bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sample Size and Geometric Morphometrics Methodology Impact the Evaluation of Morphological Variation
Authors: Rummel A D , Sheehy E T , Schachner E R , Hedrick B P 
Published: January 2024

Synopsis
Geometric morphometrics has had a profound impact on our understanding of morphological evolution. However, factors such as sample size and the views and elements selected for two-dimensional geometric morphometric (2DGM) analyses, which are often dictated by specimen availability and time rather than study design, may affect the outcomes of those analyses. Leveraging large intraspecific sample sizes (n &gt; 70) for two bat species, Lasiurus borealis and Nycticeius humeralis, we evaluate the impact of sample size on calculations of mean shape, shape variance, and centroid size. Additionally, we assessed the concordance of multiple skull 2D views with one another and characterized morphological variation in skull shape in L. borealis and N. humeralis, as well as a closely related species, Lasiurus seminolus. Given that L. seminolus is a morphologically cryptic species with L. borealis, we assessed whether differences in skull shape and in 2DGM approach would allow species discrimination. We found that reducing sample size impacted mean shape and increased shape variance, that shape differences were not consistent across views or skull elements, and that trends shown by the views and elements were not all strongly associated with one another. Further, we found that L. borealis and L. seminolus were statistically different in shape using 2DGM in all views and elements. These results underscore the importance of selecting appropriate sample sizes, 2D views, and elements based on the hypothesis being tested. While there is likely not a generalizable sample size or 2D view that can be employed given the wide variety of research questions and systems evaluated using 2DGM, a generalizable solution to issues with 2DGM presented here is to run preliminary analyses using multiple views, elements, and sample sizes, thus ensuring robust conclusions.
Pledge and Forget? Testing the Effects of NATO’s Wales Pledge on Defense Investment
Authors: Becker Jordan 
Published: January 2024

AbstractDo informal international agreements without coercive mechanisms affect states’ behavior? While scholars have long been interested in this question, answering it often poses empirical challenges, particularly in the arena of international security. By asking and answering a narrower question—Is NATO’s Wales Pledge on defense spending working?—I can empirically test the extent to which states have adhered to a public agreement without formal or coercive enforcement mechanisms. I argue that the Wales Pledge has led to higher spending because NATO the organization uniquely enables allies to influence one another’s defense planning, publicly and privately. I find support for this argument by interrogating disaggregated defense expenditures of NATO and EU members, and by comparing NATO allies Denmark and Norway with non-allies Finland and Sweden. Although the Wales Pledge has been maligned, it served its purpose by encouraging allies to spend more on defense, particularly on equipment modernization.
Grace periods in comparative effectiveness studies of sustained treatments
Authors: Wanis Kerollos Nashat , Sarvet Aaron L , Wen Lan , Block Jason P , Rifas-Shiman Sheryl L , Robins James M , Young Jessica G 
Published: January 2024

Abstract
Researchers are often interested in estimating the effect of sustained use of a treatment on a health outcome. However, adherence to strict treatment protocols can be challenging for individuals in practice and, when non-adherence is expected, estimates of the effect of sustained use may not be useful for decision making. As an alternative, more relaxed treatment protocols which allow for periods of time off treatment (i.e. grace periods) have been considered in pragmatic randomized trials and observational studies. In this article, we consider the interpretation, identification, and estimation of treatment strategies which include grace periods. We contrast natural grace period strategies which allow individuals the flexibility to take treatment as they would naturally do, with stochastic grace period strategies in which the investigator specifies the distribution of treatment utilization. We estimate the effect of initiation of a thiazide diuretic or an angiotensin-converting enzyme inhibitor in hypertensive individuals under various strategies which include grace periods.
Exploring the radio loudness of SDSS quasars with spectral stacking
Authors: Arnaudova M I , Smith D J B , Hardcastle M J , Das S , Drake A , Duncan K , Gürkan G , Magliocchetti M , Morabito L K , Petley J W , Shenoy S , Tasse C 
Published: January 2024

