bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prologue: Contemplating the quantum revolution, commencing the dialogue
Authors: Vishveshwara Smitha , Vishveshwara C V 
Published: December 2024

Abstract
In the opening chapter on relativity, C. V. Vishveshwara (Vishu) takes the reader through an excursion on how Einstein laid down the remarkable foundations of special relativity. The chapter begins with an early treatment of relativity, namely Galilean relativity, which while successful with classical mechanics was not tenable with electromagnetism. Working in the seclusion of a patent office, Einstein thought deeply and despairingly of relativity that would encompass electromagnetism. He realized that not only spatial measures but also time varied among inertial observers moving with constant relative velocities. Thus, Einstein’s special theory of relativity came to be, and along with it, his celebrated equation, E = mc2. The chapter then surveys bizarre, observable consequences of this special relativity and how they all beautifully fit into a mathematical framework created by Minkowski in which space and time become united. The chapter concludes by describing physicists’ reactions to this radical new theory and its role in different areas, such as elementary particle physics and astrophysics. In the opening chapter of quantum physics, Smitha describes the circuitous historic path taken by many a physicist explorer that led to the establishment of its mind-boggling fundamentals. This revolutionary branch of physics was seeded by puzzles posed in the late 1800s related to the behavior of light from radiating objects. The chapter begins by exploring the nature of light and the story of blackbody radiation that led to Planck introducing the notion of the quantum. It then surveys the photoelectric effect, which heralds the concept of the photon, and wave-particle duality, which applies both to light and matter. The excursion continues into Schrödinger’s description of matter acting as a wave and its consequences, including energy quantization and quantum tunneling. The chapter then explains Heisenberg’s uncertainty principle from multiple angles. Finally, it presents the quantum picture of the atom and how it resolved some of the deep puzzles, a crowning testament to quantum theory.
Nitrogen deficiency influences strigolactone levels in basal parts of shoots and shoot branching phenotype in Arabidopsis thaliana
Authors: Sakioka Riko , Yoneyama Kaori 
Published: December 2024

Abstract
Strigolactones (SLs) are allelochemicals attracting both symbiotic arbuscular mycorrhizal (AM) fungi and root parasitic plants and a novel class of phytohormones inhibiting lateral shoot branching. In general, nutrient deficiency significantly promotes SL production in roots and exudation into the rhizosphere, and also induces suppressed shoot branching phenotype in host plants of AM fungi, including rice, tomato, and maize. Nutrient deficiencies also inhibit the shoot branching in Arabidopsis thaliana (hereafter Arabidopsis), a nonhost of AM fungi, while the level of carlactone, a noncanonical SL and the SL precursor for the other SLs, was reported to be unaffected. Because Arabidopsis SLs, including CL and methyl carlactonoate, are highly unstable, relationships between SL levels and shoot branching in Arabidopsis remain elusive. Herein, we demonstrate that nitrogen deficiency increases SL levels in the basal part of shoots in Arabidopsis and lateral shoot branching appears to be strongly regulated by these SLs.
VSS-Hi-C: variance-stabilized signals for chromatin contacts
Authors: Kenari Neda Shokraneh , Bayat Faezeh , Libbrecht Maxwell W 
Published: December 2024

Abstract

Motivation
The genome-wide chromosome conformation capture assay Hi-C is widely used to study chromatin 3D structures and their functional implications. Read counts from Hi-C indicate the strength of chromatin contact between each pair of genomic loci. These read counts are heteroskedastic: that is, a difference between the interaction frequency of 0 and 100 is much more significant than a difference between the interaction frequency of 1000 and 1100. This property impedes visualization and downstream analysis because it violates the Gaussian variable assumption of many computational tools. Thus heuristic transformations aimed at stabilizing the variance of signals like the shifted-log transformation are typically applied to data before its visualization and inputting to models with Gaussian assumption. However, such heuristic transformations cannot fully stabilize the variance because of their restrictive assumptions about the mean–variance relationship in the data.

