bluuebunny/crossref_metadata_2025 huggingface dataset:
Concluding Remarks
Authors: Castater Eric G , Han Kyung Joon
Published: February 2025

This chapter concludes the book by summarizing its theoretical contribution and empirical results, as well as by delving deeper into the implications of the book for politics in wealthy democracies and the comparative political economy literature. The book provides an implication on the study of economic inequality by implying that economic inequality is self-reinforcing because it weakens the class identity of people who belong to the lower socio-economic class and even dismantles institutional bases that promote economic equality such as trade unions and corporatist institutions. The book also implies that higher inequality is contributing to the ‘crisis of democracy’ in Western Europe and the United States by leading the working class to focus more on social change and cultural issues, areas where their lower levels of formal education make them more susceptible to prejudice and authoritarian inclinations.
Impact of in-hospital medication changes on clinical outcomes in older inpatients: the journey and destination
Authors: Masnoon Nashwa , Lo Sarita , Gnjidic Danijela , McLachlan Andrew J , Blyth Fiona M , Burke Rosemary , Capuano Ana W , Hilmer Sarah N
Published: February 2025

Background

Medication review is integral in the pharmacological management of older inpatients.

Objective

To assess the association of in-hospital medication changes with 28-day postdischarge clinical outcomes.

Methods

Retrospective cohort of 2000 inpatients aged ≥75 years. Medication changes included the number of increases (medications started or dose-increased) and decreases (medications stopped or dose-decreased) for (i) all medications, (ii) Drug Burden Index (DBI)–contributing medications and (iii) Beers Criteria 2015 medications (potentially inappropriate medications, PIMs). Changes also included differences in (i) the number of medications, (ii) the number of PIMs and (iii) DBI score, at discharge versus admission. Associations with clinical outcomes (28-day ED visit, readmission and mortality) were ascertained using logistic regression, adjusted for age, gender and principal diagnosis. For mortality, sensitivity analysis excluded end-of-life patients due to higher death risk. Patients were stratified into : (i) ≤4, (ii) 5–9 and (iii) ≥10 discharge medications.

Results

The mean age was 86 years (SD = 5.8), with 59.1% female. Medication changes reduced ED visits and readmission risk for patients prescribed five to nine discharge medications, with no associations in patients prescribed ≤4 and ≥ 10 medications. In the five to nine medications group, decreasing PIMs reduced risks of ED visit (adjusted odds ratio, aOR 0.55, 95% CI 0.34–0.91, P = .02) and readmission (aOR 0.62, 95% CI 0.38–0.99, P = .04). Decreasing DBI-contributing medications reduced readmission risk (aOR 0.71, 95% CI 0.51–0.99, P = .04). Differences in PIMs reduced ED visit risk (aOR 0.65, 95% CI 0.43–0.99, P = .04). There were no associations with mortality in sensitivity analyses in all groups.

Discussion

Medication changes were associated with reduced ED visits and readmission for patients prescribed five to nine discharge medications.
MUSET: Set of utilities for constructing abundance unitig matrices from sequencing data
Authors: Vicedomini Riccardo , Andreace Francesco , Dufresne Yoann , Chikhi Rayan , Duitama González Camila
Published: February 2025

MUSET is a novel set of utilities designed to efficiently construct abundance unitig matrices from sequencing data. Unitig matrices extend the concept of k-mer matrices by merging overlapping k-mers that unambiguously belong to the same sequence. MUSET addresses the limitations of current software by integrating k-mer counting and unitig extraction to generate unitig matrices containing abundance values, as opposed to only presence-absence in previous tools. These matrices preserve variations between samples while reducing disk space and the number of rows compared to k-mer matrices. We evaluated MUSET’s performance using datasets derived from a 618-GB collection of ancient oral sequencing samples, producing a filtered unitig matrix that records abundances in less than 10 hours and 20 GB memory.

Availability and Implementation

MUSET is open source and publicly available under the AGPL-3.0 licence in GitHub at https://github.com/CamilaDuitama/muset. Source code is implemented in C ++ and provided with kmat_tools, a collection of tools for processing k-mer matrices. Version v0.5.1 is available on Zenodo with DOI 10.5281/zenodo.14164801.

Supplementary Information

Supplementary data are available at Bioinformatics online.
ipd: an R package for conducting inference on predicted data
Authors: Salerno Stephen , Miao Jiacheng , Afiaz Awan , Hoffman Kentaro , Neufeld Anna , Lu Qiongshi , McCormick Tyler H , Leek Jeffrey T
Published: February 2025

ipd is an open-source R software package for the downstream modeling of an outcome and its associated features where a potentially sizable portion of the outcome data has been imputed by an artificial intelligence or machine learning prediction algorithm. The package implements several recent proposed methods for inference on predicted data with a single, user-friendly wrapper function, ipd. The package also provides custom print, summary, tidy, glance, and augment methods to facilitate easy model inspection. This document introduces the ipd software package and provides a demonstration of its basic usage.

