bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gaussian Process Regression for foreground removal in H i Intensity Mapping experiments
Authors: Soares Paula S , Watkinson Catherine A , Cunnington Steven , Pourtsidou Alkistis 
Published: September 2021

ABSTRACT
We apply for the first time Gaussian Process Regression (GPR) as a foreground removal technique in the context of single-dish, low redshift H i intensity mapping, and present an open-source python toolkit for doing so. We use MeerKAT and SKA1-MID-like simulations of 21 cm foregrounds (including polarization leakage), H i cosmological signal, and instrumental noise. We find that it is possible to use GPR as a foreground removal technique in this context, and that it is better suited in some cases to recover the H i power spectrum than principal component analysis (PCA), especially on small scales. GPR is especially good at recovering the radial power spectrum, outperforming PCA when considering the full bandwidth of our data. Both methods are worse at recovering the transverse power spectrum, since they rely on frequency-only covariance information. When halving our data along frequency, we find that GPR performs better in the low-frequency range, where foregrounds are brighter. It performs worse than PCA when frequency channels are missing, to emulate RFI flagging. We conclude that GPR is an excellent foreground removal option for the case of single-dish, low-redshift H i intensity mapping in the absence of missing frequency channels. Our python toolkit gpr4im and the data used in this analysis are publicly available on GitHub.
Revisiting the evolution of non-radiative supernova remnants: a hydrodynamical-informed parametrization of the shock positions
Authors: Bandiera R , Bucciantini N , Martín J , Olmi B , Torres D F 
Published: September 2021

ABSTRACT
Understanding the evolution of a supernova remnant shell in time is fundamental. Such understanding is critical to build reliable models of the dynamics of the supernova remnant shell interaction with any pulsar wind nebula it might contain. Here, we perform a large study of the parameter space for the 1D spherically symmetric evolution of a supernova remnant, accompanying it by analytical analysis. Assuming, as is usual, an ejecta density profile with a power-law core and an envelope, and a uniform ambient medium, we provide a set of highly accurate approximations for the evolution of the main structural features of supernova remnants, such as the reverse and forward shocks and the contact discontinuity. We compare our results with previously adopted approximations, showing that existing simplified prescriptions can easily lead to large errors. In particular, in the context of pulsar wind nebulae modelling, an accurate description for the supernova remnant reverse shock is required. We also study in depth the self-similar solutions for the initial phase of evolution, when the reverse shock propagates through the envelope of the ejecta. Since these self-similar solutions are exact, but not fully analytical, we here provide highly accurate approximations as well.
Measuring the baryonic Tully–Fisher relation below the detection threshold
Authors: Pan Hengxing , Jarvis Matt J , Ponomareva Anastasia A , Santos Mario G , Allison James R , Maddox Natasha , Frank Bradley S 
Published: September 2021

ABSTRACT
We present a novel 2D flux density model for observed H i emission lines combined with a Bayesian stacking technique to measure the baryonic Tully–Fisher relation below the nominal detection threshold. We simulate a galaxy catalogue, which includes H i lines described with either Gaussian or busy function profiles, and H i data cubes with a range of noise and survey areas similar to the MeerKAT International Giga-Hertz Tiered Extragalactic Exploration (MIGHTEE) survey. With prior knowledge of redshifts, stellar masses, and inclinations of spiral galaxies, we find that our model can reconstruct the input baryonic Tully–Fisher parameters (slope and zero-point) most accurately in a relatively broad redshift range from the local Universe to z = 0.3 for all the considered levels of noise and survey areas and up to z = 0.55 for a nominal noise of 90 $\mu$Jy/channel over 5 deg2. Our model can also determine the $M_{\rm H\, \small {I}} - M_{\star }$ relation for spiral galaxies beyond the local Universe and account for the detailed shape of the H i emission line, which is crucial for understanding the dynamics of spiral galaxies. Thus, we have developed a Bayesian stacking technique for measuring the baryonic Tully–Fisher relation for galaxies at low stellar and/or H i masses and/or those at high redshift, where the direct detection of H i requires prohibitive exposure times.
Animal-eRNAdb: a comprehensive animal enhancer RNA database
Authors: Jin Weiwei , Jiang Guanghui , Yang Yanbo , Yang Jianye , Yang Wenqian , Wang Dongyang , Niu Xiaohui , Zhong Rong , Zhang Zhao , Gong Jing 
Published: September 2021

