bluuebunny/crossref_metadata_2025_split huggingface dataset:
The effect of noise artefacts on gravitational-wave searches for neutron star post-merger remnants
Authors: Panther F H , Lasky P D 
Published: May 2023

ABSTRACT
Gravitational waves from binary neutron star post-merger remnants have the potential to uncover the physics of the hot nuclear equation of state. These gravitational-wave signals are high frequency (∼kHz) and short-lived ($\mathcal {O}(10\, \mathrm{ms})$), which introduces potential problems for data analysis algorithms due to the presence of non-stationary and non-Gaussian noise artefacts in gravitational-wave observatories. We quantify the degree to which these noise features in LIGO data may affect our confidence in identifying post-merger gravitational-wave signals. We show that the combination of vetoing data with non-stationary glitches and the application of the Allen χ2 veto (usually reserved for long-lived lower frequency gravitational-wave signals), allows one to confidently detect post-merger signals with signal-to-noise ratio ρ ≳ 8. We discuss the need to incorporate the data quality checks and vetoes into realistic post-merger gravitational-wave searches, and describe their relevance to calculating realistic false-alarm and false-dismissal rates.
Zarlino’sComporre di fantasiaand Canon
Authors: Schubert Peter 
Published: May 2023

AbstractIn the Istitutioni harmoniche, Zarlino describes a compositional process in which a countermelody that is introduced against a principal soggetto can itself become a soggetto for the next phrase, and the process can be repeated in subsequent phrases. This study shows how comporre di fantasia functions in passages from Martini, Févin, Isaac, and Josquin. The technique can also inform our understanding of canon composition, which is illustrated with two examples by Pierre de la Rue. For the study of canons at different time intervals, I also invoke the neglected theories of Robert Morris, Robert Gauldin, and Immanuel Ott. Comporre di fantasia is a structural category that provides insight into compositional process in Renaissance polyphony.
Actin nucleators safeguard replication forks by limiting nascent strand degradation
Authors: Nieminuszczy Jadwiga , Martin Peter R , Broderick Ronan , Krwawicz Joanna , Kanellou Alexandra , Mocanu Camelia , Bousgouni Vicky , Smith Charlotte , Wen Kuo-Kuang , Woodward Beth L , Bakal Chris , Shackley Fiona , Aguilera Andrés , Stewart Grant S , Vyas Yatin M , Niedzwiedz Wojciech 
Published: May 2023

Abstract
Accurate genome replication is essential for all life and a key mechanism of disease prevention, underpinned by the ability of cells to respond to replicative stress (RS) and protect replication forks. These responses rely on the formation of Replication Protein A (RPA)-single stranded (ss) DNA complexes, yet this process remains largely uncharacterized. Here, we establish that actin nucleation-promoting factors (NPFs) associate with replication forks, promote efficient DNA replication and facilitate association of RPA with ssDNA at sites of RS. Accordingly, their loss leads to deprotection of ssDNA at perturbed forks, impaired ATR activation, global replication defects and fork collapse. Supplying an excess of RPA restores RPA foci formation and fork protection, suggesting a chaperoning role for actin nucleators (ANs) (i.e. Arp2/3, DIAPH1) and NPFs (i.e, WASp, N-WASp) in regulating RPA availability upon RS. We also discover that β-actin interacts with RPA directly in vitro, and in vivo a hyper-depolymerizing β-actin mutant displays a heightened association with RPA and the same dysfunctional replication phenotypes as loss of ANs/NPFs, which contrasts with the phenotype of a hyper-polymerizing β-actin mutant. Thus, we identify components of actin polymerization pathways that are essential for preventing ectopic nucleolytic degradation of perturbed forks by modulating RPA activity.
NBBC: a non-B DNA burden explorer in cancer
Authors: Xu Qi , Kowalski Jeanne 
Published: May 2023

Abstract
Alternate (non-B) DNA-forming structures, such as Z-DNA, G-quadruplex, triplex have demonstrated a potential role in cancer etiology. It has been found that non-B DNA-forming sequences can stimulate genetic instability in human cancer genomes, implicating them in the development of cancer and other genetic diseases. While there exist several non-B prediction tools and databases, they lack the ability to both analyze and visualize non-B data within a cancer context. Herein, we introduce NBBC, a non-B DNA burden explorer in cancer, that offers analyses and visualizations for non-B DNA forming motifs. To do so, we introduce ‘non-B burden’ as a metric to summarize the prevalence of non-B DNA motifs at the gene-, signature- and genomic site-levels. Using our non-B burden metric, we developed two analyses modules within a cancer context to assist in exploring both gene- and motif-level non-B type heterogeneity among gene signatures. NBBC is designed to serve as a new analysis and visualization platform for the exploration of non-B DNA, guided by non-B burden as a novel marker.
A conserved motif in the disordered linker of human MLH1 is vital for DNA mismatch repair and its function is diminished by a cancer family mutation
Authors: Wolf Karla , Kosinski Jan , Gibson Toby J , Wesch Nicole , Dötsch Volker , Genuardi Maurizio , Cordisco Emanuela Lucci , Zeuzem Stefan , Brieger Angela , Plotz Guido 
Published: May 2023