Availability

ipd is freely available on CRAN or as a developer version at our GitHub page: github.com/ipd-tools/ipd. Full documentation, including detailed instructions and a usage ‘vignette’ are available at github.com/ipd-tools/ipd.
COBREXA 2: tidy and scalable construction of complex metabolic models
Authors: Kratochvíl Miroslav , Wilken St Elmo , Ebenhöh Oliver , Schneider Reinhard , Satagopam Venkata P
Published: February 2025

Constraint-based metabolic models offer a scalable framework to investigate biological systems using optimality principles. Construction and simulation of detailed models that utilize multiple kinds of constraint systems pose a significant coding overhead, complicating implementation of new types of analyses. We present an improved version of the constraint-based metabolic modeling package COBREXA, which utilizes a hierarchical model construction framework that decouples the implemented analysis algorithms into independent, yet re-combinable, building blocks. By removing the need to re-implement modeling components, assembly of complex metabolic models is simplified, which we demonstrate on use-cases of resource-balanced models, and enzyme-constrained flux balance models of interacting bacterial communities. Notably, these models show improved predictive capabilities in both monoculture and community settings. In perspective, the re-usable model-building components in COBREXA 2 provide a sustainable way to handle increasingly complex models in constraint-based modeling.

Availability and Implementation

COBREXA 2 is available from https://github.com/COBREXA/COBREXA.jl, and from Julia package repositories. COBREXA 2 works on all major operating systems and computer architectures. Documentation is available at https://cobrexa.github.io/COBREXA.jl/.
Humanitarianism From Below: Border Police, Professional Identities and Moral Dilemmas
Authors: Aliverti Ana , Dufraix Tapia Roberto , Ramos Rodríguez Romina , Tapia Ladino Marcela , García España Elisa
Published: February 2025

In this article, we empirically document the changing dynamics of border controls in the context of the COVID pandemic, and its consequences for border control workers, particularly police, border agents and the military. We focus on three areas: the Anglo-French (Dover-Calais) maritime border, the Euro-African border (Ceuta-Tetuán) and the South American border of Tarapacá-Oruro between Chile and Bolivia. We explore how sovereign strategies of containment and closure, and the diplomatic tensions that arise from them, sometimes operate uneasily with on-the-ground attempts to save lives and provide care in the most precarious situations. These competing institutional demands and moral and professional tensions and dilemmas, we argue, shape an emerging form of management of social precarity that we conceptualize as ‘humanitarianism from below’.
Leveraging genotypes and phenotypes to implement precision medicine in hidradenitis suppurativa management
Authors: Petukhova Lynn , Colvin Annelise , Koerts Nicole D K , Horváth Barbara
Published: February 2025

Hidradenitis suppurativa (HS) is a chronic inflammatory skin condition with many unmet needs. It is characterized by significant clinical heterogeneity, which suggests that a diagnosis of HS captures multiple distinct disease entities and that research aimed at identifying medically relevant HS subtypes will improve its management. Precision medicine is an approach to disease management that uses information encoded in a patient’s genome, and operationalized in clinical presentations and drug responses, to identify disease subtypes. Prior research aimed at identifying HS subtypes has largely focused on phenotypic classifications derived from clinical features of cutaneous lesions. Limitations of existing HS taxonomies emphasize a need for a more nuanced understanding of disease subtypes. Evidence that has emerged from initial genetic studies of HS suggests the presence of at least three HS subtypes, each of which has different clinical implications in terms of disease risks and drug responses. These preliminary findings are instructive in terms of expanding our definitions of HS phenotypes to not only include characteristics of skin lesions, but also disease comorbidities and molecular and cellular phenotypes. Here we provide a comprehensive review of HS phenotype and genotype knowledge, and propose a strategic framework for implementing precision medicine in HS management. Future research should focus on expanding phenotype assessments to include data on multiple scales. Iterative research designs performed with phenotype and genotype data from large diverse cohorts are needed to rigorously define clinically relevant HS subtypes.
Perspectives from the frontline: Exploring the implementation of legislative change into social work practice for brothers and sisters in care in Scotland
Authors: Thomson Lizzie
Published: February 2025

Legislative changes aiming to protect and support relationships between brothers and sisters in Scotland’s care system came into force in July 2021. These changes strengthened existing duties on local authorities to ensure siblings live together if they are in care, and to support them to keep in touch if they cannot live together. Drawing on literature and theory concerning policy implementation in a social work practice context, particularly the concept of ‘street-level bureaucracy’, this small-scale qualitative study used focus groups with social workers (n = 7) from three Scottish local authority areas one year after the enactment of the legislative changes, and thematic analysis of the findings, to explore the implementation of legislative change into practice. The findings highlight a range of factors facilitating implementation, including increased momentum from broader care system reform in Scotland and enhanced focus on sibling relationships in care planning and review processes. Limited resources were seen to constrain implementation, particularly a lack of suitable placement options for larger sibling groups and limited time for social workers to spend supporting children to have contact with their siblings. The findings inform recommendations in relation to resources, training and learning, and assessment and planning, necessary to facilitate successful implementation efforts.
Efficacy and Drug Survival of Tralokinumab in Severe Atopic Dermatitis: An 18-Month Multicenter Experience
Authors: Barei Francesca , Calzari Paolo , Pezzolo Elena , Napolitano Maddalena , Rossi Mariateresa , Guanti Mario Bruno , Caroppo Francesca , Belloni Fortina Anna , Patruno Cataldo , Campanati Anna , Bianchelli Tommaso , D’Agostino Giovanni Marco , Nettis Eustachio , Pugliese Francesco , Picone Vincenzo , Trave Ilaria , Cozzani Emanuele , Stingeni Luca , Hansel Katharina , Dall'Olio Matilde , Galli Benedetta , Coppola Rosa , Panasiti Vincenzo , Maurelli Martina , Girolomoni Giampiero , Ortoncelli Michela , Ribero Simone , Marzano Angelo V , Ferrucci Silvia
Published: February 2025

Background

Tralokinumab has demonstrated efficacy in the treatment atopic dermatitis (AD) in both clinical trials and real-world settings. However, limited data exists on the long-term use of tralokinumab in real-world settings.