Abstract
Enhancer RNAs (eRNAs) are a class of non-coding RNAs transcribed from enhancers. As the markers of active enhancers, eRNAs play important roles in gene regulation and are associated with various complex traits and characteristics. With increasing attention to eRNAs, numerous eRNAs have been identified in different human tissues. However, the expression landscape, regulatory network and potential functions of eRNAs in animals have not been fully elucidated. Here, we systematically characterized 185 177 eRNAs from 5085 samples across 10 species by mapping the RNA sequencing data to the regions of known enhancers. To explore their potential functions based on evolutionary conservation, we investigated the sequence similarity of eRNAs among multiple species. In addition, we identified the possible associations between eRNAs and transcription factors (TFs) or nearby genes to decipher their possible regulators and target genes, as well as characterized trait-related eRNAs to explore their potential functions in biological processes. Based on these findings, we further developed Animal-eRNAdb (http://gong_lab.hzau.edu.cn/Animal-eRNAdb/), a user-friendly database for data searching, browsing and downloading. With the comprehensive characterization of eRNAs in various tissues of different species, Animal-eRNAdb may greatly facilitate the exploration of functions and mechanisms of eRNAs.
A simple and rapid method for enzymatic synthesis of CRISPR-Cas9 sgRNA libraries
Authors: Yates Joshua D , Russell Robert C , Barton Nathaniel J , Yost H Joseph , Hill Jonathon T 
Published: September 2021

Abstract
CRISPR-Cas9 sgRNA libraries have transformed functional genetic screening and have enabled several innovative methods that rely on simultaneously targeting numerous genetic loci. Such libraries could be used in a vast number of biological systems and in the development of new technologies, but library generation is hindered by the cost, time, and sequence data required for sgRNA library synthesis. Here, we describe a rapid enzymatic method for generating robust, variant-matched libraries from any source of cDNA in under 3 h. This method, which we have named SLALOM, utilizes a custom sgRNA scaffold sequence and a novel method for detaching oligonucleotides from solid supports by a strand displacing polymerase. With this method, we constructed libraries targeting the E. coli genome and the transcriptome of developing zebrafish hearts, demonstrating its ability to expand the reach of CRISPR technology and facilitate methods requiring custom libraries.
USP37 regulates DNA damage response through stabilizing and deubiquitinating BLM
Authors: Wu Chenming , Chang Yiming , Chen Junliang , Su Yang , Li Lei , Chen Yuping , Li Yunhui , Wu Jinhuan , Huang Jinzhou , Zhao Fei , Wang Wenrui , Yin Hui , Wang Shunli , Jin Mingpeng , Lou Zhenkun , Zhu Wei-Guo , Luo Kuntian , Zhang Jie , Yuan Jian 
Published: September 2021

Abstract
The human RecQ helicase BLM is involved in the DNA damage response, DNA metabolism, and genetic stability. Loss of function mutations in BLM cause the genetic instability/cancer predisposition syndrome Bloom syndrome. However, the molecular mechanism underlying the regulation of BLM in cancers remains largely elusive. Here, we demonstrate that the deubiquitinating enzyme USP37 interacts with BLM and that USP37 deubiquitinates and stabilizes BLM, thereby sustaining the DNA damage response (DDR). Mechanistically, DNA double-strand breaks (DSB) promotes ATM phosphorylation of USP37 and enhances the binding between USP37 and BLM. Moreover, knockdown of USP37 increases BLM polyubiquitination, accelerates its proteolysis, and impairs its function in DNA damage response. This leads to enhanced DNA damage and sensitizes breast cancer cells to DNA-damaging agents in both cell culture and in vivo mouse models. Collectively, our results establish a novel molecular mechanism for the USP37–BLM axis in regulating DSB repair with an important role in chemotherapy and radiotherapy response in human cancers.
Clinical and genetic spectra of autosomal dominant tubulointerstitial kidney disease
Authors: Mabillard Holly , Sayer John A , Olinger Eric 
Published: September 2021

