bluuebunny/crossref_metadata_2025_split huggingface dataset:
Radio and X-ray observations of giant pulses from XTE J1810 − 197
Authors: Caleb M , Rajwade K , Desvignes G , Stappers B W , Lyne A G , Weltevrede P , Kramer M , Levin L , Surnis M 
Published: November 2021

ABSTRACT
We present the results of two years of radio and X-ray monitoring of the magnetar XTE J1810 − 197 since the radio re-activation in late 2018. Single pulse analysis of radio observations from the Lovell and MkII telescopes at 1564 MHz and the Effelsberg telescope at 6 GHz has resulted in the detection of a total of 91 giant pulses (GPs) between MJDs 58858 and 59117. These GPs appear to be confined to two specific phase ranges (0.473 ≤ ϕ ≤ 0.502 and 0.541 ≤ ϕ ≤ 0.567). We also observe that the first detection of GP emission corresponds to a minimum in the spin-down rate. Simultaneous radio and X-ray observations were performed on MJDs 59009 and 59096. The 0.5–10 keV X-ray spectrum from NICER is well characterized by a two-component blackbody model that can be interpreted as two hot spots on the polar cap of the neutron star. The blackbody temperature decreases with time, consistent with the previous outburst, while the change in the pulsed fraction does not follow the same trend as was seen in the previous outburst. The radio and X-ray flux of XTE J1810 − 197 are correlated during the initial phase of the outburst (MJD 58450 – MJD 58550) and an increase in the radio flux is observed later that may be correlated to the onset of GPs. We argue that the disparity in the evolution of the current outburst compared to the previous one can be attributed to a change in geometry of the neutron star.
PHI-base in 2022: a multi-species phenotype database for Pathogen–Host Interactions
Authors: Urban Martin , Cuzick Alayne , Seager James , Wood Valerie , Rutherford Kim , Venkatesh Shilpa Yagwakote , Sahu Jashobanta , Iyer S Vijaylakshmi , Khamari Lokanath , De Silva Nishadi , Martinez Manuel Carbajo , Pedro Helder , Yates Andrew D , Hammond-Kosack Kim E 
Published: November 2021

Abstract
Since 2005, the Pathogen–Host Interactions Database (PHI-base) has manually curated experimentally verified pathogenicity, virulence and effector genes from fungal, bacterial and protist pathogens, which infect animal, plant, fish, insect and/or fungal hosts. PHI-base (www.phi-base.org) is devoted to the identification and presentation of phenotype information on pathogenicity and effector genes and their host interactions. Specific gene alterations that did not alter the in host interaction phenotype are also presented. PHI-base is invaluable for comparative analyses and for the discovery of candidate targets in medically and agronomically important species for intervention. Version 4.12 (September 2021) contains 4387 references, and provides information on 8411 genes from 279 pathogens, tested on 228 hosts in 18, 190 interactions. This provides a 24% increase in gene content since Version 4.8 (September 2019). Bacterial and fungal pathogens represent the majority of the interaction data, with a 54:46 split of entries, whilst protists, protozoa, nematodes and insects represent 3.6% of entries. Host species consist of approximately 54% plants and 46% others of medical, veterinary and/or environmental importance. PHI-base data is disseminated to UniProtKB, FungiDB and Ensembl Genomes. PHI-base will migrate to a new gene-centric version (version 5.0) in early 2022. This major development is briefly described.
Reasons for Preoperative Opioid Use Are Associated with Persistent Use following Surgery Among Patients Undergoing Total Knee and Hip Arthroplasty
Authors: Ervin-Sikhondze Brittany A , Moser Stephanie E , Pierce Jennifer , Dickens Joseph R , Lagisetty Pooja A , Urquhart Andrew G , Hallstrom Brian R , Brummett Chad M , McAfee Jenna 
Published: November 2021

Abstract

Objective
Most studies on preoperative opioid use only describe whether or not patients use opioids without characterizing reasons for use. Knowing why patients use opioids can help inform perioperative opioid management. The objective of this study was to explore pain specific reasons for preoperative opioid use prior to total hip and knee arthroplasty (THA and TKA) and their association with persistent use.

Methods
This is a prospective study of 197 patients undergoing THA (n = 99) or TKA (n = 98) enrolled in the Analgesic Outcomes Study between December 2015 and November 2018. All participants reported preoperative opioid use.