Objective

A multicentric Italian study, evaluating tralokinumab's drug survival (DS) and efficacy up to 18 months of treatment among 471 patients with severe AD was conducted.

Methods

EASI (Eczema Area and Severity Index), P-NRS (Pruritus Numerical Rating Scale), SD-NRS (Sleep Disturbance NRS), DLQI (Dermatology Life Quality Index) and ADCT (Atopic Dermatitis Control Tool) were recorded up to 18 months of treatment. DS was analyzed using Kaplan-Meier methodic.

Results

Overall DS rate was 81.5% at 12 months. A significant higher DS was found for females (p<0.001, log-rank=11.90), patients with negative family history (FH) of AD (p=0.015, log-rank=5.96) and patients ≥60-year-old (p=0.018; log-rank=5.6) when considering DS due to inefficacy. The study demonstrates a significant reduction in the clinical scores evaluated, with patients naïve to biologics or Janus kinase inhibitors (JAKi) showing a faster improvement. In the univariate regression analysis, females (p=0.038, OR=1.613; C.I. 1.026-2.534), having no atopic comorbidity (p=0.039; OR=1.692; C.I. 1.027-2.783), negative FH of AD (p=0.031; OR=1.665; C.I. 1.047-2.649) and not using concomitant systemic treatment in the previous months (p=0.003; OR=22.065; C.I. 2.803-173.691) were associated with an increased likelihood of reaching EASI-75. In the multivariate analysis, only the latter variable remained significant (p=0.004, OR=23.037, C.I. 2.793-190.052).

Conclusion

A significant improvement in clinical scores was observed, with patients naïve to biologics or JAKi experiencing faster progress. Female sex, absence of atopic comorbidities, and a negative FH of AD were linked to a higher likelihood of achieving EASI-75 in the univariate analysis but lost significance in the multivariate analysis. For discontinuation due to inefficacy, patients aged 60 and older, females, and those with a negative FH of AD had significantly better survival rates.
Electrophysiological activity underlying motor inhibition facilitated by touch
Authors: Tang Yuting , Zhang Xiaotong , Wang Houmin , Gao Yuxin , Ou Jianlin , Chen Zhuoming , Long Jinyi
Published: February 2025

Tactile sensory information obtained from oneself or others may provide a calming effect and has been shown to enhance participants’ motor control. The extent to which these touch activities may support motor inhibition and the related electrophysiological mechanisms remain unknown. Here, we investigated these effects in twenty healthy volunteers via electroencephalography under 3 touching conditions (self-touch, other-touch, and no-touch) during a stop-signal task. We found that both the self-touch and other-touch conditions resulted in better stopping accuracy and lower stop-signal reaction times than the no-touch condition. Additionally, these 2 touch conditions elicited larger N2 and P3 responses during successful inhibition of planned finger movements. Time-varying network analysis based on electroencephalography was further used to explore the differences in brain networks during conflict monitoring substages under different touch conditions. A top–down projection from the frontal cortex (Fz) to the parietal and occipital cortices was observed along with increased functional connectivity efficiency under touch conditions. These results indicate that tactile information may enhance neural processing efficiency in the human brain by eliciting larger event-related potential components and promoting information processing in the brain network during conflict monitoring processes, thereby contributing to the reactive inhibitory component of motor inhibition.
Anti-SARS-CoV-2 IgG Antibody Titers in Cotemporary lots of Intravenous Immune Globulin and Fresh Frozen Plasma Compared to COVID Convalescent Plasma
Authors: Smith Ethan A , Javier Ginny M , Multani Ashrit , Beaird Omer Eugene , Gaynor Pryce , Yanagimoto-Ogawa Lauren , Schaenman Joanna , Allyn Paul , Alfarhat George , Vijayan Tara , Ziman Alyssa , Garner Omai
Published: February 2025

Given declining COVID convalescent plasma (CCP) collection and increasing scarcity, we compared anti-SARS-CoV-2 IgG antibody titers between CCP, intravenous immunoglobulin (IVIG) and fresh frozen plasma (FFP). Herein, we report comparative anti-SARS-CoV-2 IgG antibody titers between five lots of each blood product, using the DiaSorin Liaison® SARS-CoV-2 TrimericS IgG assay.
Feather Evolution Following Flight Loss In Crown Group Birds: Relaxed Selection And Developmental Constraints
Authors: Saitta Evan T , Carden Lilja , Mitchell Jonathan S , Makovicky Peter J
Published: February 2025

Feathers are complex structures exhibiting structural/functional disparity across species and plumage. Flight was lost in >30 extant lineages from ~79.58 Ma–15 Ka. Effects of flight loss on senses, neuroanatomy, and skeletomusculature are known. To study how flightlessness affects feathers, we measured 11 feather metrics across the plumage of 30 flightless taxa and their phylogenetically closest volant taxa, with broader sampling of primaries across all orders of crown birds. Our sample includes 27 independent flight losses, representing nearly half of extant flightless species. Feather asymmetry measured by barb angle differences between trailing and leading vanes decreases in flightless lineages, most prominently in flight feathers and weakest in contour feathers. Greatest changes in feather anatomy occur in older flightless lineages (penguins, ratites). Comparative methods show some microscopic feather traits are not dramatically modified after flightlessness compared to body mass increase and relative wing and tail fan reduction, but changes toward greater symmetry are stronger. Relaxing selection for flight does not rapidly modify feather flight adaptations, apart from asymmetry. Feathers of recently flightless lineages resemble their volant relatives. Developmental constraints and relaxed selection for novel feather morphologies may explain some observed changes. Macroscopic changes to flight apparati (skeletomusculature, airfoil size) are more evident in recently flightless taxa and could more reliably detect flightlessness in fossils, with increased feather symmetry as a potential microscopic signal. We observed apical modification in later stages of feather development (asymmetric displacement of barb loci), while morphologies arising during early developmental stages are only altered after millions of years of flightlessness.
Quantitative differences in rumen epithelium proteins and detection of lysine acetylation in lambs fed a low or high metabolizable energy diet
Authors: Bond Judith J , Hudson Nicholas J , Kamath Karthik S , Wheeler David , Woodgate Serey , Oddy Victor H
Published: February 2025

