bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wide binary pulsars from electron-capture supernovae
Authors: Stevenson Simon , Willcox Reinhold , Vigna-Gómez Alejandro , Broekgaarden Floor 
Published: May 2022

ABSTRACT
Neutron stars receive velocity kicks at birth in supernovae. Those formed in electron-capture supernovae from superasymptotic giant branch stars – the lowest mass stars to end their lives in supernovae – may receive significantly lower kicks than typical neutron stars. Given that many massive stars are members of wide binaries, this suggests the existence of a population of low-mass (1.25 &lt; Mpsr/M⊙ &lt; 1.3), wide (Porb ≳ 104 d), eccentric (e ∼ 0.7), unrecycled (Pspin ∼ 1 s) binary pulsars. The formation rate of such binaries is sensitive to the mass range of (effectively) single stars leading to electron capture supernovae, the amount of mass lost prior to the supernova, and the magnitude of any natal kick imparted on the neutron star. We estimate that one such binary pulsar should be observable in the Milky Way for every 10 000 isolated pulsars, assuming that the width of the mass range of single stars leading to electron-capture supernovae is ≲0.2 M⊙, and that neutron stars formed in electron-capture supernovae receive typical kicks less than 10 km s−1. We have searched the catalogue of observed binary pulsars, but find no convincing candidates that could be formed through this channel, consistent with this low predicted rate. Future observations with the Square Kilometre Array may detect this rare sub-class of binary pulsar and provide strong constraints on the properties of electron-capture supernovae and their progenitors.
LyMAS reloaded: improving the predictions of the large-scale Lyman-α forest statistics from dark matter density and velocity fields
Authors: Peirani S , Prunet S , Colombi S , Pichon C , Weinberg D H , Laigle C , Lavaux G , Dubois Y , Devriendt J 
Published: May 2022

ABSTRACT
We present LyMAS2, an improved version of the ‘Lyman-α Mass Association Scheme’ aiming at predicting the large-scale 3D clustering statistics of the Lyman-α forest (Ly α) from moderate-resolution simulations of the dark matter (DM) distribution, with prior calibrations from high-resolution hydrodynamical simulations of smaller volumes. In this study, calibrations are derived from the Horizon-AGN suite simulations, (100 Mpc h)−3 comoving volume, using Wiener filtering, combining information from DM density and velocity fields (i.e. velocity dispersion, vorticity, line-of-sight 1D-divergence and 3D-divergence). All new predictions have been done at z = 2.5 in redshift space, while considering the spectral resolution of the SDSS-III BOSS Survey and different DM smoothing (0.3, 0.5, and 1.0 Mpc h−1 comoving). We have tried different combinations of DM fields and found that LyMAS2, applied to the Horizon-noAGN DM fields, significantly improves the predictions of the Ly α 3D clustering statistics, especially when the DM overdensity is associated with the velocity dispersion or the vorticity fields. Compared to the hydrodynamical simulation trends, the two-point correlation functions of pseudo-spectra generated with LyMAS2 can be recovered with relative differences of ∼5 per cent even for high angles, the flux 1D power spectrum (along the light of sight) with ∼2 per cent and the flux 1D probability distribution function exactly. Finally, we have produced several large mock BOSS spectra (1.0 and 1.5 Gpc h−1) expected to lead to much more reliable and accurate theoretical predictions.
Study on the magnetic field strength of NGC 300 ULX1
Authors: Pan Y Y , Li Z S , Zhang C M , Zhong J X 
Published: May 2022

ABSTRACT
NGC 300 ULX1 is a pulsating ultraluminous X-ray source (PULX) with the longest spin period of $P\simeq 31.6\, \rm s$ and a high spin-up rate of $\dot{P}\simeq -5.56\times 10^{-7}\, \rm s\, s^{-1}$ that is ever seen in the confirmed PULXs. In this paper, the inferred magnetic field of NGC 300 ULX1 is $\sim 3.0\times 10^{14}\, \rm G$ using the recent observed parameters after its first detection of pulsations. According to the evolved simulation of the magnetic field and the spin period, it will become a recycled pulsar or a millisecond pulsar under the conditions of the companion mass and the accretion rate limitation. We suggest that NGC 300 ULX1 is an accreting magnetar accounting for its super Eddington luminosity. We also propose that there might be other accreting magnetars in the confirmed PULXs. Such PULXs will be helpful for understanding the magnetar evolution and the millisecond pulsar formation whose magnetic field is stronger than $\sim 10^{9}\, \rm G$.
A bioinformatics pipeline for estimating mitochondrial DNA copy number and heteroplasmy levels from whole genome sequencing data
Authors: Battle Stephanie L , Puiu Daniela ,   TOPMed mtDNA Working Group, Verlouw Joost , Broer Linda , Boerwinkle Eric , Taylor Kent D , Rotter Jerome I , Rich Stephan S , Grove Megan L , Pankratz Nathan , Fetterman Jessica L , Liu Chunyu , Arking Dan E 
Published: May 2022