ABSTRACT
We use new 144 MHz observations over 5634 deg2 from the LOFAR (Low Frequency Array) Two-metre Sky Survey (LoTSS) to compile the largest sample of uniformly selected, spectroscopically confirmed quasars from the 14th data release of the Sloan Digital Sky Survey (SDSS-DR14). Using the classical definition of radio loudness, R = log (L1.4GHz/Li), we identify 3697 radio-loud (RL) and 111 132 radio-quiet (RQ) sources at 0.6 &lt; z &lt; 3.4. To study their properties, we develop a new rest-frame spectral stacking algorithm, designed with forthcoming massively multiplexed spectroscopic surveys in mind, and use it to create high signal-to-noise composite spectra of each class, matched in redshift and absolute i-band magnitude. We show that RL quasars have redder continuum and enhanced [O ii] emission than their RQ counterparts. These results persist when additionally matching in black hole mass, suggesting that this parameter is not the defining factor in making a quasi-stellar object (QSO) RL. We find that these features are not gradually varying as a function of radio loudness, but are maintained even when probing deeper into the RQ population, indicating that a clear-cut division in radio loudness is not apparent. Upon examining the star formation rates (SFRs) inferred from the [O ii] emission line, with the contribution from active galactic nucleus removed using the [Ne v] line, we find that RL quasars have a significant excess of star formation relative to RQ quasars out to z = 1.9 at least. Given our findings, we suggest that RL sources either preferably reside in gas-rich systems with rapidly spinning black holes, or represent an earlier obscured phase of QSO evolution.
Virialized equation of state for warm and dense stellar plasmas in proto-neutron stars and supernova matter
Authors: Barba-González D , Albertus C , Pérez-García M A 
Published: January 2024

ABSTRACT
We present microscopic molecular dynamics simulations including the efficient Ewald sum procedure to study warm and dense stellar plasmas consisting of finite-size ion charges immerse in a relativistic neutralizing electron gas. For densities typical of Supernova matter and crust in a proto-neutron star, we select a representative single ion composition and obtain the virialized equation of state (vEoS). We scrutinize the finite-size and screening corrections to the Coulomb potential appearing in the virial coefficients B2, B3, and B4 as a function of temperature. In addition, we study the thermal heat capacity at constant volume, CV, and the generalized Mayer’s relation i.e. the difference CP − CV with CP being the heat capacity at constant pressure, obtaining clear features signalling the onset of the liquid–gas phase transition. Our findings show that microscopic simulations reproduce the discontinuity in CV, whose value lies between that of idealized gas and crystallized configurations. We study the pressure isotherms marking the boundary of the metastable region before the gaseous transition takes place. The resulting vEoS displays a behaviour where effective virial coefficients include extra density dependence showing a generalized density–temperature form. As an application we parametrize pressure as a function of density and temperature under the form of an artificial neural network showing the potential of machine learning for future regression analysis in more refined multicomponent approaches. This is of interest to size the importance of these corrections in the liquid–gas phase transition in warm and dense plasma phases contributing to the cooling behaviour of early Supernova phases and proto-neutron stars.
Genomic profiling of six human somatic histone H1 variants denotes that H1X accumulates at recently incorporated transposable elements
Authors: Salinas-Pena Mónica , Serna-Pujol Núria , Jordan Albert 
Published: January 2024

Abstract
Histone H1, a vital component in chromatin structure, binds to linker DNA and regulates nuclear processes. We have investigated the distribution of histone H1 variants in a breast cancer cell line using ChIP-Seq. Two major groups of variants are identified: H1.2, H1.3, H1.5 and H1.0 are abundant in low GC regions (B compartment), while H1.4 and H1X preferentially localize in high GC regions (A compartment). Examining their abundance within transposable elements (TEs) reveals that H1X and H1.4 are enriched in recently-incorporated TEs (SVA and SINE-Alu), while H1.0/H1.2/H1.3/H1.5 are more abundant in older elements. Notably, H1X is particularly enriched in SVA families, while H1.4 shows the highest abundance in young AluY elements. Although low GC variants are generally enriched in LINE, LTR and DNA repeats, H1X and H1.4 are also abundant in a subset of recent LINE-L1 and LTR repeats. H1X enrichment at SVA and Alu is consistent across multiple cell lines. Further, H1X depletion leads to TE derepression, suggesting its role in maintaining TE repression. Overall, this study provides novel insights into the differential distribution of histone H1 variants among repetitive elements, highlighting the potential involvement of H1X in repressing TEs recently incorporated within the human genome.
Coordinated evolution of the SNORD115 and SNORD116 tandem repeats at the imprinted Prader–Willi/Angelman locus
Authors: Guibert Mathilde , Marty-Capelle Hélène , Robert Anne , Charpentier Bruno , Labialle Stéphane 
Published: January 2024