Thirty-six Merino wethers (10-month-old) were fed ad libitum for 30 days two diets;1) low metabolizable energy diet (LME; 30% lucerne: 70% cereal chaff) and 2) high ME diet (HME; 40% rolled barley grain: 50% lucerne: 10% cereal chaff). Effects of diet on dry matter intake (DMI), metabolizable energy intake (MEI), liveweight (LWT), average daily gain (ADG), carcass lean or fat gain, liver and empty rumen weight and plasma metabolites were analysed. A membrane enriched protein fraction of rumen epithelium isolated enzymatically from whole depth rumen wall was quantified for each sheep using tandem mass tag mass spectrometry (TMT-MS). The presence or absence of acetylation of lysine residues on identified proteins was counted and the position of the lysine acetylation recorded. In lambs fed the HME diet, DMI (P<0.001), MEI (P<0.001), ADG (P<0.001), fat (P<0.001) and lean gain (P<0.001), as well as liver (P<0.001) and empty rumen (P<0.009) weight were greater than those fed the LME diet. Plasma glucose (P<0.001) and β hydroxybutyrate (P<0.001) at 3 and 5 h after feeding was greater in HME diet than in the LME fed lambs. Changes in rumen epithelium protein abundance in the LME versus HME fed lambs were associated with metabolism in the peroxisome, protein processing in the endoplasmic reticulum (ER), valine, leucine and isoleucine degradation and carbon metabolism. Acetylation of lysine was detected in enzymes involved in glycolysis, tricarboxylic acid (TCA) cycle and fatty acid (FA) metabolism. Quantitative differences in the abundance of rumen epithelium proteins that carry out intracellular processes of energy expenditure were associated with the concentration of ME (MJ/ kg DM) in the diet of growing lambs. The detection of lysine acetylation sites suggests a difference in the ME of the diet regulates enzymatic activity in central metabolic pathways in the rumen epithelium cells.
Factors associated with longitudinal progression of the cumulative burden of morbidity and overall mortality after cisplatin-based chemotherapy for testicular cancer
Authors: Kerns Sarah L , Dinh Paul C , Monahan Patrick O , Stump Timothy , Fung Chunkit , Sesso Howard D , Feldman Darren R , Hamilton Robert J , Vaughn David J , Huddart Robert , Kollmannsberger Christian , Martin Neil E , Nevel Kathryn , Kincaid John , Einhorn Lawrence H , Travis Lois B
Published: February 2025

Background

To comprehensively evaluate the longitudinal progression of cumulative burden of morbidity (CBM) in testicular cancer survivors (TCS) following standard-dose cisplatin-chemotherapy and the impact of modifiable risk factors on morbidity and early-mortality.

Methods

Participants completed first-line chemotherapy ≥6 months before baseline assessments with comprehensive questionnaires and physical-examinations. Based on follow-up assessments (median: 7 years later), longitudinal progression of adverse health outcomes (AHOs) and CBM score (encompassing AHO number and severity) was examined. Baseline health behaviors and AHOs were evaluated for associations with mortality using mixed-effects parametric proportional-hazards regression to identify modifiable risk factors.

Results

Among 616 TCS longitudinally assessed, 23% experienced worsening CBM post-chemotherapy (median: 11 years [IQR = 7-15]). Declines were driven by worsening treatment-related AHOs: tinnitus (29.7%), hearing loss (24.4%), Raynaud’s (22.6%), neuropathy (18.5%), and neuropathic-pain (10.7%). Baseline factors associated with worsening neuropathy included lack of aerobic physical-activity (OR = 1.98, 95%CI = 1.06-3.72) and obesity (OR = 1.85, 95%CI = 1.17-2.92). These were also related to worsening neuropathic-pain (OR = 2.82, p = .009; and OR = 2.29; p = .023). Twenty-nine deaths occurred among 1,830 five-year TCS (4.2% cumulative hazard) (median age: 48-years [range = 22-74]). Participants reporting neuropathic-pain (HR = 3.64, 95%CI = 1.45-9.10), no aerobic (HR = 6.56, 95%CI = 2.73-15.8), or no low-impact physical-activity (HR = 3.96, 95%CI = 1.40-11.2) had significantly higher mortality, as did TCS indicating fair (HR = 9.23, 95%CI = 3.08-27.8) or poor (HR = 18.5, 95%CI = 3.30-103) health. Relationships between pain and mortality were mediated through lowered physical-activity (p = .036).

Conclusions

Clinically-actionable factors associated with early mortality identify high-risk TCS in need of closer monitoring and targeted interventions. The significant relationship between neuropathic-pain and mortality, mediated by low physical-activity, is the first to our knowledge in TCS.
Alcohol consumption, polygenic risk score and the risk of colorectal neoplasia
Authors: Fu Ruojin , Chen Xuechen , Seum Teresa , Hoffmeister Michael , Brenner Hermann
Published: February 2025

Introduction

Excess alcohol consumption is associated with increased risk of colorectal cancer (CRC), but the evidence on the individual and joint effects of alcohol consumption and genetic risk on the occurrence of various stages of colorectal carcinogenesis is limited.

