bluuebunny/crossref_metadata_2025_split huggingface dataset:
Forecasts for broad-band intensity mapping of the ultraviolet-optical background with CASTOR and SPHEREx
Authors: Scott Bryan R , Upton Sanderbeck Phoebe , Bird Simeon 
Published: February 2022

ABSTRACT
Broad-band tomography statistically extracts the redshift distribution of frequency dependent emission from the cross-correlation of intensity maps with a reference catalog of galaxy tracers. We make forecasts for the performance of future all-sky UV experiments doing broad-band tomography. We consider the Cosmological Advanced Survey Telescope for Optical-UV Research (castor) and the Spectro-Photometer for the History of the Universe, Epoch of Reionization, and Ices Explorer (SPHEREx). The dominant uncertainty is from variability in the photometric zero-point, which scales with limiting magnitude and mirror size. With this scaling and assuming a galaxy number density characteristic of future spectroscopic data sets, we find that castor measures the UV background SED 2–10 times better than existing data. The applicable redshift range will expand from the current z &lt; 1 to z ≈ 0–3 with castor and z = 5–9 with SPHEREx. We show that castor can provide competitive constraints on the EBL monopole to those available from galaxy number counts and direct measurement techniques. At high redshift especially, these results will help understand galaxy formation and reionization. Our modelling code and chains are publicly available.
Bursty star formation during the Cosmic Dawn driven by delayed stellar feedback
Authors: Furlanetto Steven R , Mirocha Jordan 
Published: February 2022

ABSTRACT
In recent years, several analytic models have demonstrated that simple assumptions about halo growth and feedback-regulated star formation can match the (limited) existing observational data on galaxies at $z \gtrsim6$. By extending such models, we demonstrate that imposing a time delay on stellar feedback (as inevitably occurs in the case of supernova explosions) induces burstiness in small galaxies. Although supernova progenitors have short lifetimes (∼5–30 Myr), the delay exceeds the dynamical time of galaxies at such high redshifts. As a result, star formation proceeds unimpeded by feedback for several cycles and ‘overshoots’ the expectations of feedback-regulated star formation models. We show that such overshoot is expected even in atomic cooling haloes, with halo masses up to ∼1010.5 M⊙ at z ≳ 6. However, these burst cycles damp out quickly in massive galaxies, because large haloes are more resistant to feedback so retain a continuous gas supply. Bursts in small galaxies – largely beyond the reach of existing observations – induce a scatter in the luminosity of these haloes (of ∼1 mag) and increase the time-averaged star formation efficiency by up to an order of magnitude. This kind of burstiness can have substantial effects on the earliest phases of star formation and reionization.
The spins of compact objects born from helium stars in binary systems
Authors: Fuller Jim , Lu Wenbin 
Published: February 2022

ABSTRACT
The angular momentum (AM) content of massive stellar cores helps us to determine the natal spin rates of neutron stars and black holes. Asteroseismic measurements of low-mass stars have proven that stellar cores rotate slower than predicted by most prior work, so revised models are necessary. In this work, we apply an updated AM transport model based on the Tayler instability to massive helium stars in close binaries, in which tidal spin-up can greatly increase the star’s AM. Consistent with prior work, these stars can produce highly spinning black holes upon core-collapse if the orbital period is less than $P_{\rm orb} \lesssim \! 1 \, {\rm d}$. For neutron stars, we predict a strong correlation between the pre-explosion mass and the neutron star rotation rate, with millisecond periods ($P_{\rm NS} \lesssim 5 \, {\rm ms}$) only achievable for massive ($M \gtrsim 10 \, M_\odot$) helium stars in tight ($P_{\rm orb} \lesssim 1 \, {\rm d}$) binaries. Finally, we discuss our models in relation to type Ib/c supernovae, superluminous supernove, gamma-ray bursts, and LIGO/Virgo measurements of black hole spins. Our models are roughly consistent with the rates and energetics of these phenomena, with the exception of broad-lined Ic supernovae, whose high rates and ejecta energies are difficult to explain.
Key sequence features of CRISPR RNA for dual-guide CRISPR-Cas9 ribonucleoprotein complexes assembled with wild-type or HiFi Cas9
Authors: Okada Keita , Aoki Kanae , Tabei Teruyuki , Sugio Kota , Imai Katsunori , Bonkohara Yuki , Kamachi Yusuke 
Published: February 2022