Abstract
Mitochondrial diseases are a heterogeneous group of disorders that can be caused by mutations in the nuclear or mitochondrial genome. Mitochondrial DNA (mtDNA) variants may exist in a state of heteroplasmy, where a percentage of DNA molecules harbor a variant, or homoplasmy, where all DNA molecules have the same variant. The relative quantity of mtDNA in a cell, or copy number (mtDNA-CN), is associated with mitochondrial function, human disease, and mortality. To facilitate accurate identification of heteroplasmy and quantify mtDNA-CN, we built a bioinformatics pipeline that takes whole genome sequencing data and outputs mitochondrial variants, and mtDNA-CN. We incorporate variant annotations to facilitate determination of variant significance. Our pipeline yields uniform coverage by remapping to a circularized chrM and by recovering reads falsely mapped to nuclear-encoded mitochondrial sequences. Notably, we construct a consensus chrM sequence for each sample and recall heteroplasmy against the sample's unique mitochondrial genome. We observe an approximately 3-fold increased association with age for heteroplasmic variants in non-homopolymer regions and, are better able to capture genetic variation in the D-loop of chrM compared to existing software. Our bioinformatics pipeline more accurately captures features of mitochondrial genetics than existing pipelines that are important in understanding how mitochondrial dysfunction contributes to disease.
Pervasive sequence-level variation in the transcriptome of Plasmodium falciparum
Authors: Dave Bruhad , Kanyal Abhishek , Mamatharani D V , Karmodiya Krishanpal 
Published: May 2022

Abstract
Single-nucleotide variations (SNVs) in RNA, arising from co- and post-transcriptional phenomena including transcription errors and RNA-editing, are well studied in a range of organisms. In the malaria parasite Plasmodium falciparum, stage-specific and non-specific gene-expression variations accompany the parasite's array of developmental and morphological phenotypes over the course of its complex life cycle. However, the extent, rate and effect of sequence-level variation in the parasite's transcriptome are unknown. Here, we report the presence of pervasive, non-specific SNVs in the P. falciparum transcriptome. SNV rates for a gene were correlated to gene length (r$ \approx$0.65–0.7) but not to the AT-content of that gene. Global SNV rates for the P. falciparum lines we used, and for publicly available P. vivax and P. falciparum clinical isolate datasets, were of the order of 10–3 per base, ∼10× higher than rates we calculated for bacterial datasets. These variations may reflect an intrinsic transcriptional error rate in the parasite, and RNA editing may be responsible for a subset of them. This seemingly characteristic property of the parasite may have implications for clinical outcomes and the basic biology and evolution of P. falciparum and parasite biology more broadly. We anticipate that our study will prompt further investigations into the exact sources, consequences and possible adaptive roles of these SNVs.
Accuracy of multiple sequence alignment methods in the reconstruction of transposable element families
Authors: Hubley Robert , Wheeler Travis J , Smit Arian F A 
Published: May 2022

Abstract
The construction of a high-quality multiple sequence alignment (MSA) from copies of a transposable element (TE) is a critical step in the characterization of a new TE family. Most studies of MSA accuracy have been conducted on protein or RNA sequence families, where structural features and strong signals of selection may assist with alignment. Less attention has been given to the quality of sequence alignments involving neutrally evolving DNA sequences such as those resulting from TE replication. Transposable element sequences are challenging to align due to their wide divergence ranges, fragmentation, and predominantly-neutral mutation patterns. To gain insight into the effects of these properties on MSA accuracy, we developed a simulator of TE sequence evolution, and used it to generate a benchmark with which we evaluated the MSA predictions produced by several popular aligners, along with Refiner, a method we developed in the context of our RepeatModeler software. We find that MAFFT and Refiner generally outperform other aligners for low to medium divergence simulated sequences, while Refiner is uniquely effective when tasked with aligning high-divergent and fragmented instances of a family.
Discharge planning of the preterm infant
Authors: Anderson Nicole , Narvey Michael 
Published: May 2022