Results
Here, we present VSS-Hi-C, a data-driven variance stabilization method for Hi-C data. We show that VSS-Hi-C signals have a unit variance improving visualization of Hi-C, for example in heatmap contact maps. VSS-Hi-C signals also improve the performance of subcompartment callers relying on Gaussian observations. VSS-Hi-C is implemented as an R package and can be used for variance stabilization of different genomic and epigenomic data types with two replicates available.

Availability and implementation
https://github.com/nedashokraneh/vssHiC.
Perioperative patient safety recommendations: systematic review of clinical practice guidelines
Authors: Martinez-Nicolas Ismael , Arnal-Velasco Daniel , Romero-García Eva , Fabregas Neus , Sanduende Otero Yolanda , Leon Irene , Bartakke Ashish A , Silva-Garcia Javier , Rodriguez Anna , Valli Claudia , Zamarian Sandro , Zaludek Adam , Meneses-Echavez Jose , Loaiza-Betancur Andrés F , Sousa Paulo , Orrego Carola , Soria-Aledo Victor ,   SAFEST Consortium, Baneres Joaquim , Carrasco Genis , Sunol Rosa , Vall Helena , Calsbeek Hiske , Emond Yvette , Heideveld-Chevalking Anita , Casaca-Carvalho Pedro , Leite Andreia , Nunes Ana Beatriz , Seyfulayeva Ayshe , De Robertis Edoardo , Weynants Cathy , Wittman Maria , Garel Pascal , Nabbe Marie , Groene Oliver , Wang Sophie , Kangasniemi Mari , Kommusaar Janne , Kristensen Kaja , Polluste Kaja , Pühvel Janne , Starkopf Joel , Marx David , Vlcek Frantisek , Schäfer Willemijn , Schlinkert Caroline , van der Schoot Nina , Van Tuyl Lilian , Voshaar Marieke , Wagner Cordula 
Published: December 2024

Abstract

Background
Surgical-related incidents are a common cause of in-hospital adverse events. Surgical patient safety would benefit from evidence-based practices, but a comprehensive collection of patient safety recommendations is still lacking. This study aimed to compile and assess the perioperative patient safety recommendations for adults.

Method
A systematic review of clinical practice guidelines was conducted using Medline, Embase, Cochrane, Virtual Health Library Regional Portal, and Trip Database from 2012 to 2022. Eligibility criteria followed a PICAR strategy for patient safety recommendations in the perioperative care continuum. Guidelines were appraised for quality, particularly focusing on the ‘rigour of development’ domain of the AGREE-II tool for those containing strong recommendations. Descriptive analyses were conducted, emphasizing guideline quality, recommendation strength, and the supporting level of evidence.

Results
From the 267 guidelines, 4666 perioperative patient safety recommendations were extracted, of which 44.9% (2095) were strongly recommended. Of these, 322 had the highest level of evidence, but only 18 guidelines met high standards in the AGREE-II ‘rigour of development’ domain. A subset of 78 recommendations ranked the highest in the strength of recommendation, level of evidence, and rigour of development of their guidelines. A gap was found within pre-admission and post-discharge care recommendations.

Discussion
This review highlights the noteworthy variability in the methodological quality of the guidelines, and a discordance between strength of recommendation and evidence level of the available perioperative patient safety recommendations. These findings provide valuable information for advising policy decisions and promoting best practices to enhance global surgical safety.

Registration
PROSPERO (CRD42022347449).
Extra-axial inflammatory signal and its relationship to peripheral and central immunity in depression
Authors: Eiff Brandi , Bullmore Edward T , Clatworthy Menna R , Fryer Tim D , Pariante Carmine M , Mondelli Valeria , Maccioni Lucia , Hadjikhani Nouchine , Loggia Marco L , Moskowitz Michael A , Bruner Emiliano , Veronese Mattia , Turkheimer Federico E , Schubert Julia J 
Published: December 2024

