, the associations all strengthened. Confounder correction did not influence estimates.

Conclusions
Random measurement error varies widely and is often non-negligible. For UK Biobank we provide relevant statistics and adaptable code to help other researchers explore and correct for this.
Punching before the Bell Rings: United Nations Signaling and Pre-Deployment Violence in Civil Wars
Authors: Kathman Jacob D , Benson Michelle , Diehl Paul F 
Published: June 2023

AbstractIn the post-Cold War era, United Nations (UN) peacekeeping has been an effective civil conflict mitigation tool. On the path to peacekeeping, the UN Security Council often signals its growing likelihood to deploy an operation by passing resolutions addressing the conflict. How do these signals affect violence levels in a pre-operation environment? We posit that conflict actors have incentives to improve their relative positions through violence as the UN signals its likelihood to intervene. Using a new dataset that links UNSC resolutions to active civil wars from 1989 to 2014, we find that resolution passage is significantly related to an increase in combatant use of anti-civilian violence. Additionally, as the signal strengthens with the passage of a greater number of resolutions, violence increases. Thus, although deployed peacekeeping operations may effectively protect non-combatants, the process leading to deployment can produce a dangerous environment for civilians.
When are International Organizations Responsive to Policy Problems?
Authors: Lundgren Magnus , Tallberg Jonas , Sommerer Thomas , Squatrito Theresa 
Published: June 2023

Abstract
When are international organizations (IOs) responsive to the policy problems that motivated their establishment? While it is a conventional assumption that IOs exist to address transnational challenges, the question of whether and when IO policy-making is responsive to shifts in underlying problems has not been systematically explored. This study investigates the responsiveness of IOs from a large-n, comparative approach. Theoretically, we develop three alternative models of IO responsiveness, emphasizing severeness, dependence, and power differentials. Empirically, we focus on the domain of security, examining the responsiveness of eight multi-issue IOs to armed conflict between 1980 and 2015, using a novel and expansive dataset on IO policy decisions. Our findings suggest, first, that IOs are responsive to security problems and, second, that responsiveness is not primarily driven by dependence or power differentials but by problem severity. An in-depth study of the responsiveness of the UN Security Council using more granular data confirms these findings. As the first comparative study of whether and when IO policy adapts to problem severity, the article has implications for debates about IO responsiveness, performance, and legitimacy.