Abstract
DNA mismatch repair (MMR) is essential for correction of DNA replication errors. Germline mutations of the human MMR gene MLH1 are the major cause of Lynch syndrome, a heritable cancer predisposition. In the MLH1 protein, a non-conserved, intrinsically disordered region connects two conserved, catalytically active structured domains of MLH1. This region has as yet been regarded as a flexible spacer, and missense alterations in this region have been considered non-pathogenic. However, we have identified and investigated a small motif (ConMot) in this linker which is conserved in eukaryotes. Deletion of the ConMot or scrambling of the motif abolished mismatch repair activity. A mutation from a cancer family within the motif (p.Arg385Pro) also inactivated MMR, suggesting that ConMot alterations can be causative for Lynch syndrome. Intriguingly, the mismatch repair defect of the ConMot variants could be restored by addition of a ConMot peptide containing the deleted sequence. This is the first instance of a DNA mismatch repair defect conferred by a mutation that can be overcome by addition of a small molecule. Based on the experimental data and AlphaFold2 predictions, we suggest that the ConMot may bind close to the C-terminal MLH1-PMS2 endonuclease and modulate its activation during the MMR process.
STellaris: a web server for accurate spatial mapping of single cells based on spatial transcriptomics data
Authors: Li Xiangshang , Xiao Chunfu , Qi Juntian , Xue Weizhen , Xu Xinwei , Mu Zelin , Zhang Jie , Li Chuan-Yun , Ding Wanqiu 
Published: May 2023

Abstract
Single-cell RNA sequencing (scRNA-seq) provides insights into gene expression heterogeneities in diverse cell types underlying homeostasis, development and pathological states. However, the loss of spatial information hinders its applications in deciphering spatially related features, such as cell–cell interactions in a spatial context. Here, we present STellaris (https://spatial.rhesusbase.com), a web server aimed to rapidly assign spatial information to scRNA-seq data based on their transcriptomic similarity with public spatial transcriptomics (ST) data. STellaris is founded on 101 manually curated ST datasets comprising 823 sections across different organs, developmental stages and pathological states from humans and mice. STellaris accepts raw count matrix and cell type annotation of scRNA-seq data as the input, and maps single cells to spatial locations in the tissue architecture of properly matched ST section. Spatially resolved information for intercellular communications, such as spatial distance and ligand-receptor interactions (LRIs), are further characterized between annotated cell types. Moreover, we also expanded the application of STellaris in spatial annotation of multiple regulatory levels with single-cell multiomics data, using the transcriptome as a bridge. STellaris was applied to several case studies to showcase its utility of adding value to the ever-growing scRNA-seq data from a spatial perspective.
Confinement of ionomer for electrocatalytic CO2 reduction reaction via efficient mass transfer pathways
Authors: Du Xiaowei , Zhang Peng , Zhang Gong , Gao Hui , Zhang Lili , Zhang Mengmeng , Wang Tuo , Gong Jinlong 
Published: May 2023

ABSTRACT
Gas diffusion electrodes (GDEs) mediate the transport of reactants, products and electrons for the electrocatalytic CO2 reduction reaction (CO2RR) in membrane electrode assemblies. The random distribution of ionomer, added by the traditional physical mixing method, in the catalyst layer of GDEs affects the transport of ions and CO2. Such a phenomenon results in elevated cell voltage and decaying selectivity at high current densities. This paper describes a pre-confinement method to construct GDEs with homogeneously distributed ionomer, which enhances mass transfer locally at the active centers. The optimized GDE exhibited comparatively low cell voltages and high CO Faradaic efficiencies (FE &gt; 90%) at a wide range of current densities. It can also operate stably for over 220 h with the cell voltage staying almost unchanged. This good performance can be preserved even with diluted CO2 feeds, which is essential for pursuing a high single-pass conversion rate. This study provides a new approach to building efficient mass transfer pathways for ions and reactants in GDEs to promote the electrocatalytic CO2RR for practical applications.
More Risk, More Information: How Passive Ownership Can Improve Informational Efficiency
Authors: Buss Adrian , Sundaresan Savitar 
Published: May 2023