Abstract
Although both central and peripheral inflammation have been observed consistently in depression, the relationship between the two remains obscure. Extra-axial immune cells may play a role in mediating the connection between central and peripheral immunity. This study investigates the potential roles of calvarial bone marrow and parameningeal spaces in mediating interactions between central and peripheral immunity in depression.
PET was used to measure regional TSPO expression in the skull and parameninges as a marker of inflammatory activity. This measure was correlated with brain TSPO expression and peripheral cytokine concentrations in a cohort enriched for heightened peripheral and central immunity comprising 51 individuals with depression and 25 healthy controls.
The findings reveal a complex relationship between regional skull TSPO expression and both peripheral and central immunity. Facial and parietal skull bone TSPO expression showed significant associations with both peripheral and central immunity. TSPO expression in the confluence of sinuses was also linked to both central and peripheral immune markers. Group-dependent elevations in TSPO expression within the occipital skull bone marrow were also found to be significantly associated with central inflammation.
Significant associations between immune activity within the skull, parameninges, parenchyma and periphery highlight the role of the skull bone marrow and venous sinuses as pivotal sites for peripheral and central immune interactions.
Optimizing treatment of cardiovascular risk factors in cerebral small vessel disease using genetics
Authors: Koohi Fatemeh , Harshfield Eric L , Gill Dipender , Ge Wenjing , Burgess Stephen , Markus Hugh S 
Published: December 2024

Abstract
Cerebral small vessel disease (cSVD) causes lacunar stroke (LS), intracerebral haemorrhage, and is the most common pathology underlying vascular dementia. However, there are few trials examining whether treating conventional cardiovascular risk factors reduce stroke risk in cSVD, as opposed to stroke as a whole. We used Mendelian randomization techniques to investigate which risk factors are causally related to cSVD and to evaluate whether specific drugs may be beneficial in cSVD prevention.
We identified genetic proxies for blood pressure traits, lipids, glycaemic markers, anthropometry measures, smoking, alcohol consumption, and physical activity from large-scale genome-wide association studies of European ancestry. We also selected genetic variants as proxies for drug target perturbation in hypertension, dyslipidaemia, hyperglycaemia, and obesity. Mendelian randomization was performed to assess their associations with LS from the GIGASTROKE Consortium (n = 6811) and in a sensitivity analysis in a cohort of patients with MRI-confirmed LS (n = 3306). We also investigated associations with three neuroimaging features of cSVD, namely, white matter hyperintensities (n = 55 291), fractional anisotropy (n = 36 460), and mean diffusivity (n = 36 012).
Genetic predisposition to higher systolic and diastolic blood pressure was associated with LS and cSVD imaging markers. Genetically predicted liability to diabetes, obesity, smoking, higher triglyceride levels, and the ratio of triglycerides to high density lipoprotein (HDL) also showed detrimental associations with LS risk, while genetic predisposition to higher HDL concentrations and moderate-to-vigorous physical activity showed protective associations. Genetically proxied blood pressure-lowering through calcium channel blockers (CCBs) was associated with cSVD imaging markers, while genetically proxied HDL-raising through Cholesteryl Ester Transfer Protein (CETP) inhibitors, triglyceride-lowering through lipoprotein lipase (LPL), and weight-lowering through gastric inhibitory polypeptide receptor (GIPR) were associated with lower risk of LS.
Our findings highlight the importance of some conventional cardiovascular risk factors, including blood pressure and BMI, in cSVD, but not other e.g. LDL. The findings further demonstrate the potential beneficial effects of CCBs on cSVD imaging markers and CETP inhibitors, LPL enhancement, and GIPR obesity-targeted drugs on LS. They provide useful information for initiating future clinical trials examining secondary prevention strategies in cSVD.
Rituximab versus placebo for chronic inflammatory demyelinating polyradiculoneuropathy: a randomized trial
Authors: Nobile-Orazio Eduardo , Cocito Dario , Manganelli Fiore , Fazio Raffaella , Lauria Pinter Giuseppe , Benedetti Luana , Mazzeo Anna , Peci Erdita , Spina Emanuele , Falzone Yuri , Dalla Bella Eleonora , Germano Francesco , Gentile Luca , Liberatore Giuseppe , Gallia Francesca , Collet-Vidiella Roger , Bianchi Elisa , Doneddu Pietro Emiliano 
Published: December 2024