Results
Reasons for preoperative opioid use were categorized as surgical site pain only (81 [41.1%]); pain in other body areas only (22 [11.2%]); and combined pain (94 [47.7%]). Compared to patients taking opioids for surgical site pain, those with combined reasons for use had 1.24 (P = .40) and 2.28 (P = .16) greater odds of persistent use at 3 and 6 months postoperatively, adjusting for relevant covariates.

Conclusions
This study provides novel insights into the heterogeneity of reasons for presurgical opioid use in patients undergoing a THA or TKA. One key take away is that not all preoperative opioid use is the same and many patients are taking opioids preoperatively for more than just pain at the surgical site. Combined reasons for use was associated with long-term use, suggesting nonsurgical pain, in part, drives persistent opioid use after surgery. Future directions in perioperative care should focus on pain and non-pain reasons for presurgical opioid use to create tailored postoperative opioid weaning plans.
New magic textures of Majorana neutrinos and the baryon asymmetry of the Universe
Authors: Hyodo Yuta , Kitabayashi Teruyuki 
Published: November 2021

Abstract
The magic texture is one of the successful textures of the flavor neutrino mass matrix for Majorana neutrinos. In this paper, it turns out that two new types of magic textures are also consistent with neutrino oscillation experiments, observation of cosmic microwave background radiation, and neutrinoless double beta decay experiments. The connection between these new magic textures and the leptogenesis scenario for the origin of the baryon asymmetry of the Universe is also discussed.
Pathways and obstacles to social recovery following the elimination of SARS-CoV-2 from Aotearoa New Zealand: a qualitative cross-sectional study
Authors: Long Nicholas J , Appleton Nayantara Sheoran , Davies Sharyn Graham , Deckert Antje , Fehoko Edmond , Holroyd Eleanor , Martin-Anatias Nelly , Sterling Rogena , Trnka Susanna , Tunufa’i Laumua 
Published: November 2021

Abstract

Background
Many public health experts have claimed that elimination strategies of pandemic response allow ‘normal social life’ to resume. Recognizing that social connections and feelings of normality are important for public health, this study examines whether, and for whom, that goal is realized, and identifies obstacles that may inhibit its achievement.

Methods
Thematic analysis of narratives obtained via a qualitative cross-sectional survey of a community cohort in Aotearoa | New Zealand.

Results
A majority of participants reported that life after elimination was ‘more or less the same’ as before the pandemic. Some became more social. Nevertheless, a sizeable minority reported being less social, even many months after elimination. Key obstacles to social recovery included fears that the virus was circulating undetected and the enduring impact of lockdowns upon social relationships, personal habits and mental health. Within our sample, old age and underlying health conditions were both associated with a propensity to become less social.

Conclusions
Elimination strategies can successfully allow ‘normal social life’ to resume. However, this outcome is not guaranteed. People may encounter difficulties with re-establishing social connections in Zero-COVID settings. Measures designed to overcome such obstacles should be an integral part of elimination strategies.
Working Remotely and the Supply-Side Impact of COVID-19
Authors: Papanikolaou Dimitris , Schmidt Lawrence D W 
Published: November 2021

Abstract
We analyze the supply-side disruptions associated with COVID-19. We find that sectors in which a higher fraction of the workforce is not able to work remotely experienced greater declines in employment and expected revenue growth, worse stock market performance, and higher likelihood of default. The stock market overweights low-exposure industries. Thus, our findings cast light on the disconnect between stock market indices and aggregate outcomes. We combine these ex ante heterogeneous industry exposures with daily financial market data to create a stock return portfolio that tracks news about the supply-side disruptions resulting from the pandemic. (JEL G12, D22, H25, J20, E00)
Examining Parent Adverse Childhood Experiences as a Distal Risk Factor in Pediatric Chronic Pain
Authors: Beveridge Jaimie K. , Yeates Keith O. , Madigan Sheri , Stone Amanda L. , Wilson Anna C. , Sumpton Janice E. , Salberg Sabrina , Mychasiuk Richelle , Noel Melanie 
Published: November 2021

Objectives:
Adverse childhood experiences (ACEs; ie, exposure to abuse, neglect, household dysfunction in childhood) are associated with poor mental and physical health outcomes across the lifespan. Emerging research suggests parent ACEs also confer risk for poor child outcomes. The relation between parent ACEs and child pain in youth with chronic pain has not yet been examined. The aim of the current longitudinal study was to examine the associations among parent ACEs, parent health, and child pain, in a clinical sample of youth with chronic pain.