Abstract
We identify a novel economic mechanism through which passive ownership positively affects informational efficiency in the cross-section of firms. Passive investors’ inelastic demand lowers a firm’s cost-of-capital, inducing it to take more risk. The higher cash flow variance, in turn, incentivizes active investors to acquire more precise private information, pushing up price informativeness for firms with high passive ownership. High passive ownership also implies higher stock prices and higher stock-return variances. An increase in the aggregate size of passive investors amplifies these cross-sectional differences. We also document complementarities in firms’ real investment and investors’ information choices that can cause information crashes.
Received May 31, 2020; editorial decision January 4, 2023 by Editor Holger Mueller. Authors have furnished an Internet Appendix, which is available on the Oxford University Press Web site next to the link to the final published paper online
Beyond the symptom: the biology of fatigue
Authors: Raizen David M , Mullington Janet , Anaclet Christelle , Clarke Gerard , Critchley Hugo , Dantzer Robert , Davis Ronald , Drew Kelly L , Fessel Josh , Fuller Patrick M , Gibson Erin M , Harrington Mary , Ian Lipkin W , Klerman Elizabeth B , Klimas Nancy , Komaroff Anthony L , Koroshetz Walter , Krupp Lauren , Kuppuswamy Anna , Lasselin Julie , Lewis Laura D , Magistretti Pierre J , Matos Heidi Y , Miaskowski Christine , Miller Andrew H , Nath Avindra , Nedergaard Maiken , Opp Mark R , Ritchie Marylyn D , Rogulja Dragana , Rolls Asya , Salamone John D , Saper Clifford , Whittemore Vicky , Wylie Glenn , Younger Jarred , Zee Phyllis C , Craig Heller H 
Published: May 2023

Abstract
A workshop titled “Beyond the Symptom: The Biology of Fatigue” was held virtually September 27–28, 2021. It was jointly organized by the Sleep Research Society and the Neurobiology of Fatigue Working Group of the NIH Blueprint Neuroscience Research Program. For access to the presentations and video recordings, see: https://neuroscienceblueprint.nih.gov/about/event/beyond-symptom-biology-fatigue. The goals of this workshop were to bring together clinicians and scientists who use a variety of research approaches to understand fatigue in multiple conditions and to identify key gaps in our understanding of the biology of fatigue. This workshop summary distills key issues discussed in this workshop and provides a list of promising directions for future research on this topic. We do not attempt to provide a comprehensive review of the state of our understanding of fatigue, nor to provide a comprehensive reprise of the many excellent presentations. Rather, our goal is to highlight key advances and to focus on questions and future approaches to answering them.
Propensity of Patient-Derived iPSCs for Retinal Differentiation: Implications for Autologous Cell Replacement
Authors: Cooke Jessica A , Voigt Andrew P , Collingwood Michael A , Stone Nicholas E , Whitmore S Scott , DeLuca Adam P , Burnight Erin R , Anfinson Kristin R , Vakulskas Christopher A , Reutzel Austin J , Daggett Heather T , Andorf Jeaneen L , Stone Edwin M , Mullins Robert F , Tucker Budd A 
Published: May 2023

Abstract
Prior to use, newly generated induced pluripotent stem cells (iPSC) should be thoroughly validated. While excellent validation and release testing assays designed to evaluate potency, genetic integrity, and sterility exist, they do not have the ability to predict cell type-specific differentiation capacity. Selection of iPSC lines that have limited capacity to produce high-quality transplantable cells, places significant strain on valuable clinical manufacturing resources. The purpose of this study was to determine the degree and root cause of variability in retinal differentiation capacity between cGMP-derived patient iPSC lines. In turn, our goal was to develop a release testing assay that could be used to augment the widely used ScoreCard panel. IPSCs were generated from 15 patients (14-76 years old), differentiated into retinal organoids, and scored based on their retinal differentiation capacity. Despite significant differences in retinal differentiation propensity, RNA-sequencing revealed remarkable similarity between patient-derived iPSC lines prior to differentiation. At 7 days of differentiation, significant differences in gene expression could be detected. Ingenuity pathway analysis revealed perturbations in pathways associated with pluripotency and early cell fate commitment. For example, good and poor producers had noticeably different expressions of OCT4 and SOX2 effector genes. QPCR assays targeting genes identified via RNA sequencing were developed and validated in a masked fashion using iPSCs from 8 independent patients. A subset of 14 genes, which include the retinal cell fate markers RAX, LHX2, VSX2, and SIX6 (all elevated in the good producers), were found to be predictive of retinal differentiation propensity.
Transplantation of Human Brain-Derived Ischemia-Induced Multipotent Stem Cells Ameliorates Neurological Dysfunction in Mice After Stroke
Authors: Nakagomi Takayuki , Nakano-Doi Akiko , Kubo Shuji , Sawano Toshinori , Kuramoto Yoji , Yamahara Kenichi , Matsuyama Tomohiro , Takagi Toshinori , Doe Nobutaka , Yoshimura Shinichi 
Published: May 2023