Methods

We evaluated the associations of alcohol consumption and a polygenic risk score (PRS) based on 140 CRC-related loci with findings of colorectal neoplasia among 4,662 participants in the German screening colonoscopy program. Analyses were conducted by multiple logistic regression. We determined genetic risk equivalents (GREs) to quantify the effect of alcohol consumption in terms of the difference in PRS conveying equivalent risk.

Results

Moderate and high (12-<25 and ≥25 g/day) alcohol consumption was associated with increased risk of advanced colorectal neoplasia (aOR [95% CI]: 1.28 [1.03-1.58] and 1.44 [1.14-1.81], respectively), while associations with any colorectal neoplasia were weaker. No significant interactions between alcohol consumption and PRS were observed. Participants with high alcohol consumption in the highest PRS tertile had a 3.4-fold increased risk of advanced neoplasia compared to those with low or no alcohol consumption in the lowest PRS tertile. The estimated impact of high alcohol consumption on the risk of advanced neoplasia was equivalent to the risk increase by a 26 percentiles higher PRS (GRE 26, 95% CI 9-44).

Conclusion

High alcohol consumption and PRS both have a major impact on the risk of advanced colorectal neoplasia. The estimated preventive impact of avoiding high alcohol consumption is as strong as the impact of having a substantially lower polygenic risk.
Impact of m6A Modification and Transcript Quantity on mRNA Composition in Plant Stress Granules
Authors: Kubiak Dawid Jakub , Szczesniak Michal Wojciech , Ostrowska Karolina , Bielewicz Dawid , Bhat Susheel Sagar , Niedojadlo Katarzyna , Szweykowska-Kulinska Zofia , Jarmolowski Artur , Fray Rupert George , Niedojadlo Janusz
Published: February 2025

Stress granules (SGs) are cytoplasmic structures that emerge in response to unfavorable environmental conditions. The mechanisms governing the accumulation of transcripts in SGs are only partially understood. Despite the recognized role of N6-methyladenosine (m6A) in plant transcriptome regulation, its impact on SGs' composition and assembly remains elusive. In Lupinus angustifolius, SGs display a distinctive bi-zonal structure comprising of a ring and a central area with differences in ultrastructure and composition. Subsequent to the transcriptome analysis, specific mRNA were chosen to investigate their localization within SGs and assess m6A levels. Transcripts of hypoxia-responsive genes (ADH1 and HUP7) showed significantly lower levels of m6A compared to housekeeping genes, but only ADH1 was absent in SGs. HUP7 mRNA, characterized by a low quantity of m6A, is present both in the SGs and cytoplasm, probably due to extremely high expression level. The m6A was observed only during the assembly of SGs. In mutants of Arabidopsis thaliana with reduced levels of m6A, ECT2 (reader of m6A) was not observed in SGs, and poly(A) RNA levels and the number of SGs were reduced. In summary, our findings demonstrate a limited impact of m6A modification on SGs assembly. However, the interplay between m6A modification and the overall transcript quantity in the cytoplasm appears to play a regulatory role in mRNA partitioning and assembly of SGs.
Atlas of Fourier Transforms
Authors: Shah Miti , Millsaps William , Sung Suk Hyun , Hovden Robert
Published: February 2025

The book Atlas of Fourier Transforms caters to enthusiasts of all proficiency levels. Here, the reader embarks into the world of Fourier transforms through carefully curated images of over 650 Fourier pairs. As the atlas unfurls, it includes concepts of symmetry, rotation, translation, addition, multiplication, and interference. For those well-versed in the art of Fourier analysis, the Atlas of Fourier Transforms offers an unparalleled dictionary of structures and their corresponding Fourier counterparts.
Quantitative Large-Area Polarized-Light Microscopy
Authors: Hoover Brian G , Ornelas-Rascon Cesar H
Published: February 2025

This article describes the elevation of polarized-light microscopy (PLM) to a technique for quantitative large-area material characterization in the Microscopy Today Innovation Award-winning CrystalViewTM laser PLM. CrystalView is enabled by narrow-band laser illumination, bistatic design, and strict qualification of polarization optics, resulting in accurate polarization imaging over an instant field-of-view (FOV) that exceeds 2 cm2. This FOV is effectively demonstrated by the critical concept of seamless stitching, which confirms low error and is then applied to obtain even larger effective FOVs with industrial utility. Linear combinations of image irradiances, known as polarization features, are related to physical material properties, for instance, crystal orientation, through the combination of Mueller matrix polarimeter design and classical electrodynamics. While CrystalView is applicable to any reflective or transmissive material that exhibits PLM contrast, in this article it is demonstrated for orientation imaging of hexagonal and cubic metal polycrystals, titanium and stainless-steel alloys respectively, the latter printed by laser powder-bed fusion (LPBF) and reliant, for texture imaging, on chemical etching that can also reveal phase structure.
Thinking Outside the Box in Making Cryo-EM More Accessible for Everyone
Authors: Berensmann Heather Rose , Humphreys Theo
Published: February 2025