Methods:
In total, 192 youth (75.5% female, 10 to 18 y old) and one of their parents (92.2% female) were recruited from tertiary pediatric chronic pain clinics in Canada. At baseline, parents completed self-report measures of ACEs, chronic pain status, anxiety and depressive symptoms, and posttraumatic stress disorder symptoms. At a 3-month follow-up, youth completed self-report measures of pain intensity and pain interference.

Results:
Regression and mediation analyses revealed that parent ACEs significantly predicted parent chronic pain status and depressive symptoms, but not parent anxiety or posttraumatic stress disorder symptoms. Moreover, parent ACEs were not significantly related to youth pain, either directly or indirectly through parent health variables.

Discussion:
Findings suggest that an intergenerational cascade from parent ACEs to parent health to child pain was not present in the current sample. Further research that examines the role of parent ACEs in the development of child chronic pain, as well as other risk and resiliency factors that may mediate or moderate the association between parent ACEs and child chronic pain, is needed.
Acute Corneal Epithelial Rejection of LR-CLAL After SARS-CoV-2 Vaccination
Authors: de la Presa Martin , Govil Amit , Chamberlain Winston D. , Holland Edward J. 
Published: November 2021

Purpose:
The purpose of this study was to report a case of acute corneal epithelial rejection of living-related conjunctival limbal allograft (LR-CLAL) after severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccination.

Observations:
A 27-year-old woman developed acute epithelial rejection of LR-CLAL 2 weeks after receiving the SARS-CoV-2 vaccine. She received the LR-CLAL transplant 4 years and 7 months previously and had a stable clinical course with no history of rejection. She had an ABO blood group and human leukocyte antigen compatible donor, no systemic comorbidities, and no rejection risk factors.

Conclusions:
The novel SARS-CoV-2 vaccine upregulates the immune system to produce an adaptive immune response. The SARS-CoV-2 vaccine may potentially be associated with increased risk of rejection in those with ocular surface transplants.
Measuring G Protein Activation with Spectrally Resolved Fluorescence Fluctuation Spectroscopy
Authors: Foust Daniel J. , Piston David W. 
Published: November 2021

AbstractG protein-coupled receptor signaling has been posited to occur through either collision coupling or pre-assembled complexes with G protein transducers. To investigate the dynamics of G protein signaling, we introduce fluorescence covariance matrix analysis (FCMA), a novel implementation of fluorescence cumulant analysis applied to spectrally resolved fluorescence images. We labeled the GPCR, Gα, and Gβγ units with distinct fluorescent protein labels and we applied FCMA to measure directly the complex formation during stimulation of dopamine and adrenergic receptors. To determine the prevalence of hetero-oligomers, we compared the GPCR data to those from control samples expressing three fluorescent protein labels with known stoichiometries. Interactions between Gα and Gβγ subunits determined by FCMA were sensitive to stimulation with GPCR ligands. However, GPCR/G protein interactions were too weak to be distinguished from background. These findings support a collision coupling mechanism rather than pre-assembled complexes for the two GPCRs studied.
The effect of the preceding masking noise on monaural and binaural release from masking
Authors: Kim Hyojin , Ratkute Viktorija , Epp Bastian 
Published: November 2021

ABSTRACTAuditory stream segregation can be facilitated when the maskers share coherent amplitude modulations or by utilizing spatial cues. The effectiveness of each cue can be quantified as a decrease in masked thresholds, termed as comodulated masking release (CMR) and binaural masking level difference (BMLD). Prolonged exposure to the masker can influence following target segregation. However, the collective impact preceding noise on target segregation in the presence of comodulation and interaural phase difference (IPD) cues is unclear. Stimuli were used to induce noise streams by altering the duration and temporal coherence of the envelope of the preceding masker. The effect on following target detection with CMR and BMLD induced by an IPD of the target tone was investigated. The results indicate that the effect of the preceding stream formation on CMR operates on different time scales, extending beyond 200 ms, depending on the spectrotemporal characteristics of the maskers. However, the effect on IPD-induced BMLD was not significant across time. Under the simplifying assumption that peripheral processing operates on shorter time scales than cortical processing, the results of the present study may provide insights into auditory signal processing in the presence of beneficial cues for target stream segregation.
Common resistance mechanisms are deployed by plants against sap-feeding herbivorous insects: insights from a meta-analysis and systematic review
Authors: Leybourne DJ , Aradottir GI 
Published: November 2021