Abstract
Chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) often requires prolonged ongoing treatment to prevent worsening. The efficacy of rituximab in preventing worsening after the discontinuation of immunoglobulin therapy in patients with CIDP was assessed.
In this randomized, double-blind, placebo-controlled study, conducted at seven Italian hospitals, CIDP patients under immunoglobulin therapy were assigned to receive either rituximab (1 g on Days 1, 15 and 180 ± 7) or placebo. Both groups continued their regular immunoglobulin doses for 6 months post-intervention. The primary end point was the proportion of patients who worsened in any of the following three measures at Month 12, within 6 months after immunoglobulin discontinuation: a decrease of at least one point on the adjusted INCAT score, two points on the MRC sum score, or four points on the RODS centile score. Secondary end points included the proportion of patients deteriorating at Month 18 (within 12 months after immunoglobulin discontinuation), treatment cessation due to adverse events or voluntary reasons, and the time until deterioration after immunoglobulin discontinuation. This study was registered with ClinicalTrials.gov (NCT06325943) and EUDRACT (number 2017-005034-36), and is now complete.
From April 2019 to March 2022, 39 patients were recruited; two withdrew consent. The remaining 37 patients were assigned to rituximab (n = 19) or placebo (n = 18). Median age was 53 (interquartile range 45–64), with 11 (30%) females. A similar proportion of patients in both the rituximab (12/19, 63.2%) and placebo (12/18, 66.6%) groups worsened at Month 12 [odds ratio (OR) 0.86; 95% confidence interval (CI) 0.22–3.32]. No significant differences were noted at Month 18 (OR 0.62; 95% CI 0.14–2.70), or in the mean scores of each scale at Months 6, 12 and 18. The median time to worsening was 5 months for rituximab and 2 months for placebo (Log-rank P = 0.4372). Treatment was suspended due to adverse events in one rituximab patient.
In this study, rituximab was not more effective than placebo in preventing clinical deterioration following the discontinuation of immunoglobulin therapy in CIDP. Further studies might evaluate the efficacy of more frequent or earlier administration of rituximab.
Clinical characterization of a novel ATP1A2 p.Gly615Glu mutation in nine family members with familial hemiplegic migraine
Authors: Romozzi Marina , Spartano Serena , L’Erario Federica Francesca , Iannone Luigi Francesco , Trigila Vincenzo , Gentile Annalisa , Sanginario Pasquale , Calabresi Paolo , Tiziano Francesco Danilo , Vollono Catello 
Published: December 2024

Abstract
Familial hemiplegic migraine type 2 results from pathogenic variants in the ATP1A2 gene, which encodes for a catalytic subunit of sodium/potassium ATPase. This extremely rare autosomal dominant disorder manifests with a spectrum of symptoms, most commonly pure hemiplegic phenotype, epilepsy, and/or intellectual disability. In this study, we detail the clinical features and genetic analysis of nine patients from a large family spanning four generations, with all carrying a previously unreported likely pathogenic variant, p.Gly615Glu, in ATP1A2, compatible with a diagnosis of familial hemiplegic migraine type 2, fully penetrant with variable expressivity. This newly identified likely pathogenic variant primarily presented with psychiatric disturbances and a non-hemiplegic phenotype. Only one patient presented hemiplegic attacks, while seven were diagnosed with migraine with aura, including visual, sensory, and speech/language aura, and one with migraine without aura. The identification of the genes responsible for the more common forms of migraine, both with and without aura, remains a significant challenge in migraine genetics and is critical for advancing personalized medicine.
Acquired autoinflammatory disorders: a dermatologist’s perspective
Authors: Bishnoi Anuradha , Sharma Apoorva , Baskaran Narayanan , Mehta Hitaishi , Chatterjee Debajyoti , Vinay Keshavamurthy 
Published: December 2024