Abstract
The Prader–Willi/Angelman syndrome (PWS/AS) locus is regulated by the epigenetic mechanism of parental genomic imprinting. This region holds two eutherian-specific, large tandem repeats of box C/D small nucleolar RNA (Snord) genes called SNORD115 and SNORD116, whose loss of paternal expression is key in the development of the PWS. Snords represent an ancient class of noncoding RNAs that typically direct the 2′-O-methylation of specific nucleotides of ribosomal RNAs. However, Snord115 and Snord116 belong to the large class of orphan Snords whose functions remain unclear. The constraints that generated and maintained their unusual genetic organization for mammalian genomes have been poorly addressed to date. Here, a comparative analysis of the evolutionary history of both tandem repeats reveals that several genetic events affected them concomitantly, including copy gains and losses between species, emergence of gene subfamilies in catarrhines or partial tandem duplication in rats. Several indications suggest that parental genomic imprinting orchestrated this coordination of events, adding a new effect on mammalian genome structure and evolution to its roles in gene dosage, meiotic recombination and replication timing. Finally, our work provides a functional rationale for the existence of closely located tandem repeats of small RNA genes in mammalian genomes.
Inducing mitochondriopathy-like damages by transformable nucleopeptide nanoparticles for targeted therapy of bladder cancer
Authors: Hou Da-Yong , Zhang Ni-Yuan , Wang Lu , Lv Mei-Yu , Li Xiang-Peng , Zhang Peng , Wang Yue-Ze , Shen Lei , Wu Xiu-Hai , Fu Bo , Guo Peng-Yu , Wang Zi-Qi , Cheng Dong-Bing , Wang Hao , Xu Wanhai 
Published: January 2024

ABSTRACT
Mitochondriopathy inspired adenosine triphosphate (ATP) depletions have been recognized as a powerful way for controlling tumor growth. Nevertheless, selective sequestration or exhaustion of ATP under complex biological environments remains a prodigious challenge. Harnessing the advantages of in vivo self-assembled nanomaterials, we designed an Intracellular ATP Sequestration (IAS) system to specifically construct nanofibrous nanostructures on the surface of tumor nuclei with exposed ATP binding sites, leading to highly efficient suppression of bladder cancer by induction of mitochondriopathy-like damages. Briefly, the reported transformable nucleopeptide (NLS-FF-T) self-assembled into nuclear-targeted nanoparticles with ATP binding sites encapsulated inside under aqueous conditions. By interaction with KPNA2, the NLS-FF-T transformed into a nanofibrous-based ATP trapper on the surface of tumor nuclei, which prevented the production of intracellular energy. As a result, multiple bladder tumor cell lines (T24, EJ and RT-112) revealed that the half-maximal inhibitory concentration (IC50) of NLS-FF-T was reduced by approximately 4-fold when compared to NLS-T. Following intravenous administration, NLS-FF-T was found to be dose-dependently accumulated at the tumor site of T24 xenograft mice. More significantly, this IAS system exhibited an extremely antitumor efficacy according to the deterioration of T24 tumors and simultaneously prolonged the overall survival of T24 orthotopic xenograft mice. Together, our findings clearly demonstrated the therapeutic advantages of intracellular ATP sequestration-induced mitochondriopathy-like damages, which provides a potential treatment strategy for malignancies.
Ginger intervention on body weight and body composition in adults: a GRADE-assessed systematic review and dose-response meta-analysis of 27 randomized controlled trials
Authors: Rafieipour Nastaran , Gharbi Negin , Rahimi Homan , Kohansal Atefeh , Sadeghi-Dehsahraei Hamed , Fadaei Marjan , Tahmasebi Marzieh , Momeni Seyed Aref , Ostovar Navid , Ahmadi Mohammad , Majd Sara Sadeghi , Mohammadi-Sartang Mohsen 
Published: January 2024

Abstract

Context
Ginger consumption may have an inverse relationship with obesity and metabolic syndrome parameters; however, clinical trials have reported contradictory results.