Abstract
Autosomal dominant tubulointerstitial kidney disease (ADTKD) is a clinical entity defined by interstitial fibrosis with tubular damage, bland urinalysis and progressive kidney disease. Mutations in UMOD and MUC1 are the most common causes of ADTKD but other rarer (REN, SEC61A1), atypical (DNAJB11) or heterogeneous (HNF1B) subtypes have been described. Raised awareness, as well as the implementation of next-generation sequencing approaches, have led to a sharp increase in reported cases. ADTKD is now believed to be one of the most common monogenic forms of kidney disease and overall it probably accounts for ∼5% of all monogenic causes of chronic kidney disease. Through international efforts and systematic analyses of patient cohorts, critical insights into clinical and genetic spectra of ADTKD, genotype–phenotype correlations as well as innovative diagnostic approaches have been amassed during recent years. In addition, intense research efforts are addressed towards deciphering and rescuing the cellular pathways activated in ADTKD. A better understanding of these diseases and of possible commonalities with more common causes of kidney disease may be relevant to understand and target mechanisms leading to fibrotic kidney disease in general. Here we highlight recent advances in our understanding of the different subtypes of ADTKD with an emphasis on the molecular underpinnings and its clinical presentations.
Constitutional Transformation and Gender Equality: The Case of the Post-Arab Uprisings North African Constitutions
Authors: Porras-Gómez Antonio-Martín 
Published: September 2021

Abstract
The recognition of gender equality has become one of the most important trends in contemporary constitutional law. Nonetheless, a crucial question lingers: is it leading to material constitutional transformation? In order to better understand it, this article presents a case study on the constitutional reconfigurations undergone in Morocco, Tunisia and Egypt after the Arab uprisings. The main vectors of constitutional change are identified from a descriptive-analytical perspective. Even if they kept idiosyncratic elements of persistent discrimination, the new charters were inserted in the globalised trends of constitutional design, bringing about a strong formal expansion of gender equality rights. On the whole, however, little material progress has been made. This suboptimal material transformation is explained by means of research arguments framed in legal evolutionist theories. Finally, the article elucidates why the greater constitutional verbosity in the recognition of gender equality did not translate into greater parity.
‘A General Insurrection in the Countries with Slaves’: The US Civil War and the Origins of an Atlantic Revolution, 1861–1866
Authors: Payne Samantha 
Published: September 2021

Abstract
This article reveals how the beginning of US Reconstruction precipitated a revolutionary crisis in Cuba and Brazil, the last two slave societies in the Atlantic World. Throughout the US Civil War, slave-owners in Cuba and Brazil faced the immense challenge of containing black revolutionary currents across the Atlantic. Despite their intensive policing of black transnational networks, many slaves in Cuba and Brazil learned of the Civil War and became convinced that it heralded their emancipation. In response, they walked off plantations, fled to maroon communities, and organized and launched revolts. Although the scale of this insurrectionary violence never reached the same heights as in the Confederacy, the beginning of Reconstruction transformed the political implications of slave rebellion across the hemisphere. The fall of the Confederacy forced slave-owners in Cuba and Brazil to confront the possibility of their violent destruction at the same moment that the apparent radicalization of Republican politics stirred fears of US support for an international slave insurrection. It was in this context that many white elites in both nations became convinced of the necessity for a gradual abolition measure, which they hoped would ensure subaltern loyalty at a moment when revolutionary violence threatened the future of slavery.
Super-resolution imaging illuminates new dynamic behaviors of cellulose synthase
Authors: Duncombe Sydney G , Chethan Samir G , Anderson Charles T 
Published: September 2021

Abstract
Confocal imaging has shown that CELLULOSE SYNTHASE (CESA) particles move through the plasma membrane as they synthesize cellulose. However, the resolution limit of confocal microscopy circumscribes what can be discovered about these tiny biosynthetic machines. Here, we applied Structured Illumination Microscopy (SIM), which improves resolution two-fold over confocal or widefield imaging, to explore the dynamic behaviors of CESA particles in living plant cells. SIM imaging reveals that Arabidopsis thaliana CESA particles are more than twice as dense in the plasma membrane as previously estimated, helping explain the dense arrangement of cellulose observed in new wall layers. CESA particles tracked by SIM display minimal variation in velocity, suggesting coordinated control of CESA catalytic activity within single complexes and that CESA complexes might move steadily in tandem to generate larger cellulose fibrils or bundles. SIM data also reveal that CESA particles vary in their overlaps with microtubule tracks and can complete U-turns without changing speed. CESA track patterns can vary widely between neighboring cells of similar shape, implying that cellulose patterning is not the sole determinant of cellular growth anisotropy. Together, these findings highlight SIM as a powerful tool to advance CESA imaging beyond the resolution limit of conventional light microscopy.
Plant cell mechanobiology: Greater than the sum of its parts
Authors: Codjoe Jennette M , Miller Kari , Haswell Elizabeth S 
Published: September 2021