Abstract
We recently demonstrated that injury/ischemia-induced multipotent stem cells (iSCs) develop within post-stroke human brains. Because iSCs are stem cells induced under pathological conditions, such as ischemic stroke, the use of human brain-derived iSCs (h-iSCs) may represent a novel therapy for stroke patients. We performed a preclinical study by transplanting h-iSCs transcranially into post-stroke mouse brains 6 weeks after middle cerebral artery occlusion (MCAO). Compared with PBS-treated controls, h-iSC transplantation significantly improved neurological function. To identify the underlying mechanism, green fluorescent protein (GFP)-labeled h-iSCs were transplanted into post-stroke mouse brains. Immunohistochemistry revealed that GFP+ h-iSCs survived around the ischemic areas and some differentiated into mature neuronal cells. To determine the effect on endogenous neural stem/progenitor cells (NSPCs) by h-iSC transplantation, mCherry-labeled h-iSCs were administered to Nestin-GFP transgenic mice which were subjected to MCAO. As a result, many GFP+ NSPCs were observed around the injured sites compared with controls, indicating that mCherry+ h-iSCs activate GFP+ endogenous NSPCs. In support of these findings, coculture studies revealed that the presence of h-iSCs promotes the proliferation of endogenous NSPCs and increases neurogenesis. In addition, coculture experiments indicated neuronal network formation between h-iSC- and NSPC-derived neurons. These results suggest that h-iSCs exert positive effects on neural regeneration through not only neural replacement by grafted cells but also neurogenesis by activated endogenous NSPCs. Thus, h-iSCs have the potential to be a novel source of cell therapy for stroke patients.
Rehabilitation Interventions for Complex Regional Pain Syndrome: An Overview of Systematic Reviews
Authors: Shafiee Erfan , MacDermid Joy , Packham Tara , Grewal Ruby , Farzad Maryam , Bobos Pavlos , Walton David 
Published: May 2023

Objectives:
An increasing number of systematic reviews have been conducted on various conservative management of complex regional pain syndrome (CRPS) targeting different rehabilitation interventions and objectives. The intent of this article was to summarize and critically appraise the body of evidence on conservative management of the CRPS and to provide an overall picture of the current state of the literature.

Methods:
This study was an overview of systematic reviews on conservative treatments for CRPS. We conducted a literature search from inception to January 2023 in the following databases: Embase, Medline, CINAHL, Google Scholar, Cochrane Library, and Physiotherapy Evidence Database (PEDro). Two independent reviewers conducted study screening, data extraction, and methodological quality assessment (using AMSTAR-2). Qualitative synthesis was the preferred method for reporting the findings of our review. We calculated the corrected covered area index to account for the proportion of overlapping primary studies that were included in multiple reviews.

Result:
We identified 214 articles, and a total of 9 systematic reviews of randomized controlled trials were eligible for inclusion. Pain and disability were the most common outcomes evaluated in the reviews. There were 6 (6/9; 66%) high-quality, 2 (2/9; 22%) moderate-quality, and 1 critically low-quality systematic review (1/9;11%), with the quality of the included trials ranging from very low to high. There was a large overlap across primary studies that were included in the systematic reviews (corrected covered area=23%). The findings of high-quality reviews support the effectiveness of mirror therapy (MT) and graded motor imagery (GMI) programs on pain and disability improvement in CRPS patients. The large effect size was reported for the effectiveness of MT on pain and disability (SMD:1.88 (95% CI: 0.73–3.02) and 1.30 (95% CI: 0.11–2.49), respectively) and the effectiveness of GMI program (GMIP) on pain and disability improvement (SMD: 1.36 (95% CI: 0.75–1.96) and 1.64 (95% CI: 0.53–2.74), respectively).