Abstract
“When will my baby come home?” is one of the most common questions asked by parents of preterm infants admitted to the neonatal intensive care unit (NICU). While the hospital course varies based on the gestational age at birth and the attainment of “physiological maturity,” the aim of this statement is to provide guidance for the safe discharge of infants born before 37 weeks. The discharge process should start at the time of admission to NICU, and with a plan for assessing physiological markers including thermoregulation, control of breathing, respiratory stability, and adequate weight gain as an indication of feeding skills. Importantly, the infant’s family unit is a crucial part of the care team and their involvement in the NICU will promote confidence, decrease anxiety, increase resilience, and help ensure a safe discharge environment.
Low Nitrogen Enhances Apoplastic Phloem Loading and Improves the Translocation of Photoassimilates in Rice Leaves and Stems
Authors: Li Guohui , Zhou Chiyan , Yang Zijun , Zhang Chenhui , Dai Qigen , Huo Zhongyang , Xu Ke 
Published: May 2022

Abstract
The grain filling of rice depends on photoassimilates from leaves and stems. Phloem loading is the first crucial step for the transportation of sucrose to grains. However, phloem loading mechanisms in rice leaves and stems and their response to nitrogen (N) remain unclear. Here, using a combination of electron microscopy, transportation of a phloem tracer and 13C labeling, phloem loading was studied in rice leaves and stems. The results showed that the sieve element–companion cell complex lacked a symplastic connection with surrounding parenchyma cells in leaves and stems. The genes expression and protein levels of sucrose transporter (SUTs) and sugars will eventually be exported transporters (SWEETs) were detected in the vascular bundle of leaves and stems. A decrease in the 13C isotope remobilization from leaves to stems and panicles following treatment with p-chloromercuribenzenesulfonic acid indicated that rice leaves and stems actively transport sucrose into the phloem. Under low-N (LN) treatment, the activities of α-amylase, β-amylase and sucrose phosphate synthase (SPS) in stems and activity of SPS in leaves increased; genes expression and protein levels of SUTs and SWEETs in leaves and stems increased; the 13C isotope reallocation in panicles increased. These indicated that LN enhanced apoplastic phloem loading in stems and leaves. This improved the translocation of photoassimilates and consequently increased grain filling percentage, grain weight and harvest index. This study provides evidence that rice leaves and stems utilize an apoplastic loading strategy and respond to N stimuli by regulating the genes expression and protein levels of SUTs and SWEETs.
MOR1/MAP215 acts synergistically with katanin to control cell division and anisotropic cell elongation in Arabidopsis
Authors: Chen Yu , Liu Xiayan , Zhang Wenjing , Li Jie , Liu Haofeng , Yang Lan , Lei Pei , Zhang Hongchang , Yu Fei 
Published: May 2022

Abstract
The MAP215 family of microtubule (MT) polymerase/nucleation factors and the MT severing enzyme katanin are widely conserved MT-associated proteins (MAPs) across the plant and animal kingdoms. However, how these two essential MAPs coordinate to regulate plant MT dynamics and development remains unknown. Here, we identified novel hypomorphic alleles of MICROTUBULE ORGANIZATION 1 (MOR1), encoding the Arabidopsis thaliana homolog of MAP215, in genetic screens for mutants oversensitive to the MT-destabilizing drug propyzamide. Live imaging in planta revealed that MOR1-green fluorescent protein predominantly tracks the plus-ends of cortical MTs (cMTs) in interphase cells and labels preprophase band, spindle and phragmoplast MT arrays in dividing cells. Remarkably, MOR1 and KATANIN 1 (KTN1), the p60 subunit of Arabidopsis katanin, act synergistically to control the proper formation of plant-specific MT arrays, and consequently, cell division and anisotropic cell expansion. Moreover, MOR1 physically interacts with KTN1 and promotes KTN1-mediated severing of cMTs. Our work establishes the Arabidopsis MOR1–KTN1 interaction as a central functional node dictating MT dynamics and plant growth and development.
MAMP-elicited changes in amino acid transport activity contribute to restricting bacterial growth
Authors: Zhang Xiaomu , Khadka Pramod , Puchalski Patryk , Leehan Joss D , Rossi Franco R , Okumoto Sakiko , Pilot Guillaume , Danna Cristian H 
Published: May 2022