Abstract
The ability to sense and respond to physical forces is critical for the proper function of cells, tissues, and organisms across the evolutionary tree. Plants sense gravity, osmotic conditions, pathogen invasion, wind, and the presence of barriers in the soil, and dynamically integrate internal and external stimuli during every stage of growth and development. While the field of plant mechanobiology is growing, much is still poorly understood—including the interplay between mechanical and biochemical information at the single-cell level. In this review, we provide an overview of the mechanical properties of three main components of the plant cell and the mechanoperceptive pathways that link them, with an emphasis on areas of complexity and interaction. We discuss the concept of mechanical homeostasis, or “mechanostasis,” and examine the ways in which cellular structures and pathways serve to maintain it. We argue that viewing mechanics and mechanotransduction as emergent properties of the plant cell can be a useful conceptual framework for synthesizing current knowledge and driving future research.
A Poem by Sir Julius Caesar, Judge of the Admiralty, 1589
Authors: Bajetta Carlo M 
Published: September 2021

Abstract
A courtier of Elizabeth I and later James I, Sir Julius Caesar (Giulio Cesare Adelmare, 1558–1636) is remembered today chiefly for his place in the history of the English legal system. His role as a lover and writer of poetry, however, has been almost entirely ignored by historians and literary scholars alike, even though a poem of his was found and published as early as the nineteenth century. A manuscript collection containing many of Caesar’s business and family papers confirms his authorship of these verses and provides a date, a new context, and a far superior (and longer) text. Surrounded by documents relating to the literary exchanges of the Adelmare family, original letters by members of the Elizabethan élite, and presenting some disquieting references to treason, this apparently naive composition proves to be deeply connected with both Caesar’s life and the politics of his time.
Composing Well-being: Mental Health and the Mass Observation Project in Twentieth-Century Britain
Authors: Burchell Andrew , Thomson Mathew 
Published: September 2021

Summary
This article argues that the Mass Observation Project (MOP) at the University of Sussex offers a unique window onto the history of mental health and the voices of those who have lived with mental health conditions during the late-twentieth century. This article analyses how a sample of MOP participants use their writing to reflect on their experiences, and compose narratives about, mental illness over time. More specifically, we suggest that MOP’s capacity for the longitudinal study of individual respondents (underutilised by historians of mental health) offers exciting historiographical and methodological possibilities, not just in the history of mental health but for historians of medicine more generally. We conclude by considering how, for a handful of the participants in the project, mental health is entwined with MOP, as project participants deploy the archive to write about their experiences and even find something akin to therapy in the narrative act.
XVI American Literature: The Twentieth Century
Authors: Gifford James , Clawson James M , Foltz Mary , Kidder Orion Ussner , Peppard Anna , Parker Lindsay 
Published: September 2021

AbstractThis chapter has eight sections: 1. Poetry; 2. Fiction 1900–1945; 3. Fiction since 1945; 4. Drama; 5. Comics; 6. African American Writing; 7. Native Writing; 8. Latino/a, Asian American, and General Ethnic Writing. Section 1 is by James Gifford; section 2 is by James M. Clawson; section 3 is by Mary Foltz; section 4 will resume next year; section 5(a) is by Anna Peppard; section 5(b) is by Orion Ussner Kidder; section 6 is by Adam Rudder; section 7 is by James Gifford and Lindsay Parker; section 8 will resume next year.
Evaluation of a Risk-Stratified, Heparin-Based, Obstetric Thromboprophylaxis Protocol
Authors: Lu Michelle Y. , Blanchard Christina T. , Ausbeck Elizabeth B. , Oglesby Kacie R. , Page Margaret R. , Lazenby Allison J. , Cozzi Gabriella D. , Muñoz Rogers Rodrigo D. , Bushman Elisa T. , Kaplan Elle R. , Ruzic Martha F. , Mahalingam Mythreyi , Dunk Sarah , Champion Macie , Casey Brian M. , Tita Alan T. , Kim Dhong-Jin , Szychowski Jeff M. , Subramaniam Akila 
Published: September 2021

OBJECTIVE:
To evaluate outcomes before and after implementation of a risk-stratified heparin-based obstetric thromboprophylaxis protocol.