Abstract
Specific sequence features of the protospacer and protospacer-adjacent motif (PAM) are critical for efficient cleavage by CRISPR-Cas9, but current knowledge is largely derived from single-guide RNA (sgRNA) systems assessed in cultured cells. In this study, we sought to determine gRNA sequence features of a more native CRISPR-Cas9 ribonucleoprotein (RNP) complex with dual-guide RNAs (dgRNAs) composed of crRNA and tracrRNA, which has been used increasingly in recent CRISPR-Cas9 applications, particularly in zebrafish. Using both wild-type and HiFi SpCas9, we determined on-target cleavage efficiencies of 51 crRNAs in zebrafish embryos by assessing indel occurrence. Statistical analysis of these data identified novel position-specific mononucleotide features relevant to cleavage efficiencies throughout the protospacer sequence that may be unique to CRISPR-Cas9 RNPs pre-assembled with perfectly matched gRNAs. Overall features for wild-type Cas9 resembled those for HiFi Cas9, but specific differences were also observed. Mutational analysis of mononucleotide features confirmed their relevance to cleavage efficiencies. Moreover, the mononucleotide feature-based score, CRISPR-kp, correlated well with efficiencies of gRNAs reported in previous zebrafish RNP injection experiments, as well as independently tested crRNAs only in RNP format, but not with Cas9 mRNA co-injection. These findings will facilitate design of gRNA/crRNAs in genome editing applications, especially when using pre-assembled RNPs.
Tatajuba: exploring the distribution of homopolymer tracts
Authors: de Oliveira Martins Leonardo , Bloomfield Samuel , Stoakes Emily , Grant Andrew J , Page Andrew J , Mather Alison E 
Published: February 2022

Abstract
Length variation of homopolymeric tracts, which induces phase variation, is known to regulate gene expression leading to phenotypic variation in a wide range of bacterial species. There is no specialized bioinformatics software which can, at scale, exhaustively explore and describe these features from sequencing data. Identifying these is non-trivial as sequencing and bioinformatics methods are prone to introducing artefacts when presented with homopolymeric tracts due to the decreased base diversity. We present tatajuba, which can automatically identify potential homopolymeric tracts and help predict their putative phenotypic impact, allowing for rapid investigation. We use it to detect all tracts in two separate datasets, one of Campylobacter jejuni and one of three Bordetella species, and to highlight those tracts that are polymorphic across samples. With this we confirm homopolymer tract variation with phenotypic impact found in previous studies and additionally find many more with potential variability. The software is written in C and is available under the open source licence GNU GPLv3.
nf-core/mag: a best-practice pipeline for metagenome hybrid assembly and binning
Authors: Krakau Sabrina , Straub Daniel , Gourlé Hadrien , Gabernet Gisela , Nahnsen Sven 
Published: February 2022

AbstractThe analysis of shotgun metagenomic data provides valuable insights into microbial communities, while allowing resolution at individual genome level. In absence of complete reference genomes, this requires the reconstruction of metagenome assembled genomes (MAGs) from sequencing reads. We present the nf-core/mag pipeline for metagenome assembly, binning and taxonomic classification. It can optionally combine short and long reads to increase assembly continuity and utilize sample-wise group-information for co-assembly and genome binning. The pipeline is easy to install-all dependencies are provided within containers-portable and reproducible. It is written in Nextflow and developed as part of the nf-core initiative for best-practice pipeline development. All codes are hosted on GitHub under the nf-core organization https://github.com/nf-core/mag and released under the MIT license.
Longitudinal Electronic Cigarette Use Among Patients Recently Diagnosed With Cancer Enrolled in a Smoking Cessation Trial
Authors: Kalkhoran Sara , Streck Joanna M , Kruse Gina R , Rigotti Nancy A , Perez Giselle K , Regan Susan , Ponzani Colin J , Muzikansky Alona , Park Elyse R , Ostroff Jamie S 
Published: February 2022

Abstract

Introduction
Many cancer patients who smoke report concurrent e-cigarette use. Using a mixed-methods approach, we aimed to (1) describe longitudinal e-cigarette use over 6 months after a cancer diagnosis and (2) assess the association between e-cigarette use and smoking cessation, among cancer patients in a smoking cessation trial.

Aims and Methods
Data were from a 2-site randomized controlled trial of Standard (brief counseling) versus Intensive treatment (sustained counseling plus smoking cessation medication) in individuals who smoke recently diagnosed with cancer. Participants (n = 303) reported e-cigarette use at baseline, 3 months, and 6 months. Biochemically-verified past 7-day cigarette abstinence was collected at 6 months. Qualitative interviews at 6 months explored factors related to e-cigarette use.

