bluuebunny/crossref_metadata_2025_split huggingface dataset:
Breast Implant Illness as a Clinical Entity: A Systematic Review of the Literature
Authors: Kabir Raeesa , Stanton Eloise , Sorenson Thomas J , Hemal Kshipra , Boyd Carter J , Karp Nolan S , Choi Mihye 
Published: April 2024

Abstract

Background
Breast implant illness (BII) has become a contentious subject in recent years. Although some studies have reported associations between breast implants and autoimmune diseases, others have failed to establish a definitive link.

Objectives
The objective of this study was to provide a comprehensive, up-to-date evaluation of the literature surrounding BII, with an emphasis on identifying patient-related factors that may be associated with BII.

Methods
A systematic review was performed following PRISMA guidelines by searching the PubMed (MEDLINE), Embase, and Cochrane databases for relevant studies published in the last 20 years.

Results
Thirty-one studies were included, which covered 39,505 implant patients with a mean [standard deviation] age of 44.2 [9.30] years. Fifteen studies reported implant explantation status, with 72.4% patients choosing to remove their implants. Among these, 9 studies reported symptom improvement in 83.5% patients. Fifty-three percent of patients undergoing explantation had total capsulectomy. Twenty-eight studies documented total numbers of patients experiencing symptoms related to BII, with 31.3% patients reporting such symptoms. Among these, 16 studies of 4109 BII patients distinguished whether the reason for implantation was cosmetic augmentation or reconstruction. When specified, more patients experiencing BII-related symptoms received implants for “cosmetic” vs “reconstructive” reasons (cosmetic, 3864/4109 [94.0%] vs reconstruction, 245/4109 [5.96%]; P &lt; .001).

Conclusions
This review provides an overview of the current state of knowledge regarding BII. The study highlights a potential relationship between BII and indication for implants (cosmetic vs reconstructive) among other variables, offering valuable insight on factors associated with BII and directions for future research.

Level of Evidence: 3
TMBstable: a variant caller controls performance variation across heterogeneous sequencing samples
Authors: Wang Shenjie , Zhu Xiaoyan , Wang Xuwen , Liu Yuqian , Zhao Minchao , Chang Zhili , Wang Xiaonan , Shao Yang , Wang Jiayin 
Published: April 2024

Abstract
In cancer genomics, variant calling has advanced, but traditional mean accuracy evaluations are inadequate for biomarkers like tumor mutation burden, which vary significantly across samples, affecting immunotherapy patient selection and threshold settings. In this study, we introduce TMBstable, an innovative method that dynamically selects optimal variant calling strategies for specific genomic regions using a meta-learning framework, distinguishing it from traditional callers with uniform sample-wide strategies. The process begins with segmenting the sample into windows and extracting meta-features for clustering, followed by using a pre-trained meta-model to select suitable algorithms for each cluster, thereby addressing strategy-sample mismatches, reducing performance fluctuations and ensuring consistent performance across various samples. We evaluated TMBstable using both simulated and real non-small cell lung cancer and nasopharyngeal carcinoma samples, comparing it with advanced callers. The assessment, focusing on stability measures, such as the variance and coefficient of variation in false positive rate, false negative rate, precision and recall, involved 300 simulated and 106 real tumor samples. Benchmark results showed TMBstable’s superior stability with the lowest variance and coefficient of variation across performance metrics, highlighting its effectiveness in analyzing the counting-based biomarker. The TMBstable algorithm can be accessed at https://github.com/hello-json/TMBstable for academic usage only.
The effects of cholecalciferol and afamelanotide on vitamin D levels in erythropoietic protoporphyria: a multicentre cohort study
Authors: Kluijver Louisa G , Nekouei Shahraki Mitra , Wagenmakers Margreet A E M , Hanssen Bettina E , Kuerten Viola , Schelonke Kathrin , Homey Bernhard , Langendonk Janneke G 
Published: April 2024

Abstract

Background
Patients with erythropoietic protoporphyria experience lifelong painful photosensitivity resulting in a lack of sunlight exposure. Previous studies have shown that 47–63% of patients with EPP suffer from vitamin D deficiency and a high prevalence of osteoporosis. An effective treatment for EPP has been available since 2016: the α-melanocyte stimulating hormone analogue afamelanotide. So far, studies on vitamin D levels in EPP have only investigated patients who have not been treated with afamelanotide.