AbstractSap-feeding insects cause significant yield losses to the world’s crops, these insects feed using syringe-like mouthparts and electrophysiology can be used to compare feeding behaviour on susceptible and resistant plants to identify the mechanistic processes behind resistant phenotypes. Data extracted from 129 studies, comprising 41 insect species across eight insect taxa and 12 host-plant families representing over 30 species, demonstrates that mechanisms deployed by resistant plants have common consequences on the feeding behaviour of diverse insect groups. We show that insects feeding on resistant plants take longer to establish a feeding site and have their feeding duration suppressed two-fold compared with insects feeding on susceptible plants. Our results reveal that the underlying traits contributing towards resistant phenotypes are conserved across plant families, deployed against taxonomically diverse insect groups, and that the underlying resistance mechanisms are conserved. These findings provide new insight that will be beneficial when developing future crop varieties.
Open-ended molecular recording of sequential cellular events into DNA
Authors: Loveless Theresa B. , Carlson Courtney K. , Dentzel Helmy Catalina A. , Hu Vincent J. , Ross Sara K. , Demelo Matt C. , Murtaza Ali , Liang Guohao , Ficht Michelle , Singhai Arushi , Pajoh-Casco Marcello J. , Liu Chang C. 
Published: November 2021

Genetically encoded DNA recorders noninvasively convert transient biological events into durable mutations in a cell’s genome, allowing for the later reconstruction of cellular experiences using high-throughput DNA sequencing1. Existing DNA recorders have achieved high-information recording2–15, durable recording3,5–10,13,15–19, multiplexed recording of several cellular signals5–8,19,20, and temporally resolved signal recording5–8,19,20, but not all at the same time in mammalian cells. We present a DNA recorder called peCHYRON (prime editing21Cell HistorY Recording by Ordered iNsertion) that does. In peCHYRON, mammalian cells are engineered to express prime editor and a collection of prime editing guide RNAs21(pegRNAs) that facilitate iterative rounds of prime editing. In each round of editing, prime editor inserts a variable triplet DNA sequence alongside a constant propagator sequence that deactivates the previous and activates the next step of insertion. Editing can continue indefinitely because each insertion adds the complete sequence needed to initiate the next step. Because only one active target site is present at any given time, insertions accumulate sequentially, in a unidirectional order. Thus, temporal information is preserved in the order of insertions. Durability is achieved through the use of a prime editor that only nicks a single DNA strand, effectively avoiding deletion mutations that could otherwise corrupt the information stored at the recording locus. High-information content is established by co-expressing a variety of pegRNAs, each harboring unique triplet DNA sequences. We demonstrate that constitutive expression of such a library of pegRNAs generates insertion patterns that support straightforward reconstruction of cell lineage relationships. In an alternative pegRNA expression scheme, we also achieve multiplexed recording by manually pulsing expression of different pegRNAs, then reconstructing pulse sequences from the peCHYRON records. Additionally, we coupled the expression of specific pegRNAs to specific biological stimuli, which allowed temporally resolved, multiplexed recording of chemical exposures in populations of mammalian cells.Graphical abstract
A framework for detecting noncoding rare variant associations of large-scale whole-genome sequencing studies
Authors: Li Zilin , Li Xihao , Zhou Hufeng , Gaynor Sheila M. , Selvaraj Margaret S. , Arapoglou Theodore , Quick Corbin , Liu Yaowu , Chen Han , Sun Ryan , Dey Rounak , Arnett Donna K. , Bielak Lawrence F. , Bis Joshua C. , Blackwell Thomas W. , Blangero John , Boerwinkle Eric , Bowden Donald W. , Brody Jennifer A. , Cade Brian E. , Conomos Matthew P. , Correa Adolfo , Cupples L. Adrienne , Curran Joanne E. , de Vries Paul S. , Duggirala Ravindranath , Freedman Barry I. , Göring Harald H. H. , Guo Xiuqing , Kalyani Rita R. , Kooperberg Charles , Kral Brian G. , Lange Leslie A. , Manichaikul Ani , Martin Lisa W. , Mitchell Braxton D. , Montasser May E. , Morrison Alanna C. , Naseri Take , O’Connell Jeffrey R. , Palmer Nicholette D. , Peyser Patricia A. , Psaty Bruce M. , Raffield Laura M. , Redline Susan , Reiner Alexander P. , Reupena Muagututi‘a Sefuiva , Rice Kenneth M. , Rich Stephen S. , Smith Jennifer A. , Taylor Kent D. , Vasan Ramachandran S. , Weeks Daniel E. , Wilson James G. , Yanek Lisa R. , Zhao Wei ,   NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium,   TOPMed Lipids Working Group, Rotter Jerome I. , Willer Christen J. , Natarajan Pradeep , Peloso Gina M. , Lin Xihong 
Published: November 2021

