bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extending protein interaction networks using proteoforms and small molecules
Authors: Hernández Sánchez Luis Francisco , Burger Bram , Castro Campos Rodrigo Alexander , Johansson Stefan , Njølstad Pål Rasmus , Barsnes Harald , Vaudel Marc 
Published: September 2023

Abstract

Motivation
Biological network analysis for high-throughput biomedical data interpretation relies heavily on topological characteristics. Networks are commonly composed of nodes representing genes or proteins that are connected by edges when interacting. In this study, we use the rich information available in the Reactome pathway database to build biological networks accounting for small molecules and proteoforms modeled using protein isoforms and post-translational modifications to study the topological changes induced by this refinement of the network representation.

Results
We find that improving the interactome modeling increases the number of nodes and interactions, but that isoform and post-translational modification annotation is still limited compared to what can be expected biologically. We also note that small molecule information can distort the topology of the network due to the high connectedness of these molecules, which does not necessarily represent the reality of biology. However, by restricting the connections of small molecules to the context of biochemical reactions, we find that these improve the overall connectedness of the network and reduce the prevalence of isolated components and nodes. Overall, changing the representation of the network alters the prevalence of articulation points and bridges globally but also within and across pathways. Hence, some molecules can gain or lose in biological importance depending on the level of detail of the representation of the biological system, which might in turn impact network-based studies of diseases or druggability.

Availability and implementation
Networks are constructed based on data publicly available in the Reactome Pathway knowledgebase: reactome.org.
Risk factors for postoperative complications after adrenalectomy for phaeochromocytoma: multicentre cohort study
Authors: Parente Alessandro , Kamarajah Sivesh K , Thompson Joseph P , Crook Charlotte , Aspinall Sebastian , Melvin Ross , Stechman Michael J , Perry Helen , Balasubramanian Sabapathy P , Pannu Arslan , Palazzo Fausto F , Van Den Heede Klaas , Eatock Fiona , Anderson Hannah , Doran Helen , Wang Kelvin , Hubbard Johnathan , Aldrees Abdulaziz , Shore Susannah L , Fung Clare , Waghorn Alison , Ayuk John , Bennett Davinia , Sutcliffe Robert P 
Published: September 2023

Abstract

Background
To determine the incidence and risk factors for postoperative complications and prolonged hospital stay after adrenalectomy for phaeochromocytoma.

Methods
Demographics, perioperative outcomes and complications were evaluated for consecutive patients who underwent adrenalectomy for phaeochromocytoma from 2012 to 2020 in nine high-volume UK centres. Odds ratios were calculated using multivariable models. The primary outcome was postoperative complications according to the Clavien–­­Dindo classification and secondary outcome was duration of hospital stay.

Results
Data were available for 406 patients (female n = 221, 54.4 per cent). Two patients (0.5 per cent) had perioperative death, whilst 148 complications were recorded in 109 (26.8 per cent) patients. On adjusted analysis, the age-adjusted Charlson Co-morbidity Index ≥3 (OR 8.09, 95 per cent c.i. 2.31 to 29.63, P = 0.001), laparoscopic converted to open (OR 10.34, 95 per cent c.i. 3.24 to 36.23, P &lt;0.001), and open surgery (OR 11.69, 95 per cent c.i. 4.52 to 32.55, P &lt;0.001) were independently associated with postoperative complications. Overall, 97 of 430 (22.5 per cent) had a duration of stay ≥5 days and this was associated with an age-adjusted Charlson Co-morbidity Index ≥3 (OR 4.31, 95 per cent c.i. 1.08 to 18.26, P = 0.042), tumour size (OR 1.15, 95 per cent c.i. 1.05 to 1.28, P = 0.006), laparoscopic converted to open (OR 32.11, 95 per cent c.i. 9.2 to 137.77, P &lt;0.001), and open surgery (OR 28.01, 95 per cent c.i. 10.52 to 83.97, P &lt;0.001).

