bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Lick Observatory Supernova Search follow-up program: photometry data release of 70 SESNe
Authors: Zheng WeiKang , Stahl Benjamin E , de Jaeger Thomas , Filippenko Alexei V , Wang Shan-Qin , Gan Wen-Pei , Brink Thomas G , Altunin Ivan , Baer-Way Raphael , Bigley Andrew , Blanchard Kyle , Blanchard Peter K , Bradley James , Cargill Samantha K , Casper Chadwick , Chapman Teagan , Chander Vidhi , Channa Sanyum , Choi Byung Yun , Choksi Nick , Chu Matthew , Clubb Kelsey I , Cohen Daniel P , Dalba Paul A , deGraw Asia , de Kouchkovsky Maxime , Ellison Michael , Falcon Edward , Fox Ori D , Fuller Kiera , Ganeshalingam Mohan , Girish Nachiket , Gould Carolina , Halevi Goni , Halle Andrew , Hayakawa Kevin T , Hardy Romain , Hestenes Julia , Hoffman Andrew M , Hyland Michael , Jeffers Benjamin T , Jennings Connor , Kandrashoff Michael T , Khodanian Anthony , Kim Minkyu , Kim Haejung , Kislak Michelle E , Krishnan Daniel , Kumar Sahana , Kumar Snehaa Ganesh , Leja Joel , Leonard Erin J , Li Gary Z , Li Weidong , Lian Ji-Shun , Liu Evelyn , Lowe Thomas B , Lu Philip , Ma Emily , Mason Michelle N , May Michael , McAllister Kyle , McGinness Emma , Modak Shaunak , Molloy Jeffrey , Murakami Yukei S , Nayak Omnarayani , Perera Derek , Pina Kenia , Punjabi Druv , Rikhter Andrew , Ross Timothy W , Sipple Jackson , Soler Costas , Stegman Samantha , Stephens Haynes , Sunseri James , Tang Kevin , Taylor Stephen , Thrasher Patrick , Van Dyk Schuyler D , Wang Xiang-Gao , Wayland Jeremy , Wilkins Andrew , Yagubyan Abel , Yuk Heechan , Yunus Sameen , Zhang Keto D 
Published: March 2022

ABSTRACT
We present BVRI and unfiltered (Clear) light curves of 70 stripped-envelope supernovae (SESNe), observed between 2003 and 2020, from the Lick Observatory Supernova Search follow-up program. Our SESN sample consists of 19 spectroscopically normal SNe Ib, 2 peculiar SNe Ib, six SNe Ibn, 14 normal SNe Ic, 1 peculiar SN Ic, 10 SNe Ic-BL, 15 SNe IIb, 1 ambiguous SN IIb/Ib/c, and 2 superluminous SNe. Our follow-up photometry has (on a per-SN basis) a mean coverage of 81 photometric points (median of 58 points) and a mean cadence of 3.6 d (median of 1.2 d). From our full sample, a subset of 38 SNe have pre-maximum coverage in at least one passband, allowing for the peak brightness of each SN in this subset to be quantitatively determined. We describe our data collection and processing techniques, with emphasis toward our automated photometry pipeline, from which we derive publicly available data products to enable and encourage further study by the community. Using these data products, we derive host-galaxy extinction values through the empirical colour evolution relationship and, for the first time, produce accurate rise-time measurements for a large sample of SESNe in both optical and infrared passbands. By modelling multiband light curves, we find that SNe Ic tend to have lower ejecta masses and lower ejecta velocities than SNe Ib and IIb, but higher 56Ni masses.
Regulatory elements can be essential for maintaining broad chromatin organization and cell viability
Authors: Liu Ying , Ding Bo , Zheng Lina , Xu Ping , Liu Zhiheng , Chen Zhao , Wu Peiyao , Zhao Ying , Pan Qian , Guo Yu , Wang Wei , Wei Wensheng 
Published: March 2022

Abstract
Increasing evidence shows that promoters and enhancers could be related to 3D chromatin structure, thus affecting cellular functions. Except for their roles in forming canonical chromatin loops, promoters and enhancers have not been well studied regarding the maintenance of broad chromatin organization. Here, we focused on the active promoters/enhancers predicted to form many 3D contacts with other active promoters/enhancers (referred to as hotspots) and identified dozens of loci essential for cell growth and survival through CRISPR screening. We found that the deletion of an essential hotspot could lead to changes in broad chromatin organization and the expression of distal genes. We showed that the essentiality of hotspots does not result from their association with individual genes that are essential for cell viability but rather from their association with multiple dysregulated non-essential genes to synergistically impact cell fitness.
The DNA polymerase of bacteriophage YerA41 replicates its T-modified DNA in a primer-independent manner
Authors: Gomez-Raya-Vilanova Miguel V , Leskinen Katarzyna , Bhattacharjee Arnab , Virta Pasi , Rosenqvist Petja , Smith Jake L R , Bayfield Oliver W , Homberger Christina , Kerrinnes Tobias , Vogel Jörg , Pajunen Maria I , Skurnik Mikael 
Published: March 2022