The iterative nature of grid screening for single-particle analysis often requires a microscope that efficiently bridges the gap between sample preparation and high-resolution data collection. However, such a system is often specialized solely for cryogenic applications and may present substantial financial barriers. Enhancing the versatility of a thermionic TEM to support both room-temperature and cryogenic-temperature applications can provide more laboratories with greater accessibility to cryo-electron microscopy equipment. Through the experimental evaluations of Hitachi’s innovative retractable cold finger design, coupled with Simple Origin’s transfer holder and SerialEM, Hitachi’s HT7800 TEM was shown to be an effective screening tool in multiple environments.
Holistic Tri-Service Military Pathology: A Proposed Paradigm for Consolidation
Authors: Smith Nathaniel E , O’Connell William , Johnson Rebecca , Leonard George
Published: February 2025

Historically, military anatomic pathology (AP) services have been significantly compartmentalized, with each branch independently executing its laboratory support mission. The result is redundant and costly duplication of nearly identical services in close geographic proximity. The duplication of AP services disperses the overall caseload, resulting in pathologist diagnostic acumen atrophy, excessive support personnel requirements, inadequate utilization of subspecialty expertise, and overall lower-quality patient care. Unlike many medical specialties, implementing AP services does not require direct patient interaction and is principally not as time-sensitive as other clinical laboratory testing. The practice of AP is conducive to a more consolidatory paradigm to achieve economies of scale. Pathology service unification would also afford the stationing of predominantly subspecialists at tertiary care centers to handle higher caseloads. Larger groups of pathologists increase patient safety enhancing peer-to-peer and subspeciality quality assurance processes during case review. Conversely, the nature of clinical pathology services requires a more widespread presence—even at the smaller, auxiliary clinics throughout the military health system. Clinical pathology services would also benefit from additional triservice cooperation including standardization of quality management processes, increased resource sharing, exchange, and cooperative contingency planning. Laboratory directorships also benefit from consolidating expertise, where pathologists could be physically located at a central site with remote oversight of laboratory services. Here, we propose a holistic triservice consolidation plan for military pathology to optimize resource utilization and ultimately realize the overarching strategic plan for military medicine set forth by the Defense Health Agency.
The Romantic-Virtuosic Sentence in Liszt’s B Minor Sonata, or, Positive Feedback as Formal Accelerator
Authors: Smith Kenneth
Published: February 2025

The classical sentence (Schoenberg’s ‘Satz’), or ‘Bar form’ (Alfred Lorenz), have long been discussed in music theoretic terms. Existing studies of the sentence in Romantic music have focused on the music of Wagner or Liszt’s symphonic poems, but study of Liszt’s pianism is perhaps even more revealing because it allows us to consider the sentence in energetic terms as a formal accelerator, a coefficient of Liszt’s virtuosity. To appreciate the extent of the sentence’s dramatic energy, this article borrows from the meta-discipline of cybernetics, which concerns systems of control and communication through feedback loops. Feedback loops, particularly the ‘positive feedback’ that leads to a system’s collapse, speaks to the dialectic between virtuosity and form. Exploring Liszt’s B minor Sonata, I examine sentences which, under Liszt’s control, become forces of ‘positive feedback’, constantly breaking the phrase structures apart under their own weight.
Antagonistic roles by the conserved nuclear poly(A)-binding proteins PABPN1 and ZC3H14 in nuclear RNA surveillance
Authors: Latour Mélodie , Kwiatek Lauren , Landry-Voyer Anne-Marie , Bachand François
Published: February 2025

Most eukaryotic genomes are transcribed pervasively, thereby producing an array of long non-coding RNAs (lncRNAs) in addition to protein-coding mRNAs. A large fraction of these lncRNAs is targeted by polyadenylation-dependent decay via the poly(A)-binding protein nuclear 1 (PABPN1) and the RNA exosome. Yet, how PABPN1 contributes to nuclear RNA surveillance by facilitating lncRNA turnover by the RNA exosome remains largely unclear. Here, we show that PABPN1 is important for the nuclear retention of polyadenylated lncRNAs, such that PABPN1 loss of function allows target lncRNAs to evade nuclear decay, leading to cytoplasmic accumulation. Interestingly, we found that another nuclear PABP, ZC3H14, functions antagonistically to PABPN1 and the poly(A)-tail exosome targeting (PAXT) connection in the control of nuclear lncRNA turnover. Collectively, our findings disclose the critical interplay between two conserved nuclear PABPs, PABPN1 and ZC3H14, in RNA surveillance via the control of nuclear RNA export.
Nuclear NAD+ Synthase NMNAT1 Contributes to Nuclear Atypia and Promotes Glioma Growth
Authors: Liu Jiaqi , Zhu Yi , Canic Tijana , Diaz-Perez Zoraida , Gultekin Sakir Humayun , Zhai R Grace
Published: February 2025

Background

Glioma is a malignant primary brain tumor with a poor prognosis and short survival. NAD+ is critical for cancer growth, however, clinical trials targeting NAD+ biosynthesis had limited success, indicating the need for mechanistic characterization. Nuclear atypia, aberrations in the size and shape of the nucleus, is widely observed in cancer and is often considered a distinctive feature in diagnosis, however, the molecular underpinnings are unclear.

Methods

We carried out high-resolution immunohistochemical analyses on glioma tissue samples from 19 patients to analyze the expression of NAD+ synthase nicotinamide mononucleotide adenylyltransferase (NMNAT1), and its correlation with nuclear atypia in gliomas. Utilizing a Drosophila model of glial neoplasia, we investigated the genetic role of nuclear NMNAT in glioma growth in vivo, elucidating the cellular mechanisms of NMNAT1 in promoting nuclear atypia and glioma growth.