Conclusion
Adrenalectomy for phaeochromocytoma is associated with a very low mortality rate, whilst postoperative complications are common. Several risk factors, including co-morbidities and operative approach, are independently associated with postoperative complications and/or prolonged hospitalization, and should be considered when counselling patients.
B-301 In-vivo Continuous Therapeutic Drug Monitoring With Electrochemical Aptamer-based Sensors
Authors: Goncales V , Chamazketi A A , Harrison M , Leung K , Gerson J , Batchelor R H , Farnkopf A , Hodges A , Plaxco K 
Published: September 2023

Abstract
Therapeutic drug monitoring (TDM) is a clinical practice involving quantification of plasma drug concentrations to adjust treatment efficacy and minimize toxicity in patient care. TDM is relevant for drugs with a narrow therapeutic index, defined as the plasma concentration range over which a molecule is therapeutically effective without causing significant adverse effects. For narrow therapeutic index drugs, indirect predictors of a patient’s metabolism, such as age, body mass, or genotype, are insufficient to ensure effective dosing, and metabolic variability across different individuals needs to be considered. The importance of TDM is illustrated by the difficulty in treating a patient with vancomycin, an essential antibiotic used to combat gram-positive bacterial infections. The practice typically involves determining trough concentration, peak concentration, or exposure to the vancomycin area under the curve, necessitating blood sampling. After sampling, the current practices require patient blood to be sent to a laboratory, which can only provide an answer from hours after sample collection. Electrochemical aptamer-based (E-AB) sensors provide significant opportunities to make TDM a practice as frequent and convenient as the measurement of blood sugar has become for people with diabetes. This is because E-AB sensing is a molecular approach to continuously measuring concentrations of specific molecules. We present the selection of an aptamer against vancomycin and its adaptation into an E-AB sensor. Using this sensor, we then demonstrate the opportunities for rapid (seconds) measurement of plasma vancomycin and the real-time measurement of subject-specific vancomycin pharmacokinetics on rats (Fig. 1) [3]. Such capability provides a route toward improving TDM and the personalized delivery of pharmacological interventions.Fig. 1.Real-time continuous monitoring of subject-specific vancomycin pharmacokinetics with electrochemical aptamer-based sensors. Reprinted with permission from the American Chemical Society.
SLPs’ perceptions of language learning myths about children who are DHH
Authors: McDaniel Jena , Krimm Hannah , Schuele C Melanie 
Published: September 2023

Abstract
This article reports on speech-language pathologists’ (SLPs’) knowledge related to myths about spoken language learning of children who are deaf and hard of hearing (DHH). The broader study was designed as a step toward narrowing the research-practice gap and providing effective, evidence-based language services to children. In the broader study, SLPs (n = 106) reported their agreement/disagreement with myth statements and true statements (n = 52) about 7 clinical topics related to speech and language development. For the current report, participant responses to 7 statements within the DHH topic were analyzed. Participants exhibited a relative strength in bilingualism knowledge for spoken languages and a relative weakness in audiovisual integration knowledge. Much individual variation was observed. Participants’ responses were more likely to align with current evidence about bilingualism if the participants had less experience as an SLP. The findings provide guidance on prioritizing topics for speech-language pathology preservice and professional development.
Incidence and individual risk prediction of post-COVID-19 cardiovascular disease in the general population: a multivariable prediction model development and validation study
Authors: la Roi-Teeuw Hannah M , van Smeden Maarten , Geersing Geert-Jan , Klungel Olaf H , Rutten Frans H , Souverein Patrick C , van Doorn Sander 
Published: September 2023

Abstract

Aims
Previous studies suggest relatively increased cardiovascular risk after COVID-19 infection. This study assessed incidence and explored individual risk and timing of cardiovascular disease occurring post-COVID-19 in a large primary care database.