Abstract
Yersinia phage YerA41 is morphologically similar to jumbo bacteriophages. The isolated genomic material of YerA41 could not be digested by restriction enzymes, and used as a template by conventional DNA polymerases. Nucleoside analysis of the YerA41 genomic material, carried out to find out whether this was due to modified nucleotides, revealed the presence of a ca 1 kDa substitution of thymidine with apparent oligosaccharide character. We identified and purified the phage DNA polymerase (DNAP) that could replicate the YerA41 genomic DNA even without added primers. Cryo-electron microscopy (EM) was used to characterize structural details of the phage particle. The storage capacity of the 131 nm diameter head was calculated to accommodate a significantly longer genome than that of the 145 577 bp genomic DNA of YerA41 determined here. Indeed, cryo-EM revealed, in contrast to the 25 Å in other phages, spacings of 33–36 Å between shells of the genomic material inside YerA41 heads suggesting that the heavily substituted thymidine increases significantly the spacing of the DNA packaged inside the capsid. In conclusion, YerA41 appears to be an unconventional phage that packages thymidine-modified genomic DNA into its capsids along with its own DNAP that has the ability to replicate the genome.
Trends in pneumoconiosis in Brazil, 1979–2019
Authors: Penteado Júlia Oliveira , Peres Tyele Goulart , Ramires Paula Florencio , de Lima Brum Rodrigo , da Silva Freitas Livia , Volcão Lisiane Martins , dos Santos Marina , Da Silva Júnior Flavio Manoel Rodrigues 
Published: March 2022

AbstractBackgroundPneumoconiosis is a lung disease related to exposure to dust in the workplace. The disease can induce irreversible damage to health, especially in lung tissue, and can cause progressive and permanent physical disabilities.AimsThis study evaluated the temporal and spatial distribution of mortality rates (1979–2019) and hospital admissions (1995–2019) for pneumoconiosis in Brazil.MethodsThe outcomes were hospitalization and death due to pneumoconiosis: codes 500–506 according to the ICD-9 and J60–J66 according to the ICD-10. Data from this retrospective ecological study were collected from the Brazilian Ministry of Health database.ResultsHospitalization for pneumoconiosis has decreased in all regions of Brazil. Hospitalizations occurred predominantly in men aged over 40 years. Death rates showed a temporal increase in all regions. Deaths occurred predominantly in men aged over 50 years. The highest hospitalization and death rates were in the states of the Midwest and South Regions.ConclusionsPneumoconiosis is a preventable occupational disease, and ongoing occurrences of hospitalizations and deaths highlight the importance of inspecting industries and controlling occupational and environmental exposures.
Functional nuclear retention of pre-mRNA involving Cajal bodies during meiotic prophase in European larch (Larix decidua)
Authors: Rudzka Magda , Wróblewska-Ankiewicz Patrycja , Majewska Karolina , Hyjek-Składanowska Malwina , Gołębiewski Marcin , Sikora Marcin , Smoliński Dariusz Jan , Kołowerzo-Lubnau Agnieszka 
Published: March 2022

AbstractGene regulation ensures that the appropriate genes are expressed at the proper time. Nuclear retention of incompletely spliced or mature mRNAs is emerging as a novel, previously underappreciated layer of posttranscriptional regulation. Studies on this phenomenon indicated that it exerts a significant influence on the regulation of gene expression by regulating export and translation delay, which allows the synthesis of specific proteins in response to a stimulus or at strictly controlled time points, for example, during cell differentiation or development. Here, we show that transcription in microsporocytes of European larch (Larix decidua) occurs in a pulsatile manner during prophase of the first meiotic division. Transcriptional activity was then silenced after each pulse. However, the transcripts synthesized were not exported immediately to the cytoplasm but were retained in the nucleoplasm and Cajal bodies (CBs). In contrast to the nucleoplasm, we did not detect mature transcripts in CBs, which only stored nonfully spliced transcripts with retained introns. Notably, the retained introns were spliced at precisely defined times, and fully mature mRNAs were released into the cytoplasm for translation. As similar processes have been observed during spermatogenesis in animals, our results illustrate an evolutionarily conserved mechanism of gene expression regulation during generative cells development in Eukaryota.
A synthetic switch based on orange carotenoid protein to control blue–green light responses in chloroplasts
Authors: Piccinini Luca , Iacopino Sergio , Cazzaniga Stefano , Ballottari Matteo , Giuntoli Beatrice , Licausi Francesco 
Published: March 2022