Results

In low-grade glioma and GBM, higher transcription level of NMNAT1 is correlated with poorer disease-free survival. Samples of high-grade gliomas contained a higher percentage of glial cells enriched with NMNAT1 protein. We identified a specific correlation between nuclear NMNAT1 protein level with nuclear atypia. Mechanistic studies in human glioma cell lines and in vivo Drosophila model suggest that NMNAT1 disrupts the integrity of the nuclear lamina by altering the distribution of lamin A/C, and promotes glioma growth.

Conclusions

Our study uncovers a novel functional connection between the NAD+ metabolic pathway and glioma growth, reveals the contribution of the NAD+ biosynthetic enzyme NMNAT1 to nuclear atypia, and underscores the role of nuclear NMNAT1 in exacerbating glioma pathology.
Refugee Resettlement: A Durable Solution at a Crossroads
Authors: Fee Molly , Darrow Jessica , Howsam Scholl Jess , Cureton Ashley , Gonzalez Benson Odessa
Published: February 2025

The future of refugee resettlement stands at a crossroads. This Special Issue brings together an interdisciplinary and international group of scholars to tackle questions and dilemmas central to the durable solution of third country resettlement. The original articles in this Special Issue engage with the policy and practice of resettlement, taking stock of traditional approaches and future possibilities. Drawing on the experiences and voices of arriving refugees, service providers, and civil society partners, these papers examine key developments in the resettlement landscape over the past ten years. Each article takes on a distinct issue or problem, from racialization and incorporation to private sponsorship and notions of success, and is set against the backdrop of critical socio-political shifts to refugee admissions over the last decade. As a cohesive compilation, this Special Issue addresses entrenched problems and creative solutions in both the policy and practice of refugee resettlement.
Effects of a botanical feed additive blend of capsicum oleoresin, clove and garlic essential oils on growth performance and fecal dry matter in nursery pigs
Authors: Kim Ty H , Woodworth Jason C , Tokach Mike D , DeRouchey Joel M , Goodband Robert D , Gebhardt Jordan T , Knauer Mark T , van de Ligt Christiaan P A , Wall Emma H
Published: February 2025

Two experiments were conducted to determine the effects of a botanical-derived feed additive containing capsicum oleoresin, clove and garlic essential oils (CCG; Fytera Start, Selko, Indianapolis, IN) in nursery pigs fed with or without pharmacological levels of Zn and Cu. In Exp. 1, 756 pigs (Duroc × Landrace/Large White composite (Smithfield Premium Genetics), initially 7.8 ± 0.09 kg) were used in a 40-d study to determine the effects of CCG level on growth performance of nursery pigs fed pharmacological levels of Zn and Cu. In Exp. 2, 340 barrows (DNA 200 × 400, initially 6.1 ± 0.08 kg) were used in 38-d study to determine the effect of CCG in diets with or without pharmacological levels of Zn and Cu on growth performance and fecal dry matter (DM). For both experiments, pigs were randomly allotted to pens which were allotted to 1 of 4 dietary treatments in a completely randomized design. There were 9 pigs per pen and 21 pens per treatment in Exp. 1 and 5 pigs per pen and 17 pens per treatment in Exp. 2. Dietary treatments in Exp. 1 were corn-soybean meal based with pharmacological levels of Zn and Cu and included either 0, 25, 50, or 100 mg/kg of CCG. Dietary treatments in Exp. 2 were arranged in a 2 × 2 factorial with main effects of CCG (none or 100 mg/kg) and nutritional or pharmacological levels of Zn and Cu. All Exp. 2 diets contained 110 mg/kg of Zn and 16.5 mg/kg of Cu from the trace mineral premix. For both experiments, pharmacological levels of Zn were added at 3,000 and 2,000 mg/kg in phase 1 and 2, respectively and Cu was added at 250 mg/kg in all phases. For Exp. 1, overall average daily gain (ADG) increased (linear, P < 0.05) and average daily feed intake (ADFI) tended to increase (linear, P < 0.10) as CCG increased from 0 to 100 mg/kg. For Exp. 2, there was a CCG × Zn/Cu interaction observed for overall ADG and ADFI (P < 0.05) where CCG numerically increased ADG and ADFI in pigs fed nutritional levels of Zn and Cu; but reduced ADG and ADFI in pigs fed pharmacological levels of Zn and Cu. There was a Zn/Cu × day interaction (P = 0.001) for fecal DM, in which there was no difference (P > 0.10) in fecal DM on d 10, but pigs fed pharmacological levels of Zn and Cu had lower (P < 0.001) fecal DM on d 21 compared to pigs fed nutritional levels of Zn and Cu. In summary, when included in diets with pharmacological levels of Zn and Cu, feeding increasing levels of CCG increased ADG in Exp. 1 but did not improve performance in Exp 2.
Measuring Well-Being Influencers: Development and Validation of the WISH Inventory
Authors: Higgins K. Elliott , Wingert Theodora , Duggan Elizabeth W. , Mansolf Maxwell , Hernandez Carcamo Jose , Park Christine
Published: February 2025

Background:

Improving healthcare professional well-being and reducing burnout requires improving work ecosystems and cultures. Current well-being metrics focus on distal outcomes within individuals (e.g., professional fulfillment or burnout). In this study, we developed and evaluated the performance of an inventory measuring perceptions of modifiable workplace dimensions—termed influencers—that shape healthcare professionals' well-being.