Discussion:
The evidence is in favor of adopting movement representation techniques, such as MT and GMI programs, for the treatment of pain and disability in patients with CRPS. However, this is based on a small body of primary evidence, and more research is required to generate conclusions. Overall, the evidence is not comprehensive or of sufficient quality to make definitive recommendations about the effectiveness of other rehabilitation interventions in improving pain and disability.
Individualized Positive End-expiratory Pressure Titration Strategies in Superobese Patients Undergoing Laparoscopic Surgery: Prospective and Nonrandomized Crossover Study
Authors: Boesing Christoph , Schaefer Laura , Hammel Marvin , Otto Mirko , Blank Susanne , Pelosi Paolo , Rocco Patricia R. M. , Luecke Thomas , Krebs Joerg 
Published: May 2023

Background
Superobesity and laparoscopic surgery promote negative end-expiratory transpulmonary pressure that causes atelectasis formation and impaired respiratory mechanics. The authors hypothesized that end-expiratory transpulmonary pressure differs between fixed and individualized positive end-expiratory pressure (PEEP) strategies and mediates their effects on respiratory mechanics, end-expiratory lung volume, gas exchange, and hemodynamic parameters in superobese patients.

Methods
In this prospective, nonrandomized crossover study including 40 superobese patients (body mass index 57.3 ± 6.4 kg/m2) undergoing laparoscopic bariatric surgery, PEEP was set according to (1) a fixed level of 8 cm H2O (PEEPEmpirical), (2) the highest respiratory system compliance (PEEPCompliance), or (3) an end-expiratory transpulmonary pressure targeting 0 cm H2O (PEEPTranspul) at different surgical positioning. The primary endpoint was end-expiratory transpulmonary pressure at different surgical positioning; secondary endpoints were respiratory mechanics, end-expiratory lung volume, gas exchange, and hemodynamic parameters.

Results
Individualized PEEPCompliance compared to fixed PEEPEmpirical resulted in higher PEEP (supine, 17.2 ± 2.4 vs. 8.0 ± 0.0 cm H2O; supine with pneumoperitoneum, 21.5 ± 2.5 vs. 8.0 ± 0.0 cm H2O; and beach chair with pneumoperitoneum; 15.8 ± 2.5 vs. 8.0 ± 0.0 cm H2O; P < 0.001 each) and less negative end-expiratory transpulmonary pressure (supine, −2.9 ± 2.0 vs. −10.6 ± 2.6 cm H2O; supine with pneumoperitoneum, −2.9 ± 2.0 vs. −14.1 ± 3.7 cm H2O; and beach chair with pneumoperitoneum, −2.8 ± 2.2 vs. −9.2 ± 3.7 cm H2O; P < 0.001 each). Titrated PEEP, end-expiratory transpulmonary pressure, and lung volume were lower with PEEPCompliance compared to PEEPTranspul (P < 0.001 each). Respiratory system and transpulmonary driving pressure and mechanical power normalized to respiratory system compliance were reduced using PEEPCompliance compared to PEEPTranspul.

Conclusions
In superobese patients undergoing laparoscopic surgery, individualized PEEPCompliance may provide a feasible compromise regarding end-expiratory transpulmonary pressures compared to PEEPEmpirical and PEEPTranspul, because PEEPCompliance with slightly negative end-expiratory transpulmonary pressures improved respiratory mechanics, lung volumes, and oxygenation while preserving cardiac output.

Editor’s Perspective

What We Already Know about This Topic

What This Article Tells Us That Is New
Oral microbiome as a new research-target for supportive care and precision oncology
Authors: Bruno Julia Stephanie , Fregnani Eduardo Rodrigues 
Published: May 2023

Purpose of review
A growing number of studies demonstrate the oral bacterial shift in cancer patients and the enrichment of oral bacteria in distant tumours. During the oncological treatment, opportunistic oral bacteria correlate with oral toxicities. This review focused on the most recent studies to identify which genera are the most mentioned and deserved further investigation.

Recent findings
This review evaluated bacterial changes in patients with head and neck, colorectal, lung and breast cancer. Greater composition of disease-related genera (e.g., Fusobacterium, Porphyromonas, Lactobacillus, Streptococcus, and Parvimonas) are present in the oral cavity of these groups of patients. The tumour specimen characterisation of head and neck, pancreatic and colorectal cancer also describes the presence of oral taxa. No evidence indicates that commensal oral bacteria have protective roles in distant tumours. Regardless, oral care is critical to prevent the growth of oral pathogens and reduce infection foci.

Summary
Recent evidence suggests that oral microbiota is a potential biomarker for oncological clinical outcomes and oral toxicities. Currently, the literature presents a remarkable methodological variety - from the sample collection site to the preference of the data analysis tools. For the oral microbiome to achieve the stage of being used as a clinical tool in the oncological context, more studies are necessary.