Objectives
To investigate the effects of afamelanotide treatment on vitamin D levels in EPP.

Methods
A multicentre observational cohort study in adults with EPP from the Erasmus Medical Centre, the Netherlands, and the University Hospital Düsseldorf, Germany, was carried out. Routinely collected vitamin D levels between 2005 and 2021 were used for analysis. Patient exposure to cholecalciferol or afamelanotide was categorized into four treatment groups: untreated, cholecalciferol, afamelanotide and combined treatment. A linear mixed model for longitudinal data was applied to measure the effect of the treatment groups compared with the untreated groups on vitamin D levels.

Results
A total of 230 patients and 1774 vitamin D measurements were included. The prevalence of vitamin D deficiency and severe deficiency remained high despite afamelanotide treatment (&lt; 50 nmol L–1 in 71.8% of patients and &lt; 30 nmol L–1 in 48.1%, respectively). Afamelanotide treatment alone did not lead to a significant average increase in vitamin D levels [β = 0.5, 95% confidence interval (CI) –3.2 to 4.2]. In contrast, cholecalciferol and combined therapy with afamelanotide led to a significant increase in vitamin D levels [β = 11.6 (95% CI 7.2–15.9) and β = 15.2 (95% CI 12.3–18.1), respectively].

Conclusions
Cholecalciferol remains essential for the treatment of vitamin D deficiency in EPP, irrespective of new treatment options like afamelanotide. Afamelanotide treatment did not affect vitamin D levels. We suggest that future guidelines include continuous monitoring of vitamin D and a prescription for cholecalciferol in all patients with EPP, including those treated with afamelanotide.
New insight into air pollution-related cardiovascular disease: an adverse outcome pathway framework of PM2.5-associated vascular calcification
Authors: Ding Ruiyang , Huang Linyuan , Yan Kanglin , Sun Zhiwei , Duan Junchao 
Published: April 2024

Abstract
Despite the air quality has been generally improved in recent years, ambient fine particulate matter (PM2.5), a major contributor to air pollution, remains one of the major threats to public health. Vascular calcification is a systematic pathology associated with an increased risk of cardiovascular disease. Although the epidemiological evidence has uncovered the association between PM2.5 exposure and vascular calcification, little is known about the underlying mechanisms. The adverse outcome pathway (AOP) concept offers a comprehensive interpretation of all of the findings obtained by toxicological and epidemiological studies. In this review, reactive oxygen species generation was identified as the molecular initiating event (MIE), which targeted subsequent key events (KEs) such as oxidative stress, inflammation, endoplasmic reticulum stress, and autophagy, from the cellular to the tissue/organ level. These KEs eventually led to the adverse outcome, namely increased incidence of vascular calcification and atherosclerosis morbidity. To the best of our knowledge, this is the first AOP framework devoted to PM2.5-associated vascular calcification, which benefits future investigations by identifying current limitations and latent biomarkers.
Continental-scale migration patterns and origin of Helicoverpa zea (Lepidoptera: Noctuidae) based on a biogeochemical marker
Authors: Paula-Moraes Silvana V , Calixto Eduardo S , Santos Abraão A , Reay-Jones Francis P F , Reisig Dominic D , Farhan Yasmine , Smith Jocelyn L , Hutchison William D 
Published: April 2024