Methods:

A core team developed the Well-Being Influencers Survey for Healthcare (WISH), an inventory designed to measure these systemic, occupational well-being influencers (e.g., leadership support, psychological safety, working conditions). Following content validation and refinement, 223 healthcare professionals from an academic department of anesthesiology completed WISH alongside established well-being measures, including the Maslach Burnout Inventory (MBI), Professional Fulfillment Index (PFI), Perceived Stress Scale (PSS), PROMIS short forms for meaning, purpose, and life satisfaction, as well as standard items of affective commitment (AC, a measure of engagement) and a standard item assessing intention to leave (ITL). Factor analysis was used to assess WISH’s internal structure, while correlation and regression analyses assessed its criterion-related validity using the above established measures.

Results:

WISH showed expected relationships with established well-being measures, and outperformed established metrics in predicting AC and ITL after adjusting for those measures and/or covariates. Factor analysis indicated that most WISH variance reflects a single common factor, supporting the use of an instrument-level score. Unique variance at the influencer level highlights the added value of examining influencer scores.

Conclusions:

WISH fills a key gap in healthcare professional well-being improvement science by assessing causal factors of well-being and burnout, rather than the conditions themselves. Here, we established initial validity of this unique inventory and further reinforce the relevance of system-level and cultural factors in influencing healthcare professionals’ well-being. WISH is well suited to assist healthcare professional well-being improvement efforts driven by system-improvement mindsets.
GLP-1 Receptor Agonist Medications Alter Outcomes of Spine Surgery
Authors: Wiener Joshua M. , Sanghvi Parshva A. , Vlastaris Katelyn , Mroz Thomas , Belding Jonathan , Kaelber David C. , Olson Thomas , Francis Kevin P. , Adams John S. , Bernthal Nicholas , Sheppard William L.
Published: February 2025

Study Design.

retrospective cohort study.

Objective.

To investigate the relationship between perioperative Glucagon-Like Peptide-1 Receptor Agonists (GLP-1 RAs) and postoperative outcomes after spinal fusion in obese and diabetic patient populations.

Summary of Background Data.

GLP-1 RAs have been shown to be beneficial when used perioperatively in clinical orthopaedic arthroplasty literature. Minimal evidence exists showing efficacy with respect to spinal fusion.

Materials and Methods.

This retrospective, multi-center study accessed the TriNetX platform, using the research database to identify diabetic patients who underwent spinal fusion between 2008 and 2022. Cohorts were created based on Body-Mass-Index (BMI) and GLP-1 RA usage. Propensity score matching was employed to create balanced cohorts utilizing BMI, Hemoglobin A1c (HbA1c), surgical intervention, as well as other demographic characteristics. Orthopedic outcomes were compared between GLP-1 RA users and non-users. The primary outcomes included post-operative infection, readmission, revision surgery, and quality of life metrics.

Results.

After matching, the study cohort consisted of 2,263 patients, with 1,560 classified as obese. GLP-1 RA use was associated with significantly reduced post-operative infection rates (obese: HR=0.168 (0.086, 0.328), not obese: HR=0.250 (0.102, 0.612)), fewer revisions (obese: HR=0.505 (0.368, 0.693), not obese: HR=0.439 (0.272, 0.708)), decreased postoperative readmission rates (obese: HR=0.283 (0.243, 0.329), not obese: HR=0.241 (0.193, 0.301)), and reduced mobility abnormalities (obese: HR=0.355 (0.230, 0.549), not obese: HR=0.508 (0.269, 0.959)). No significant differences were observed in rates of fracture rates between GLP-1 RA users and non-users.

Conclusions.

GLP-1 RA use in spinal fusion patients was associated with improved post-operative outcomes, including lower infection rates, fewer revisions, and better quality of life metrics. These findings suggest that GLP-1 RAs may be a valuable adjunctive therapy in managing surgical outcomes in diabetic and obese patients undergoing spinal fusion. Further prospective and animal-based studies are needed to confirm these findings and explore the underlying mechanisms.
Continuation Versus Discontinuation of Angiotensin-Converting Enzyme Inhibitors and Angiotensin Receptor Blockers in Patients Undergoing Noncardiac Surgery
Authors: Kallash Mohammed , Frishman William
Published: February 2025

There has been ongoing debate about whether to continue or withhold angiotensin-converting enzyme (ACE) inhibitors or angiotensin receptor blockers (ARBs) in patients undergoing noncardiac surgery. With over 200 million surgeries performed annually worldwide and millions of patients on ACE inhibitors and ARBs, it is crucial to elucidate the best management strategy for patients undergoing noncardiac surgery while on these medications. Several large randomized controlled trials, the Stop-or-Not and the Perioperative Ischemic Evaluation-3 trials, were conducted to investigate this important issue. Both clinical trials demonstrated no difference in cardiovascular adverse events, including vascular death, myocardial injury, stroke, and cardiac arrest, with continuation versus discontinuation of ACE inhibitors or ARBs in patients undergoing noncardiac surgery. However, these clinical trials showed a higher incidence of intraoperative hypotension in patients who continued taking their ACE inhibitor or ARB through the surgery. Based on this evidence, the American College of Cardiology 2024 Perioperative Guidelines recommend that patients undergoing elevated-risk surgery should have their ACE inhibitor or ARB withheld 24 hours before the surgery; however, patients with heart failure with reduced ejection fraction undergoing noncardiac surgery should continue their regimen. Currently, while the evidence indicates no difference in adverse outcomes between continuing and discontinuing ACE inhibitors and ARBs in patients undergoing noncardiac surgery, the decision to continue or withhold these medications remains individualized. Clinicians must consider various patient and clinical factors when making this decision, including the type of surgery, the risk for intraoperative blood loss and hypotension, and the specific indication of the ACE inhibitor or ARB.