Objective
To systematically review and analyze randomized controlled trials (RCTs) assessing the effects of ginger on body weight and body composition parameters.

Methods
Databases were searched for appropriate articles up to August 20, 2022. All selected RCTs investigated the impact of ginger on glycemic indices in adults. A random effects model was used to conduct a meta-analysis, and heterogeneity was assessed using the I2 statistic. Net changes in body weight, body mass index (BMI), waist circumference (WC), and percent body fat were used to calculate the effect size, which was reported as a weighted mean difference (WMD) and 95% confidence intervals (CIs). The risk of bias was assessed.

Results
A total of 27 RCTs involving 1309 participants were included. The certainty in the evidence was very low for WC and BMI, and low for body weight and percent body fat as assessed by the GRADE evidence profiles. The meta-analysis showed a significant association between ginger supplementation and a reduction in body weight (WMD, –1.52 kg; 95%CI, –2.37, –0.66; P &lt; 0.001), BMI (WMD, –0.58 kg/m2; 95%CI, –0.87, –0.30; P &lt; 0.001), WC (WMD, –1.04 cm; 95%CI: –1.93, –0.15; P = 0.021), and percent body fat consumption (WMD, –0.87%; 95%CI, –1.71, –0.03; P = 0.042). The results of the nonlinear dose-response analysis showed a significant association between the ginger dose with body weight (Pnonlinearity = 0.019) and WC (Pnonlinearity = 0.042). The effective dose of ginger intervention for body mass reduction was determined to be 2 g/d in dose-response analysis. The duration of ginger intervention had a significant nonlinear relationship with body weight (Pnonlinearity = 0.028) with an effective duration of longer than 8 weeks.

Conclusions
Our findings provide evidence that ginger consumption may significantly affect body composition parameters nonlinearly. More, well-constructed RCTs are needed.
Sediment trap samples reveal regional differences in the population structure of Calanus hyperboreus from the Arctic Ocean
Authors: Tokuhiro Koki , Matsuno Kohei , Onodera Jonaotaro , Sampei Makoto , Fujiwara Amane , Harada Naomi , Niehoff Barbara , Nöthig Eva-Maria , Yamaguchi Atsushi 
Published: January 2024

Abstract
Calanus hyperboreus is one of the dominant copepod species in the Arctic zooplankton communities. The impact of climate change varies among regions within the Arctic, implying that C. hyperboreus populations may be differently affected at different locations, but knowledge on seasonal population dynamics in relation to biogeography is scarce. To fill this gap, we counted C. hyperboreus in samples from sediment traps that were moored from 2009 to 2014 in three regions of the Arctic Ocean (eastern Fram Strait, northern Chukchi Sea and MacKenzie Trough). The C. hyperboreus flux increased between April and May in all regions, likely associated with the ascent from overwintering depth to the surface. In the descent period, high fluxes were observed between July and September in the Fram Strait, between September and November in the northern Chukchi Sea, and between August and October in the MacKenzie Trough, suggesting that the timing of descent varied among the regions characterized by differences in light regime, phytoplankton development and water temperature. The copepodite stage composition in the eastern Fram Strait and the MacKenzie Trough varied with season, suggesting successful local reproduction while it was uniform in the northern Chukchi Sea, possibly because the population is fueled by advection.
Relationship between insomnia and pain in patients with chronic orofacial pain
Authors: Alessandri-Bonetti Anna , Sangalli Linda , Boggero Ian A 
Published: January 2024

Abstract

Objective
Few studies have investigated specific associations between insomnia and orofacial pain (OFP). The aim of this cross-sectional study was to examine relationships of insomnia with pain, mental health, and physical health variables among treatment-seeking patients with chronic OFP.

Methods
OFP diagnosis, demographics, insomnia symptoms, pain intensity, interference, and duration, mental health measures, and number of medical comorbidities were extracted from the medical records of 450 patients receiving an initial appointment at a university-affiliated tertiary OFP clinic. T-tests compared differences between patients with and without insomnia symptomatology, and between patients with different insomnia subtypes (delayed onset/early wakening).