METHODS:
We performed a retrospective cohort study of all patients who delivered at our tertiary care center from 2013 to 2018. Deliveries were categorized as preprotocol (2013–2015; no standardized heparin-based thromboprophylaxis) and postprotocol (2016–2018). Patients receiving outpatient anticoagulation for active venous thromboembolism (VTE) or high VTE risk were excluded. Coprimary effectiveness and safety outcomes were postpartum VTEs and wound hematomas, respectively, newly diagnosed after delivery and up to 6 weeks postpartum. Secondary outcomes were other wound or bleeding complications, including unplanned surgical procedures (eg, hysterectomies, wound explorations) and blood transfusions. Outcomes were compared between groups, and adjusted odds ratios (aORs) and 95% CIs were calculated using the preprotocol group as reference.

RESULTS:
Of 24,229 deliveries, 11,799 (49%) occurred preprotocol. Although patients were more likely to receive heparin-based prophylaxis postprotocol (15.6% vs 1.2%, P<.001), there was no difference in VTE frequency between groups (0.1% vs 0.1%, odds ratio 1.0, 95% CI 0.5–2.1). However, patients postprotocol experienced significantly more wound hematomas (0.7% vs 0.4%, aOR 2.34, 95% CI 1.54–3.57), unplanned surgical procedures (aOR 1.29, 95% CI 1.06–1.57), and blood transfusions (aOR 1.34, 95% CI 1.16–1.55).

CONCLUSION:
Risk-stratified heparin-based thromboprophylaxis in a general obstetric population was associated with increased wound and bleeding complications without a complementary decrease in postpartum VTE. Guidelines recommending this strategy should be reconsidered.
Evaluation of Respiratory Emissions During Labor and Delivery
Authors: Mok Thalia , Harris Elijah , Vargas Andres , Afshar Yalda , Han Christina S. , Karagozian Ann , Rao Rashmi 
Published: September 2021

OBJECTIVE:
To characterize respiratory emissions produced during labor and vaginal delivery vis-à-vis the potential for transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).

METHODS:
Observational study of three women who tested negative for SARS-CoV-2 and had uncomplicated vaginal deliveries. Using background-oriented schlieren imaging, we evaluated the propagation of respiratory emissions produced during the labor course and delivery. The primary outcome was the speed and propagation of breath over time, calculated through processed images collected throughout labor and delivery.

RESULTS:
In early labor with regular breathing, the speed of the breath was 1.37 meters/s (range 1.20–1.55 meters/s). The breath appeared to propagate faster with a cough during early labor at a speed of 1.69 meters/s (range 1.22–2.27 meters/s). During the second stage of labor with Valsalva and forced expiration, the propagation speed was 1.79 meters/s (range 1.71–1.86 meters/s).

CONCLUSION:
Labor and vaginal delivery increase the propagation of respiratory emissions that may increase risk of respiratory transmission of SARS-CoV-2.
Neonatal Outcomes After Delivery in Water
Authors: Lanier Ariel L. , Wiegand Samantha L. , Fennig Kathleen , Snow E. Kaye , Maxwell Rose A. , McKenna David 
Published: September 2021

OBJECTIVE:
To assess neonatal intensive care unit (NICU) admissions and neonatal outcomes after water birth or land birth in an alternative birthing center.

METHODS:
We conducted a prospective observational study of preselected low-risk parturients separated into three groups depending on their location for labor and delivery: land–land, water–land, and water–water. Delivery outcomes, labor length, maternal pain assessment, need for newborn resuscitation, and NICU admission and diagnoses were collected. The primary outcome was admission to the NICU.

RESULTS:
There were 2,077 total deliveries from April 2015 to December 2019, consisting of 458 land–land deliveries, 730 water–land deliveries, and 889 water–water deliveries. The rate of NICU admission was 2.8% (95% CI 1.5–4.8%) for land–land deliveries, 4.1% (2.8–5.8%) for water–land deliveries, and 2.0% (1.2–3.2%) for water–water deliveries. A post hoc power analysis revealed a 70% power to detect a 2.1% difference in NICU admissions between the water–land and water–water groups.

CONCLUSION:
In this cohort of low-risk pregnant women, births in water and on land were associated with similar rates of admission to the NICU.