AbstractLarge-scale whole-genome sequencing studies have enabled analysis of noncoding rare variants’ (RVs) associations with complex human traits. Variant set analysis is a powerful approach to study RV association, and a key component of it is constructing RV sets for analysis. However, existing methods have limited ability to define analysis units in the noncoding genome. Furthermore, there is a lack of robust pipelines for comprehensive and scalable noncoding RV association analysis. Here we propose a computationally-efficient noncoding RV association-detection framework that uses STAAR (variant-set test for association using annotation information) to group noncoding variants in gene-centric analysis based on functional categories. We also propose SCANG (scan the genome)-STAAR, which uses dynamic window sizes and incorporates multiple functional annotations, in a non-gene-centric analysis. We furthermore develop STAARpipeline to perform flexible noncoding RV association analysis, including gene-centric analysis as well as fixed-window-based and dynamic-window-based non-gene-centric analysis. We apply STAARpipeline to identify noncoding RV sets associated with four quantitative lipid traits in 21,015 discovery samples from the Trans-Omics for Precision Medicine (TOPMed) program and replicate several noncoding RV associations in an additional 9,123 TOPMed samples.
Ancient mitogenomes unravel massive genetic diversity loss during near extinction of Alpine ibex
Authors: Robin Mathieu , Ferrari Giada , Akgül Gülfirde , von Seth Johanna , Schuenemann Verena J. , Dalén Love , Grossen Christine 
Published: November 2021

AbstractPopulation bottlenecks can have dramatic consequences for the health and long-term survival of a species. A recent bottleneck event can also largely obscure our understanding of standing variation prior to the contraction. Historic population sizes can be modeled based on extant genomics, however uncertainty increases with the severity of the bottleneck. Integrating ancient genomes provides a powerful complement to retrace the evolution of genetic diversity through population fluctuations. Here, we recover 15 high-quality mitogenomes of the once nearly extinct Alpine ibex spanning 8601 ± 33 BP to 1919 CE and combine these with 60 published modern genomes. Coalescent demography simulations based on modern genomes indicate population fluctuations matching major climatic change over the past millennia. Using ancient genomes, we show that mitochondrial haplotype diversity has been reduced to a fifth of the pre-bottleneck diversity with several highly differentiated mitochondrial lineages having co-existed historically. The main collapse of mitochondrial diversity coincided with human settlement expansions in the Middle Ages. The near extinction severely reduced the mitochondrial diversity. After recovery, one lineage was spread and nearly fixed across the Alps due to recolonization efforts. Contrary to expectations, we show that a second ancestral mitochondrial lineage has survived in an isolated population further south. Our study highlights that a combined approach integrating genomic data of ancient, historic and extant populations unravels major long-term population fluctuations.
Interneuron Control of C. elegans Developmental Decision-making
Authors: Chai Cynthia M. , Torkashvand Mahdi , Seyedolmohadesin Maedeh , Park Heenam , Venkatachalam Vivek , Sternberg Paul W. 
Published: November 2021

SUMMARYAnimals integrate external stimuli to shape their physiological responses throughout development. In adverse environments, Caenorhabditis elegans larvae can enter a stress-resistant diapause state with arrested metabolism and reproductive physiology. Amphid sensory neurons feed into both rapid chemotactic and short-term foraging mode decisions, mediated by amphid and premotor interneurons, as well as the long-term diapause decision. We identify amphid interneurons that integrate pheromone cues and propagate this information via a neuropeptidergic pathways to influence larval developmental fate, bypassing the pre-motor system. AIA interneuron-derived FLP-2 neuropeptide signaling promotes reproductive growth and AIA activity is suppressed by pheromone. FLP-2 acts antagonistically to the insulin-like INS-1. FLP-2’s growth promoting effects are inhibited by upstream metabotropic glutamatergic signaling and mediated by the broadly-expressed neuropeptide receptor NPR-30. Conversely, the AIB interneurons and their neuropeptide receptor NPR-9/GALR2 promote diapause entry. These neuropeptidergic outputs allow reuse of parts of a sensory system for a decision with a distinct timescale.