Methods and results
Data were extracted from the UK’s Clinical Practice Research Datalink. Incidence rates within 180 days post-infection were estimated for arterial or venous events, inflammatory heart disease, and new-onset atrial fibrillation or heart failure. Next, multivariable logistic regression models were developed on 220 751 adults with COVID-19 infection before 1 December 2020 using age, sex and traditional cardiovascular risk factors. All models were externally validated in (i) 138 034 vaccinated and (ii) 503 404 unvaccinated adults with a first COVID-19 infection after 1 December 2020. Discriminative performance and calibration were evaluated with internal and external validation. Increased incidence rates were observed up to 60 days after COVID-19 infection for venous and arterial cardiovascular events and new-onset atrial fibrillation, but not for inflammatory heart disease or heart failure, with the highest rate for venous events (13 per 1000 person-years). The best prediction models had c-statistics of 0.90 or higher. However, &lt;5% of adults had a predicted 180-day outcome-specific risk larger than 1%. These rare outcomes complicated calibration.

Conclusion
Risks of arterial and venous cardiovascular events and new-onset atrial fibrillation are increased within the first 60 days after COVID-19 infection in the general population. Models’ c-statistics suggest high discrimination, but because of the very low absolute risks, they are insufficient to inform individual risk management.
A virus induces alterations in root morphology while exerting minimal effects on the rhizosphere and endosphere microorganisms in rice
Authors: Liu Xuewei , Wang Yirong , Han Lijuan , Xia Yuxian , Xie Jiaqin 
Published: September 2023

Abstract
The highly destructive southern rice black-streaked dwarf virus (SRBSDV) causes significant losses in rice production. To understand its impact on rice root, we studied fibrous root development and root microbiota variation (rhizosphere and endosphere) after SRBSDV infection. SRBSDV infection reduced the number and length of fibrous roots in rice. Interestingly, the rhizosphere had higher bacterial diversity and abundance at the initial (0 days) and 30-day postinfection stages, while 30-day-old roots showed increased diversity and abundance. However, there were no significant differences in microbiota diversity between infected and noninfected rice plants. The major rhizosphere microbiota included Proteobacteria, Bacteroidota, Acidobacteriota, and Planctomycetota, comprising about 80% of the community. The endosphere was dominated by Proteobacteria and Cyanobacteria, constituting over 90%, with Bacteroidota as the next most prominent group. Further, we identified differentially expressed genes related to plant–pathogen interactions, plant hormone signal, and ABC transporters, potentially affecting root morphology. Notably, specific bacteria (e.g. Inquilinus and Actinoplanes) showed correlations with these pathways. In conclusion, SRBSDV primarily influences root growth through host metabolism, rather than exerting direct effects on the root microbiota. These insights into the interactions among the pathogen, rice plant, and associated microbiota could have implications for managing SRBSDV’s detrimental effects on rice production.
‘Writing is an Act, the Poem a Weapon and Discussion an Assembly’: The Political Turn in Souffles during Morocco’s 1968
Authors: Stafford Andy 
Published: September 2023

Abstract
Using the recent publication in English translation of an anthology of texts from the Moroccan journal Souffles (Stanford University Press, 2016), this article is part of a wider project that links the journal’s moves to question Négritude with its postcolonial critique of folklorism. It considers the Moroccan journal as an archetypal May 1968 publication; first, by tracing the dramatic shift that Souffles makes between 1966 and 1969 from literary and cultural journal to revolutionary mouthpiece of Marxist anti-Zionism, and which takes place in a period of pan-Arabist crisis and during the social unrest of 1968–1971 in Morocco; and second, by looking closely at the theoretical and philosophical innovations of Abraham Serfaty, alongside the agitational poetry of Abdellatif Laâbi and the political theories emerging in sub-Saharan Africa and the Francophone Caribbean, that appear in Souffles in the wake of May 1968 in France. Finally, it locates an incipient Maoism in the radicalization of Souffles.
Dementia Prevention and Individual and Socioeconomic Barriers: Avoiding “Lifestyle” Stigma
Authors: Wilson Nikki-Anne , Anstey Kaarin J 
Published: September 2023