Results
E-cigarette use prevalence was highest between baseline and 3 months (16%) and declined over time. Participants using e-cigarettes at follow-up had higher baseline cigarette dependence and smoked more heavily. Multivariable analyses found no significant association between follow-up e-cigarette use and 6-month cigarette abstinence. E-cigarette use at follow-up was higher in the Standard versus Intensive treatment group (p = .003 and .001 at 3 and 6 mo, respectively). Smoking cessation and health concerns were primary reasons for using e-cigarettes.

Conclusions
Among individuals who smoke recently diagnosed with cancer and enrolled in a smoking cessation intervention trial, e-cigarette use during trial participation was not associated with smoking abstinence. Individuals who chose to use e-cigarettes were less likely to be receiving intensive cessation support as part of the trial. Further studies are needed to evaluate the association between e-cigarette use and smoking cessation in cancer patients.

Implications
E-cigarette use was not associated with cigarette abstinence at 6 months among adults who smoke recently diagnosed with cancer enrolled in a smoking cessation trial. Individuals with easier access to evidence-based smoking cessation treatment may be less likely to use e-cigarettes.
A pseudotyped lentivirus-based assay to titer SARS-CoV-2 neutralizing antibodies in Mexico
Authors: Cruz-Cardenas José Antonio , Gutierrez-Mayret Michelle , López-Arredondo Alejandra , Castañeda-Delgado Julio Enrique , Rojas-Martinez Augusto , García-Rivas Gerardo , Enciso-Moreno José Antonio , Palomares Laura A. , Brunck Marion E. G. 
Published: February 2022

AbstractMeasuring the neutralizing potential of SARS-CoV-2 antigens-exposed sera informs on effective humoral immunity. This is relevant to 1-monitor levels of protection within an asymptomatic population, 2-evaluate the efficacy of existing and novel vaccines against emerging variants, 3-test prospective therapeutic monoclonal neutralizing antibodies (NAbs) and, overall, to contribute to understand SARS-CoV-2 immunity. However, the gold-standard method to titer NAbs is a functional assay of virus-mediated infection, which requires biosafety level 3 (BSL-3) facilities. As these facilities are insufficient in Latin American countries, including Mexico, scant information has been obtained about NAb in these countries during the COVID-19 pandemic. An alternative solution to acquire NAb information locally is to use non-replicative viral particles that display the SARS-CoV-2 Spike (S) protein on their surface, and deliver a reporter gene into target cells upon transduction. Here we present the development of a NAb-measuring assay based on Nanoluc-mediated luminescence measurements from SARS-CoV-2 S-pseudotyped lentiviral particle-infected cells. The successive steps of development are presented, including lentiviral particles production, target cell selection, and TCID50 determination. We applied the optimized assay in a BSL-2 facility to measure NAbs in 15 pre-pandemic, 18 COVID-19 convalescent and 32 BNT162b2 vaccinated serum samples, which evidenced the assay with 100% sensitivity, 86.6% specificity and 96% accuracy. The assay highlighted heterogeneity in neutralization curves which are relevant in discussing neutralization potency dynamics. Overall, this is the first report of a BSL-2 safe functional assay to measure SARS-CoV-2 in Mexico and a cornerstone methodology necessary to measure NAb with a functional assay in the context of limited resources settings.ImportanceEvaluating effective humoral immunity against SARS-CoV-2 requires a functional assay with infectious virus. Handling the authentic SARS-CoV-2 virus requires specialized facilities that are not readily available in Latin America, including Mexico. Here we produce non-replicative viral particles pseudotyped with the SARS-CoV-2 S protein that are used as safe surrogate viral particles in an optimized BSL-2 ready neutralization assay. The establishment of this assay is critical to allow the evaluation of effective humoral immunity to SARS-CoV-2 post-infection and to monitor the efficacy of existing or novel vaccines against emerging variants in the Mexican population.
Zero-COVID Policies: Melbourne’s 112-Day Hard Lockdown Experiment Harmed Mostly Mothers
Authors: Schurer Stefanie , Atalay Kadir , Glozier Nick , Vera-Toscano Esperanza , Wooden Mark 
Published: February 2022