Abstract
Insect migrations have ecological and economic impacts, particularly in agriculture. However, there is limited knowledge about the migratory movements of pests at the continental scale, which is an important factor influencing the spread of resistance genes. Understanding the migratory patterns of economic pests, like Helicoverpa zea (Boddie), is essential for improving Integrated Pest Management (IPM) and Insect Resistance Management (IRM) strategies. In this study, we used stable hydrogen isotopic ratios in wing tissue as a biogeochemical marker to examine migratory patterns and estimate the native origins of H. zea individuals collected across a wide latitudinal gradient in North America. Samples collected at higher latitudes (Ontario, Canada and Minnesota, USA) exhibited a greater proportion (60%–96%) of nonlocal individuals, with an increased probability of origin from the southeastern United States. Populations from mid-latitudes (Florida, North Carolina, and South Carolina) showed a blend of local and nonlocal (40%–60%) individuals. Finally, 15% of the southernmost population individuals (Puerto Rico) were classified as migratory, with some having a probability of origin at higher latitudes (&gt;30°). Overall, our results provide evidence of a northward spring/summer migration of H. zea in North America and underscore the significance of the southeastern United States as a hub for genetic flow. In addition, based on stable hydrogen isotopic ratios, there is strong evidence of reverse (southward) migration of H. zea from the continental United States to Puerto Rico. Our study highlights the implications for IPM and IRM programs and the need for management strategies that account for both northward and southward migration patterns.
Reaching out to socially distant trainees: experimental evidence from variations on the standard farmer trainer system
Authors: Bertelli Olivia , Fall Fatou 
Published: April 2024

Abstract
The farmer trainer (FT) model has gained momentum as a cost-effective alternative to traditional agricultural extension systems. However, there may be friction in the transmission of information, whereby farmers closer to the FT may benefit more than socially distant farmers. This study explores whether variations on the standard FT model facilitate the diffusion of information outside the FT’s pre-existing social network. On top of a standard FT training, a sub-sample of voluntary FTs in rural Uganda was randomly assigned to receive (i) vouchers for accessing professional extension agents, (ii) a signpost advertising the trainer services or (iii) further training aimed at tailoring the training to the specific needs of the trainees. The results show that the FTs assigned these treatment variations trained more farmers, a larger proportion of whom belonged to the FT’s own close circle. The FTs who received vouchers were the only ones to reach out to more socially distant farmers and were also those who organized the most training sessions. We show that these effects are independent of any FT prominence in the village. Nevertheless, further evidence suggests exercising caution regarding the presence of friction in the transmission of knowledge, since knowledge and technology adoption appear to increase only among farmers closely connected to the FT.
Alkynyl-, vinyl-, and arylsilanes
Authors: Thomas Susan E. 
Published: April 2024

Abstract
This chapter studies the conversion of a terminal alkyne to its alkynylsilane. It displays how terminal alkynes are converted into alkynylsilanes by metallation and the addition of chlorosilane. The chapter also looks at the regioselective electrophilic attack on alkynylsilanes. It assesses how electrophiles react with alkynylsilanes at the silicon-bearing end of the alkyne. The chapter then moves to explore hydrosilylation and its application to the synthesis of vinylsilanes. It argues that the reaction is catalyssed by many transition-metal complexes — showing the mechanism for the hydrosilylation of an alkene under transition-metal catalysis. Finally, the chapter pays attention to how arylsilanes are prepared. It outlines the steps of the reaction, then shows how arylsilanes undergo a reaction with electrophiles known as ipso-desilylation.
Reactions of organoboranes
Authors: Thomas Susan E. 
Published: April 2024

Abstract
This chapter discusses the tetrahedral species known as an organoborate. It examines how the attacks by nucleophiles and subsequent 1,2-migration reactions dominate much of the reactivity of organoboranes. Organoboranes are normally handled under a nitrogen atmosphere as they are generally sensitive to oxidation processes. The chapter looks at how this is carried out using alkaline hydrogen peroxide when oxidation is required. It also reviews the oxidation of alklyboranes by using the alkaline hydrogen peroxide. Lastly, the chapter explores how aqueous chromic acid has been used to oxidize alklyboranes. It further discusses the concept of protonolysis, the hydroboration/protolytic cleavage of alkynes, and halogenolysis, the cleavage of the boron-carbon bonds by halogens.
Properties of organosilicon compounds
Authors: Thomas Susan E. 
Published: April 2024