Abstract
Recent decades have seen exponential growth in research on modifiable risk factors for dementia across the lifespan, which has considerably advanced our understanding of brain health. Not all modifiable risk factors are equal, however, in the ease with which they can be addressed. Some individuals and populations face significant barriers to engaging in dementia risk-reduction behaviors. With the evolution of the dementia prevention field, there is a need to broaden our approach from identifying individual risk factors toward addressing inclusive and globally effective intervention strategies. Here, we argue for a greater awareness of individual and socioeconomic barriers to behavior change-oriented dementia risk reduction. We caution against inadvertently increasing health inequities through “lifestyle” stigma and call for an approach that both harnesses current dementia risk-reduction knowledge and effectively addresses barriers to change. A greater focus on more positive aspects of reducing dementia risk, such as enhancing mental well-being, may also be beneficial. Evidence for the negative ramifications of stigma in dementia is discussed as well as overly simplistic media representations of dementia as a disease, which one can “stave off” through lifestyle. Further, we explore potential negative implications for research funding and policy resulting from stigma. More research regarding the experience of stigma in dementia is needed, across diverse cultural and socioeconomic groups.
The Inner Lives of Cephalopods
Authors: Schnell Alexandra K , Farndale Wright Nathaniel R , Clayton Nicola S 
Published: September 2023

Synopsis
The minds of cephalopods have captivated scientists for millennia, yet the extent that we can understand their subjective experiences remains contested. In this article, we consider the sum of our scientific progress towards understanding the inner lives of cephalopods. Here, we outline the behavioral responses to specific experimental paradigms that are helping us to reveal their subjective experiences. We consider evidence from three broad research categories, which help to illuminate whether soft-bodied cephalopods (octopus, cuttlefish, and squid) have an awareness of self, awareness of others, and an awareness of time. Where there are current gaps in the literature, we outline cephalopod behaviors that warrant experimental investigation. We argue that investigations, especially framed through the lens of comparative psychology, have the potential to extend our understanding of the inner lives of this extraordinary class of animals.
The Development and Expansion of in vivo Germline Editing Technologies in Arthropods: Receptor-Mediated Ovary Transduction of Cargo (ReMOT Control) and Beyond
Authors: Terradas Gerard , Macias Vanessa M , Peterson Hillary , McKeand Sage , Krawczyk Grzegorz , Rasgon Jason L 
Published: September 2023

Synopsis
In the past 20 years, sequencing technologies have led to easy access to genomic data from nonmodel organisms in all biological realms. Insect genetic manipulation, however, continues to be a challenge due to various factors, including technical and cost-related issues. Traditional techniques such as microinjection of gene-editing vectors into early stage embryos have been used for arthropod transgenesis and the discovery of Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR–Cas) technologies allowed for targeted mutagenesis and the creation of knockouts or knock-ins in arthropods. Receptor-Mediated Ovary Transduction of Cargo (ReMOT Control) acts as an alternative to embryonic microinjections, which require expensive equipment and extensive hands-on training. ReMOT Control’s main advantage is its ease of use coupled with the ability to hypothetically target any vitellogenic species, as injections are administered to the egg-laying adult rather than embryos. After its initial application in the mosquito Aedes aegypti, ReMOT Control has successfully produced mutants not only for mosquitoes but for multiple arthropod species from diverse orders, such as ticks, mites, wasps, beetles, and true bugs, and is being extended to crustaceans, demonstrating the versatility of the technique. In this review, we discuss the current state of ReMOT Control from its proof-of-concept to the advances and challenges in the application across species after 5 years since its development, including novel extensions of the technique such as direct parental (DIPA)-CRISPR.
Systolic anterior motion due to morphology changes in constrictive pericarditis
Authors: Kumagai Yu , Nakajima Hiroyuki , Nakajima Tomomi , Yoshitake Akihiro 
Published: September 2023