Abstract
Plants live under the constant challenge of microbes that probe the environment in search of potential hosts. Plant cells perceive microbe-associated molecular patterns (MAMPs) from incoming microbes and activate defense responses that suppress attempted infections. Despite the substantial progress made in understanding MAMP-triggered signaling pathways, the downstream mechanisms that suppress bacterial growth and disease remain poorly understood. Here, we uncover how MAMP perception in Arabidopsis (Arabidopsis thaliana) elicits dynamic changes in extracellular concentrations of free L-amino acids (AA). Within the first 3 h of MAMP perception, a fast and transient inhibition of AA uptake produces a transient increase in extracellular AA concentrations. Within 4 and 12 h of MAMP perception, a sustained enhanced uptake activity decreases the extracellular concentrations of AA. Gene expression analysis showed that salicylic acid-mediated signaling contributes to inducing the expression of AA/H+ symporters responsible for the MAMP-induced enhanced uptake. A screening of loss-of-function mutants identified the AA/H+ symporter lysin/histidine transporter-1 as an important contributor to MAMP-induced enhanced uptake of AA. Infection assays in lht1-1 seedlings revealed that high concentrations of extracellular AA promote bacterial growth in the absence of induced defense elicitation but contribute to suppressing bacterial growth upon MAMP perception. Overall, the data presented in this study reveal a mechanistic connection between MAMP-induced plant defense and suppression of bacterial growth through the modulation of AA transport activity.
Selenium-binding Protein 1 (SBD1): A stress response regulator in Chlamydomonas reinhardtii
Authors: Koletti Aikaterini , Dervisi Irene , Kalloniati Chrysanthi , Zografaki Maria-Eleftheria , Rennenberg Heinz , Roussis Andreas , Flemetakis Emmanouil 
Published: May 2022

Abstract
Selenium-binding proteins (SBPs) represent a ubiquitous protein family implicated in various environmental stress responses, although the exact molecular and physiological role of the SBP family remains elusive. In this work, we report the identification and characterization of CrSBD1, an SBP homolog from the model microalgae Chlamydomonas reinhardtii. Growth analysis of the C. reinhardtii sbd1 mutant strain revealed that the absence of a functional CrSBD1 resulted in increased growth under mild oxidative stress conditions, although cell viability rapidly declined at higher hydrogen peroxide (H2O2) concentrations. Furthermore, a combined global transcriptomic and metabolomic analysis indicated that the sbd1 mutant exhibited a dramatic quenching of the molecular and biochemical responses upon H2O2-induced oxidative stress when compared to the wild-type. Our results indicate that CrSBD1 represents a cell regulator, which is involved in the modulation of C. reinhardtii early responses to oxidative stress. We assert that CrSBD1 acts as a member of an extensive and conserved protein–protein interaction network including Fructose-bisphosphate aldolase 3, Cysteine endopeptidase 2, and Glutaredoxin 6 proteins, as indicated by yeast two-hybrid assays.
Perspective-taking is associated with increased discriminability of affective states in the ventromedial prefrontal cortex
Authors: Vaccaro Anthony G , Heydari Panthea , Christov-Moore Leonardo , Damasio Antonio , Kaplan Jonas T 
Published: May 2022

AbstractRecent work using multivariate-pattern analysis (MVPA) on functional magnetic resonance imaging (fMRI) data has found that distinct affective states produce correspondingly distinct patterns of neural activity in the cerebral cortex. However, it is unclear whether individual differences in the distinctiveness of neural patterns evoked by affective stimuli underlie empathic abilities such as perspective-taking (PT). Accordingly, we examined whether we could predict PT tendency from the classification of blood-oxygen-level-dependent (BOLD) fMRI activation patterns while participants (n = 57) imagined themselves in affectively charged scenarios. We used an MVPA searchlight analysis to map where in the brain activity patterns permitted the classification of four affective states: happiness, sadness, fear and disgust. Classification accuracy was significantly above chance levels in most of the prefrontal cortex and in the posterior medial cortices. Furthermore, participants’ self-reported PT was positively associated with classification accuracy in the ventromedial prefrontal cortex and insula. This finding has implications for understanding affective processing in the prefrontal cortex and for interpreting the cognitive significance of classifiable affective brain states. Our multivariate approach suggests that PT ability may rely on the grain of internally simulated affective representations rather than simply the global strength.
We Have Buried Our Tomahawks Very Deep in the Ground and in the Sky: Rock River Ho-Chunk Peacekeeping in the 1832 “Black Hawk War”
Authors: Tronnes Libby 
Published: May 2022