Abstract
This chapter describes the properties of bonds to silicon. It exhibits the relative strengths of bonds that silicon and carbon form with some other elements, noting that silicon forms stronger bonds than carbon to oxygen and the halogens, and weaker bonds to carbon and hydrogen. The chapter points out that much of organosilicon chemistry is driven by the formation of strong silicon-oxygen or silicon-fluorine bonds at the expense of other weaker bonds. The chapter then moves to demonstrate the relative increases in bond lengths between selected atoms attached to silicon and the corresponding bond to carbon. It then introduces the concept of bond polarization and investigates why silicon is more electropositive than carbon. Next, the chapter elaborates on the nucleophilic substitution at a silicon centre, and the stabilization of beta-carbocations and alpha-carbon-metal bonds.
Protection of hydroxy groups as silyl ethers
Authors: Thomas Susan E. 
Published: April 2024

Abstract
This chapter illustrates the formation of silyl ethers. It gives attention to the trimethylsilyl group which has been used extensively for the protection of alcohols. One of the many methods which have been used for protecting a hydroxy group as its trimethylsilyl ether involves adding trimethylsilyl chloride (trimethylchlorosilane, TMCS) to the alcohol in the presence of a weak base. The chapter then argues that silyl ethers are cleaved to their parent alcohols by nucleophiles (often alcohols) under a range of acidic or basic conditions. Finally, the chapter shows some examples of protection of hydroxy groups as silyl ethers  emphasizing the synthesis of (R)-isoproterenol and the synthesis of gephyrotoxin.
Allylsilanes and acylsilanes
Authors: Thomas Susan E. 
Published: April 2024

Abstract
This chapter reviews some methods available for making allylsilanes. It focuses on the silylation of a metal-allyl species as the most direct method available for making them as well as the use of the Wittig reaction. Allylsilanes react with electrophiles at their γ carbon atom as attack at this position generates a carbocation β to silicon. Displacement of the silyl group subsequently produces a new alkene. The chapter then shifts to detail the method of synthesizing acylsilanes which involves deprotonation and silylation of the 1,3-derivative of an aldehyde. It considers how acylsilanes have been synthesized by several other approaches: a reverse Brook rearrangement (silyl-Wittig rearrangement) of allyltrimethylsilyl ether followed by oxidation and reductive cleavage of carbon-sulphur bonds in the silylenol ethers derived from thiol esters.
Exploring the Predictive Value of Gut Microbiome Signatures for Therapy Intensification in Patients With Inflammatory Bowel Disease: A 10-Year Follow-up Study
Authors: Al Radi Zainab M A , Prins Femke M , Collij Valerie , Vich Vila Arnau , Festen Eleonora A M , Dijkstra Gerard , Weersma Rinse K , Klaassen Marjolein A Y , Gacesa Ranko 
Published: April 2024

Abstract

Background
Inflammatory bowel diseases (IBDs) pose a significant challenge due to their diverse, often debilitating, and unpredictable clinical manifestations. The absence of prognostic tools to anticipate the future complications that require therapy intensification presents a substantial burden to patient private life and health. We aimed to explore whether the gut microbiome is a potential biomarker for future therapy intensification in a cohort of 90 IBD patients.

Methods
We conducted whole-genome metagenomics sequencing on fecal samples from these patients, allowing us to profile the taxonomic and functional composition of their gut microbiomes. Additionally, we conducted a retrospective analysis of patients’ electronic records over a period of 10 years following the sample collection and classified patients into (1) those requiring and (2) not requiring therapy intensification. Therapy intensification included medication escalation, intestinal resections, or a loss of response to a biological treatment. We applied gut microbiome diversity analysis, dissimilarity assessment, differential abundance analysis, and random forest modeling to establish associations between baseline microbiome profiles and future therapy intensification.

Results
We identified 12 microbial species (eg, Roseburia hominis and Dialister invisus) and 16 functional pathways (eg, biosynthesis of L-citrulline and L-threonine) with significant correlations to future therapy intensifications. Random forest models using microbial species and pathways achieved areas under the curve of 0.75 and 0.72 for predicting therapy intensification.