Abstract
Systolic anterior motion (SAM) can be caused by multifactorial mechanisms, including structural, morphological and functional factors. We report an unusual case of a 76-year-old woman presenting with SAM associated with constrictive pericarditis. Echocardiography showed no septal hypertrophy but SAM and left ventricular outflow tract obstruction and moderate mitral regurgitation. The restoration of diastolic function after complete pericardiectomy successfully eliminated it.
Night shift work characteristics and risk of incident coronary heart disease among health care workers: national cohort study
Authors: Vestergaard Jesper Medom , Dalbøge Annett , Bonde Jens Peter Ellekilde , Garde Anne Helene , Hansen Johnni , Hansen Åse Marie , Larsen Ann Dyreborg , Härmä Mikko , Costello Sadie , Böttcher Morten , Kolstad Henrik Albert 
Published: September 2023

Abstract

Background
Night work has been associated with coronary heart disease. The present study examined exposure-response relations between quantitative night work characteristics and coronary heart disease (angina pectoris or myocardial infarction) with the aim to contribute to evidence-based recommendations for low-risk night work schedules.

Methods
We followed 100 149 night workers (80% women) and 153 882 day workers (78% women), all health care workers in Denmark with day by day payroll information on night shifts from 2007 to 2015. We analysed data with Poisson regression stratified by sex and adjusted for age, calendar year, diabetes, family history of cardiovascular disease, educational level, occupation, indicators for obesity, hypercholesterolaemia, and hypertension.

Results
Female and male night workers worked on average 1.7 and 1.8 night shifts per month for an average duration of less than 4 years. During follow-up, 1198 night and 2128 day workers were hospitalized with first-time coronary heart disease. When compared with day workers, the overall incidence rate ratios for female and male night workers were 1.06 [95% confidence interval (CI): 0.97, 1.17] and 1.22 (95% CI 1.07, 1.39). Highest risks were observed in top exposure categories for several night work characteristics. However, no consistent exposure-response relations by number of monthly night shifts, cumulative night shifts, years with rotating night shifts, years with any night shift and consecutive night shifts were observed among the night workers of either sex.

Conclusions
This study of a population with low exposure to night work does not indicate that reducing extent of monthly night shifts, cumulative night shifts, years with rotating night shifts, years with any night shift and consecutive night shifts would reduce the risk of coronary heart disease.
Spectral deconvolution of matrix models: the additive case
Authors: Tarrago Pierre 
Published: September 2023

Abstract
We implement a complex analytic method to build an estimator of the spectrum of a matrix perturbed by the addition of a random matrix noise in the free probabilistic regime. This method, which has been previously introduced by Arizmendi, Tarrago and Vargas, involves two steps: the first step consists in a fixed point method to compute the Stieltjes transform of the desired distribution in a certain domain, and the second step is a classical deconvolution by a Cauchy distribution, whose parameter depends on the intensity of the noise. This method thus reduces the spectral deconvolution problem to a classical one. We provide explicit bounds for the mean squared error of the first step under the assumption that the distribution of the noise is unitary invariant. In the case where the unknown measure is sparse or close to a distribution with a density with enough smoothness, we prove that the resulting estimator converges to the measure in the $1$-Wasserstein distance at speed $O(1/\sqrt{N})$, where $N$ is the dimension of the matrix.
Mechanisms that regulate the production of secondary siRNAs in plants
Authors: Fujimoto Yuji , Iwakawa Hiro-oki 
Published: September 2023

Abstract
Many organisms produce secondary small interfering RNAs (siRNAs) that are triggered by primary small RNAs to regulate various biological processes. Plants have evolved several types of secondary siRNA biogenesis pathways that play important roles in development, stress responses and defense against viruses and transposons. The critical step of these pathways is the production of double-stranded RNAs by RNA-dependent RNA polymerases. This step is normally tightly regulated, but when its control is released, secondary siRNA production is initiated. In this article, we will review the recent advances in secondary siRNA production triggered by microRNAs encoded in the genome and siRNAs derived from invasive nucleic acids. In particular, we will focus on the factors, events, and RNA/DNA elements that promote or inhibit the early steps of secondary siRNA biogenesis.