AbstractLockdowns were used worldwide to mitigate the spread of SARS-CoV-2. We demonstrate that the 112-day hard lockdown in Melbourne, Australia, the longest among OECD jurisdictions, exclusively penalized families with young children. To identify the causal impact of lockdown, we interrogated nationally-representative longitudinal survey data and exploited quasi- experimental variation in Melbourne’s lockdown, one that left other jurisdictions unaffected. Using difference-in-differences estimation, we found that, surprisingly, most vulnerable groups (the young, poor, lonely and those with previous mental health conditions) were left unscathed. However, we found mothers experienced significant, sizable declines in health and work hours, and increases in loneliness, despite feeling safer and being more active. Zero-COVID policies are not as harmful as may have been expected but came at high cost to mothers in society.One-Sentence Summary:Melbourne’s hard lockdown left most vulnerable groups unscathed but led to greater ill- health and loneliness in mothers.
Deep proteome analysis of plasma reveals novel biomarkers of mild cognitive impairment and Alzheimer’s disease: A longitudinal study
Authors: Kaur Gurjeet , Poljak Anne , Sachdev Perminder 
Published: February 2022

AbstractAgeing is the primary risk factor for AD; however, there is a poor understanding of the biological mechanisms by which the ageing process contributes to the development of AD in some individuals, while others progress to advanced age with relatively little AD neuropathology. To halt the progression of AD, the preclinical stage of neurodegeneration (before the onset of clinical symptoms) is anticipated to be the more effective time point for applying potentially disease-modifying interventions in AD. The main objective of this study was to understand the age and disease related proteomic changes are detectable in plasma, based on retrospective analysis of longitudinal data and cross-sectional analyses of clinically diagnosed cases. We conducted an in-depth plasma proteomics analysis using intensive depletion of high-abundant plasma proteins using the Agilent multiple affinity removal liquid chromatography (LC) column-Human 14 (Hu14) followed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS PAGE) technique. In this study, we have begun to address the following questions; (1) differences in plasma proteomic profiles between normal ageing, vs ageing with progress to cognitive decline (MCI) or disease (dementia, probable AD), (2) cross-sectional analysis of baseline data, when all subjects are clinically identified as cognitively normal, provides insight into the preclinical changes which precede subsequent progression to AD and potentially provide early biomarkers, and (3) comparison of plasma at the point of progression to clinically diagnosed onset of cognitive decline or AD, can provide potential plasma biomarkers to facilitate clinical diagnosis. Furthermore, our findings also identified some proteins previously discovered in AD CSF and brain proteomics signatures that could provide clinically meaningful information. We identified differentially expressed proteins which were associated with several biological and molecular processes that may serve as therapeutic targets and fluid biomarkers for the disease.
Inside-out tracking and projection mapping for robot-assisted transcranial magnetic stimulation
Authors: Liu Yihao , Liu Shuya (Joshua) , Sefati Shahriar , Tian Jing , Kheradmand Amir , Armand Mehran 
Published: February 2022

ABSTRACTTranscranial Magnetic Stimulation (TMS) is a neurostimulation technique based on the principle of electromagnetic induction of an electric field in the brain with both research and clinical applications. To produce an optimal neuro-modulatory effect, the TMS coil must be placed on the head and oriented accurately with respect to the region of interest within the brain. A robotic method can enhance the accuracy and facilitate the procedure for TMS coil placement. This work presents two system improvements for robot-assisted TMS (RA-TMS) application. Previous systems have used outside-in tracking method where a stationary external infrared (IR) tracker is used as a reference point to track the head and TMS coil position. This method is prone to losing track of the coil or the head if the IR camera is blocked by the robotic arm during its motion. To address this issue, we implemented an inside-out tracking method by mounting a portable IR camera on the robot end-effector. This method guarantees that the line of sight of the IR camera is not obscured by the robotic arm at any time during its motion. We also integrated a portable projection mapping device (PPMD) into the RA-TMS system to provide visual guidance during TMS application. PPMD can track the head via an IR tracker, and can project a planned contact point of the TMS coil on the head or overlay the underlying brain anatomy in real-time.
Blood Gene Expression Risk Profiles and Interstitial Lung Abnormalities: COPDGene and ECLIPSE cohort studies
Authors: Moll Matthew , Hobbs Brian D. , Menon Aravind , Ghosh Auyon J. , Putman Rachel K. , Hino Takuya , Hata Akinori , Silverman Edwin K. , Quackenbush John , Castaldi Peter J. , Hersh Craig P. , McGeachie Michael J. , Sin Don D. , Tal-Singer Ruth , Nishino Mizuki , Hatabu Hiroto , Hunninghake Gary M. , Cho Michael H. 
Published: February 2022