Abstract
Autoinflammatory disorders are characterized by a dysregulated and disproportionately heightened response by the innate immune system to PAMPs and DAMPs (pathogen- and damage-associated molecular patterns, respectively), with a crucial role played by neutrophils and macrophages in disease pathogenesis. Autoinflammatory disorders closely resemble connective tissue diseases (CTDs); however, tests for antinuclear antibodies, typically considered a marker of CTDs, are negative in autoinflammatory disorders. Many autoinflammatory disorders are monogenic and arise from inherited genetic mutations, resulting in autoinflammation. This is especially true for disorders presenting in childhood or early adulthood. However, with the relatively recent identification of VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) syndrome, the recognized genetic spectrum of these disorders has expanded, especially in the adult population, emphasizing that these mutations could either be inherited or acquired later in life. Additionally, many of the acquired autoinflammatory disorders, for example, adult-onset Still disease and Schnitzler syndrome, have a multifactorial pathogenesis and are typically polygenic. Many novel disorders are being described in this category, and the majority of them have prominent cutaneous manifestations – either at onset or during the course of disease – that are particularly important from a diagnostic point of view. In this review, we discuss the cutaneous findings of a few acquired autoinflammatory disorders, with a specific focus on adult-onset Still disease, VEXAS syndrome, Schnitzler syndrome, Kikuchi–Fujimoto disease and haemophagocytic lymphohistiocytosis.
Dioctyl-substituted dibenzotetracyanonaphthoquinodimethane for air-stable n-channel organic semiconductor
Authors: Yang Tengzhou , Xie Bing , Zhang Liang , Wei Haoming 
Published: December 2024

Abstract
In this study, a novel n-channel 11,11,12,12-tetracyanonaphtho-2,6-quinodimethane-based organic semiconductor C8-DBTNAP was synthesized. C8-DBTNAP had good solubility and low-lying lowest unoccupied molecular orbital level (−4.41 eV). The good thin-film formability of C8-DBTNAP made it produce continuous, strip-shaped and uniform crystalline films. C8-DBTNAP organic thin-film transistors demonstrated high electron mobility up to 0.4 cm2/Vs under air conditions. These findings revealed that DBTNAP skeleton can be expected as a potential building block for developing high-performance, air-stable n-channel organic semiconductors.
Recognition of mismatched sites in double-stranded DNA by a pair of partially noncomplementary peptide nucleic acids
Authors: Shibata Masanari , Shoji Osami , Aiba Yuichiro 
Published: December 2024

Abstract
We have successfully achieved efficient recognition of mismatched sites in double-stranded DNA through the formation of an invasion complex by using partially noncomplementary peptide nucleic acids (PNAs). Owing to mismatches between 2 PNAs used for invasion, the undesired PNA/PNA duplex, which inhibits invasion complex formation, was destabilized. This approach overcame an inherent challenge in PNA invasion, in particular, undesired PNA/PNA duplex formation resulting from PNA complementarity, thereby enhancing overall invasion efficiency.
A One Health Investigation into H5N1 Avian Influenza Virus Epizootics on Two Dairy Farms
Authors: Shittu Ismaila , Silva Diego , Oguzie Judith U , Marushchak Lyudmyla V , Olinger Gene G , Lednicky John A , Trujillo-Vargas Claudia M , Schneider Nicholas E , Hao Haiping , Gray Gregory C 
Published: December 2024

Abstract

Background
In early April 2024 we studied 2 Texas dairy farms that had suffered incursions of H5N1 highly pathogenic avian influenza virus (HPAIV) the previous month.

Methods
We employed molecular assays, cell and egg culture, Sanger and next generation sequencing to isolate and characterize viruses from multiple farm specimens (cow nasal swab, milk specimens, fecal slurry, and a dead bird).

Results
We detected H5N1 HPAIV in 64% (9/14) of milk specimens, 2.6% (1/39) of cattle nasal swab specimens, and none of 17 cattle worker nasopharyngeal swab specimens. We cultured and characterized virus from 8 H5N1-positive specimens. Sanger and next-generation sequencing revealed the viruses were closely related into other recent Texas epizootic H5N1 strains of clade 2.3.4.4b. Our isolates had multiple mutations associated with increased spillover potential. Surprisingly, we detected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in a nasal swab from a sick cow. Additionally, 14.3% (2/14) of the farm workers who donated sera were recently symptomatic and had elevated neutralizing antibodies against a related H5N1 strain.

Conclusions
Although our sampling was limited, these data offer additional insight into the large H5N1 HPAIV epizootic, which has rapidly spread in the United States. Due to fears that research might damage dairy businesses, studies like this one have been few. We need to find ways to work with dairy farms in collecting more comprehensive epidemiological data that are necessary for the design of future interventions against H5N1 HPAIV on cattle farms.