Abstract
In Spring 1832, a Ho-Chunk delegation attempted to resolve a refugee crisis that threatened to bring war with the Americans into their lands. The return migration of a removed multiethnic band made up primarily of Sauk and Fox families into northern Illinois precipitated a conflict known as the Black Hawk War. When direct diplomacy failed, Rock River Ho-Chunks attempted to spare the lives of their refugee kin while also protecting their cornfields from American invaders. The federal government used the crisis to force a land cession and removal treaty. Nineteenth-century American observers, and historians ever since, have generally overlooked the imaginative peacekeeping strategies deployed by the Ho-Chunk people, schemes designed to prevent troops from finding the refugees and from destroying raised field agriculture. They almost succeeded. Emphasizing Native voices and actions in the historical record and questioning accounts published by the White conflict veterans on which historians traditionally rely allows a new history of this tragic crisis that privileges Native autonomy, ingenuity, and survivance.
Ether Day Revisited
Authors: Firth Paul G. 
Published: May 2022

Background:
The details of the public demonstration of the effects of ether that initiated the modern era of surgery and anesthesia are often misreported. Existing published transcripts of the clinical records are incomplete or inaccurate.

Methods:
The patient notes of Gilbert Abbott were photographed, transcribed, and reviewed.

Results:
The records are handwritten in “Surgical Records for 1846; Volume 30,” of the Massachusetts General Hospital. The patient was admitted on September 25. The presenting condition was a congenital, mobile, compressible, multilobed, small lesion at the angle of the left mandible, and base of tongue. The operation on October 16 was an attempted ligation of the blood supply to the lesion. The postoperative diagnosis was a vascular lesion (“erectile tumor”). Postoperative management included application of sclerosants. The mass was unchanged in size on discharge on December 7. There is no documentation of the anesthetic administration in the progress note but a retrospective report of the anesthetic is pasted into the Records book. This account reported that the patient did not respond to the initial incision. He moved and cried out during the latter part of the procedure. Although he was aware of the operation taking place, he later said he had not experienced pain. The commentary concluded that the demonstration of the analgesic effectiveness of ether was inconclusive but that subsequently ether was shown to be effective.

Conclusions:
The surgery on October 16, an unsuccessful ligation of a congenital lymphovascular malformation, was performed under incomplete general anesthesia. Examination of the primary documents may allow for more accurate accounts of circumstances surrounding the discovery of anesthesia.
Devastating Independence Day fireworks hand injuries of 2020: a retrospective case series examining dramatic increase secondary to COVID-19 restrictions
Authors: Herzog Leah N. , Daley Dane N. 
Published: May 2022

Background:
To evaluate the effects of COVID-19 restrictions on the amount of fireworks injuries during the Fourth of July.

Methods:
This was a retrospective review of all fireworks injuries during the weekend of the Fourth of July at a single institution from 2014 to 2020. All patients who presented to this institution with a fireworks injury were recorded along with age, occupation, hand dominance, injured hand, smoking status, and whether the patient was transferred from an outside hospital. This information was then used to compare fireworks injuries during 2020 and the COVID-19 pandemic versus the years prior to COVID-19.

Results:
There were 24 fireworks injuries from 2014 to 2020. Most patients were males, and the average age was 25 yr old. Forty-six percent (11 patients) of these fireworks injuries occurred in 2020 during the COVID-19 pandemic. The next closest number of fireworks injuries occurred in 2015 with four patients (17%).

Conclusions:
Fireworks injuries are devastating injuries that affect all aspects of patients’ lives. With social restrictions from the COVID-19 pandemic limiting public fireworks display, there was a 275% increase in fireworks hand injuries presenting to the authors’ level #1 trauma center. The authors propose modifying the current safety guidelines to prevent injuries to minors and urge a more robust publicization of the guidelines.

Level of Evidence:
Level IV.