AbstractRationaleInterstitial lung abnormalities (ILA) are radiologic findings that may progress to idiopathic pulmonary fibrosis (IPF). Blood gene expression profiles can predict IPF mortality, but whether these same genes associate with ILA and ILA outcomes is unknown.ObjectivesTo evaluate if a previously described blood gene expression profile associated with IPF mortality is associated with ILA and all-cause mortality.MethodsIn COPDGene and ECLIPSE study participants with visual scoring of ILA and gene expression data, we evaluated the association of a previously described IPF mortality score with ILA and mortality. We also trained a new ILA score, derived using genes from the IPF score, in a subset of COPDGene. We tested the association with ILA and mortality on the remainder of COPDGene and ECLIPSE.Measurements and Main ResultsIn 1,469 COPDGene (training n=734; testing n=735) and 571 ECLIPSE participants, the IPF score was not associated with ILA or mortality. However, an ILA score derived from IPF score genes was associated with ILA (meta-analysis of test datasets OR 1.4 [95% CI: 1.2-1.6]) and mortality (HR 1.25 [95% CI: 1.12-1.41]). Six of the 11 genes in the ILA score had discordant directions of effects compared to the IPF score. The ILA score partially mediated the effects of age on mortality (11.8% proportion mediated).ConclusionsAn ILA gene expression score, derived from IPF mortality-associated genes, identified genes with concordant and discordant effects on IPF mortality and ILA. These results suggest shared, and unique biologic processes, amongst those with ILA, IPF, aging, and death.Key messagesWhat is the key questionInterstitial lung abnormalities (ILA) are radiologic findings that may progress to idiopathic pulmonary fibrosis (IPF). Do blood gene expression profiles that predict IPF mortality also associate with ILA?What is the bottom lineAn ILA gene expression score, derived from IPF mortality-associated genes, was associated with ILA and all-cause mortality. This score identified genes with concordant and discordant effects on IPF mortality and ILA. Our results suggest shared, and unique biologic processes, amongst those with ILA, IPF, aging, and death.Why read onOur results lend insight into how gene expression profiles and biological pathways associated with IPF prognosis relate to ILA and all-cause mortality
Vaginal microbiome is associated with endometrial cancer grade and histology
Authors: Hakimjavadi Hesamedin , George Sophia , Taub Michael , Dodds Leah , Sanchez-Covarrubias Alex , Huang Marilyn , Pearson Matthew , Slomovitz Brian , Kobetz Erin , Gharaibeh Raad Z. , Sowamber Ramlogan , Pinto Andre , Chamala Srikar , Schlumbrecht Matthew 
Published: February 2022

AbstractBackgroundThe vaginal microbiome is an underexplored environment which may yield insights about endometrial cancer (EC) pathophysiology and serve as an early marker of disease. Our objective was to evaluate the preoperative vaginal microbiome in women undergoing hysterectomy for benign conditions and EC to identify patterns which could segregate benign disease from EC, and to assess if the microbiome distinguishes low-grade (LG) from high-grade (HG) histologies.MethodsVaginal microbiome samples were prospectively collected at the time of hysterectomy, and clinicopathologic data collected. Extracted DNA underwent shotgun metagenomics sequencing. Microbial diversity was calculated using the Shannon Index (α-diversity) and PERMANOVA (β-diversity). Hierarchical clustering was used to describe community state types (CST), which were then compared by microbial diversity and grade. Machine learning was utilized to assess the predictive value of grade and histology based on relative bacterial abundance.Results61 patients participated: 1) benign gynecologic disease (n=11), 2) LG EC (n=30), and 3) HG EC (n=20). 40 (62.5%) were White, 22 (34.3%) were Black, and 37 (57.8%) were Hispanic. Both α- and β-diversity were associated with tumor grade (p□=□0.026 and p□=□0.035, respectively). Four CST were identified that associated with grade of disease (p=0.036). Different histologies demonstrated variation in CST even within tumor grades (p=0.017). Markers at the species level informed models that predicted benign vs cancer (AUC 0.878), HG versus benign (AUC=0.803), and HG versus LG (AUC=0.771) with high accuracy.ConclusionsThe vaginal microbiome segregates benign disease from EC, and is predictive of histology and grade, suggesting it may be an effective tool for screening.