Conclusions
The gut microbiome is a potential biomarker for therapy intensification in IBD patients and personalized management strategies. Further research should validate our findings in other cohorts to enhance the generalizability of these results.
Genomic and Epigenomic Influences on Resilience across Scales: Lessons from the Responses of Fish to Environmental Stressors
Authors: Metzger David C H , Earhart Madison L , Schulte Patricia M 
Published: April 2024

Synopsis
Understanding the factors that influence the resilience of biological systems to environmental change is a pressing concern in the face of increasing human impacts on ecosystems and the organisms that inhabit them. However, most considerations of biological resilience have focused at the community and ecosystem levels, whereas here we discuss how including consideration of processes occurring at lower levels of biological organization may provide insights into factors that influence resilience at higher levels. Specifically, we explore how processes at the genomic and epigenomic levels may cascade up to influence resilience at higher levels. We ask how the concepts of “resistance,” or the capacity of a system to minimize change in response to a disturbance, and “recovery,” or the ability of a system to return to its original state following a disturbance and avoid tipping points and resulting regime shifts, map to these lower levels of biological organization. Overall, we suggest that substantial changes at these lower levels may be required to support resilience at higher levels, using selected examples of genomic and epigenomic responses of fish to climate-change-related stressors such as high temperature and hypoxia at the levels of the genome, epigenome, and organism.
Density-dependent habitat selection and warming determine the spatial distribution of haddock (Melanogrammus aeglefinus) on Georges Bank
Authors: Wang Yanjun , Gao Jin , McCurdy Quinn 
Published: April 2024

Abstract
In an ever-changing environment, detecting shifts in the spatial distribution of marine fish and understanding the relative importance of climate change and biotic factors impacting fish distributions can improve fisheries management. Coincident with the significant increase in Haddock (Melanogrammus aeglefinus) abundance to a historically high levels on Georges Bank (GB) in the last decade, extreme ocean temperature increase was also observed in this region. In this study, the possible seasonal and inter-annual spatial distribution changes of haddock were investigated with &gt;50 years of bottom trawl survey data collected in spring and fall on GB. These data were analyzed using models with spatial, different temporal, and spatio-temporal autocorrelation structures. To characterize the directional changes in haddock spatial distribution, the Center of Gravity (CG) and Area of Occupancy (AO) in each season were estimated from the best model selected by Akaike Information Criteria (AIC). The results showed substantial range expansion/contraction and distribution changes in both spring and fall over time. The relative role of density dependence, age structure, and climate change in affecting haddock distribution was evaluated using a generalized additive model (GAM). It was found that density-dependent habitat selection made the greatest contribution to the variations of AO in both seasons, which is consistent with the MacCall’s Basin model theory. Rising ocean temperatures played a major role in shaping a northward distribution shift in fall. GB is the southern edge of haddock distribution in the Northwest Atlantic, continued warming from climate model projections in the next 50 years in this region could make it difficult to define stock boundaries between GB and adjacent Canadian and US domestic management areas. This would subsequently impact fishery management of haddock.
Transitive Centralizer and Fibered Partially Hyperbolic Systems
Authors: Damjanović Danijela , Wilkinson Amie , Xu Disheng 
Published: April 2024

Abstract
We prove several rigidity results about the centralizer of a smooth diffeomorphism, concentrating on two families of examples: diffeomorphisms with transitive centralizer, and perturbations of isometric extensions of Anosov diffeomorphisms of nilmanifolds. We classify all smooth diffeomorphisms with transitive centralizer: they are exactly the maps that preserve a principal fiber bundle structure, acting minimally on the fibers and trivially on the base. We also show that for any smooth, accessible isometric extension $f_{0}\colon M\to M$ of an Anosov diffeomorphism of a nilmanifold, subject to a spectral bunching condition, any $f\in \textrm{Diff}^{\infty }(M)$ sufficiently $C^{1}$-close to $f_{0}$ has centralizer a Lie group. If the dimension of this Lie group equals the dimension of the fiber, then $f$ is a principal fiber bundle morphism covering an Anosov diffeomorphism. Using the results of this paper, we classify the centralizer of any partially hyperbolic diffeomorphism of a $3$-dimensional, nontoral nilmanifold: either the centralizer is virtually trivial, or the diffeomorphism is an isometric extension of an Anosov diffeomorphism, and the centralizer is virtually ${{\mathbb{Z}}}\times{{\mathbb{T}}}$.