Results
Compared to patients without insomnia, those with elevated insomnia symptomatology (45.1%) reported higher pain intensity (60.70 ± 20.61 vs 44.15 ± 21.69; P &lt; .001) and interference (43.81 ± 29.84 vs 18.40 ± 23.43; P &lt; 0.001), depression/anxiety symptomatology (5.53 ± 3.32 vs 2.72 ± 2.66; P &lt; 0.001), dissatisfaction with life (21.63 ± 6.95 vs 26.50 ± 6.21; P &lt; .001), and number of medical comorbidities (6.72 ± 5.37 vs 4.37 ± 4.60; P &lt; .001). Patients with Sleep Onset Latency insomnia (SOL-insomnia) (N = 76) reported higher pain intensity (t = 3.57; P &lt; 0.001), and pain interference (t = 4.46; P &lt; .001) compared to those without SOL-insomnia. Those with Early Morning Awakening insomnia (EMA-insomnia) (N = 71) did not significantly differ from those without EMA-insomnia on any of the variables. Differences remained significant after adjusting for age, sex, primary OFP diagnosis, and pain intensity.

Conclusions
Insomnia is associated with pain outcomes and should be appropriately managed when treating patients with chronic OFP.
Monitoring drug metabolic pathways through extracellular vesicles in mouse plasma
Authors: Wu Xiaofeng , Quan Menchus , Hadisurya Marco , Hu Jianzhong , Liu Yi-Kai , Zhuang Yuxin , Li Li , Iliuk Anton B , Yang Jun J , Kuang Shihuan , Tao W Andy 
Published: January 2024

Abstract
The ability to monitor the response of metabolic enzymes to drug exposure in individuals is highly appealing and critical to personalized medicine. Although pharmacogenomics assesses genotypic differences, it does not report changes in metabolic enzyme activities due to environmental factors such as drug interactions. Here, we report a quantitative proteomics strategy to monitor drug metabolic pathways by profiling metabolic enzymes in circulating extracellular vesicles (EVs) upon drug exposure. Mass spectrometry (MS)-based measurement revealed that changes in metabolic enzyme abundance in EVs paralleled those in hepatic cells isolated from liver tissue. Coupling with multiplexed isotopic labeling, we temporally quantified 34 proteins involved in drug absorption, distribution, metabolism, and excretion (ADME) pathways. Out of 44 known ADME proteins in plasma EVs, previously annotated mouse cytochrome P450 3A11 (Cyp3a11), homolog to human CYP3A4, and uridine 5'-diphospho (UDP) glucuronosyltransferase 2A3 (Ugt2a3), increased upon daily rifampicin dosage. Dasatinib, a tyrosine kinase inhibitor to treat leukemia, also elevated Cyp3a11 levels in plasma EVs, but to a lesser extent. Altogether, this study demonstrates that measuring drug enzymes in circulating EVs as an effective surrogate is highly feasible and may transform today's drug discovery and development for personalized medicine.
The role of advanced nuclear reactors and fuel cycles in a future energy system
Authors: Kornecki Kasia , Wise Catherine F 
Published: January 2024

Abstract
Nuclear power has been an important part of the US electricity system since the 1950s and continues to be a major source of low-carbon electricity today. Despite having low emissions, high grid reliability, and an excellent track record of safety, nuclear power also demands significant time and upfront capital to deploy, can struggle to compete economically with other generation sources, has intrinsic proliferation risk by relying on fissile material for fuel, and generates radioactive waste for which there are currently no disposal sites. Given the emissions and energy security benefits of having nuclear as part of the energy mix, advanced nuclear technologies have garnered significant interest and investment in recent years. Advanced reactor designs differ from the current operating fleet and have several potential advantages, including lower cost, faster construction, smaller size, inherent safety features, and lower waste yields. Yet, many challenges related to their deployment remain, and overcoming them will dictate whether or not new nuclear technologies become a material element of the future energy infrastructure. This article synthesizes the opportunities and barriers to deploying advanced nuclear reactors and their associated fuel cycles as described in two National Academies consensus reports. It highlights the consensus recommendations that could allow these new technologies to reach commercial success as part of a long-term decarbonization strategy.