Abstract
Synthetic biology approaches to engineer light-responsive systems are widely used, but their applications in plants are still limited due to the interference with endogenous photoreceptors and the intrinsic requirement of light for photosynthesis. Cyanobacteria possess a family of soluble carotenoid-associated proteins named orange carotenoid proteins (OCPs) that, when activated by blue–green light, undergo a reversible conformational change that enables the photoprotection mechanism that occurs on the phycobilisome. Exploiting this system, we developed a chloroplast-localized synthetic photoswitch based on a protein complementation assay where two nanoluciferase fragments were fused to separate polypeptides corresponding to the OCP2 domains. Since Arabidopsis (Arabidopsis thaliana) does not possess the prosthetic group needed for the assembly of the OCP2 complex, we first implemented the carotenoid biosynthetic pathway with a bacterial β-carotene ketolase enzyme (crtW) to generate keto-carotenoid-producing plants. The photoswitch was tested and characterized in Arabidopsis protoplasts and stably transformed plants with experiments aimed to uncover its regulation by a range of light intensities, wavelengths, and its conversion dynamics. Finally, we applied the OCP-based photoswitch to control transcriptional responses in chloroplasts in response to green light illumination by fusing the two OCP fragments with the plastidial SIGMA FACTOR 2 and bacteriophage T4 anti-sigma factor AsiA. This pioneering study establishes the basis for future implementation of plastid optogenetics to regulate organelle responses upon exposure to specific light spectra.
SALT AND ABA RESPONSE ERF1 improves seed germination and salt tolerance by repressing ABA signaling in rice
Authors: Li Yuxiang , Zhou Jiahao , Li Zhe , Qiao Jinzhu , Quan Ruidang , Wang Juan , Huang Rongfeng , Qin Hua 
Published: March 2022

AbstractRice (Oryza sativa) germination and seedling establishment, particularly in increasingly saline soils, are critical to ensure successful crop yields. Seed vigor, which determines germination and seedling growth, is a complex trait affected by exogenous (environmental) and endogenous (hormonal) factors. Here, we used genetic and biochemical analyses to uncover the role of an APETALA2-type transcription factor, SALT AND ABA RESPONSE ERF1 (OsSAE1), as a positive regulator of seed germination and salt tolerance in rice by repressing the expression of ABSCISIC ACID-INSENSITIVE5 (OsABI5). ossae1 knockout lines exhibited delayed seed germination, enhanced sensitivity to abscisic acid (ABA) during germination and in early seedling growth, and reduced seedling salt tolerance. OsSAE1 overexpression lines exhibited the converse phenotype, with increased seed germination and salt tolerance. In vivo and in vitro assays indicated that OsSAE1 binds directly to the promoter of OsABI5, a major downstream component of the ABA signaling pathway and acts as a major regulator of seed germination and stress response. Genetic analyses revealed that OsABI5-mediated ABA signaling functions downstream of OsSAE1. This study provides important insights into OsSAE1 regulation of seed vigor and salt tolerance and facilitates the practical use of OsSAE1 in breeding salt-tolerant varieties suitable for direct seeding cultivation.
A maize triacylglycerol lipase inhibits sugarcane mosaic virus infection
Authors: Xu Xiao-Jie , Geng Chao , Jiang Shao-Yan , Zhu Qing , Yan Zhi-Yong , Tian Yan-Ping , Li Xiang-Dong 
Published: March 2022

Abstract
Triacylglycerol lipase (TGL) plays critical roles in providing energy for seed germination and plant development. However, the role of TGL in regulating plant virus infection is largely unknown. In this study, we adopted affinity purification coupled with mass spectrometry and identified that a maize (Zea mays) pathogenesis-related lipase protein Z. mays TGL (ZmTGL) interacted with helper component-proteinase (HC-Pro) of sugarcane mosaic virus (SCMV). Yeast two-hybrid, luciferase complementation imaging, and bimolecular fluorescence complementation assays confirmed that ZmTGL directly interacted with SCMV HC-Pro in vitro and in vivo. The 101–460 residues of SCMV HC-Pro were important for its interaction with ZmTGL. ZmTGL and SCMV HC-Pro co-localized at the mitochondria. Silencing of ZmTGL facilitated SCMV infection, and over-expression of ZmTGL reduced the RNA silencing suppression activity, most likely through reducing HC-Pro accumulation. Our results provided evidence that the lipase hydrolase activity of ZmTGL was associated with reducing HC-Pro accumulation, activation of salicylic acid (SA)-mediated defense response, and inhibition of SCMV infection. We show that ZmTGL inhibits SCMV infection by reducing HC-Pro accumulation and activating the SA pathway.
Complex Regional Pain Syndrome: Practical Diagnostic and Treatment Guidelines, 5th Edition
Authors: Harden R Norman , McCabe Candida S , Goebel Andreas , Massey Michael , Suvar Tolga , Grieve Sharon , Bruehl Stephen 
Published: March 2022

AbstractThere have been some modest recent advancements in the research of Complex Regional Pain Syndrome, yet the amount and quality of the work in this complicated multifactorial disease remains low (with some notable exceptions; e.g., the recent work on the dorsal root ganglion stimulation). The semi-systematic (though in some cases narrative) approach to review is necessary so that we might treat our patients while waiting for “better research.” This semi-systematic review was conducted by experts in the field, (deliberately) some of whom are promising young researchers supplemented by the experience of “elder statesman” researchers, who all mention the system they have used to examine the literature. What we found is generally low- to medium-quality research with small numbers of subjects; however, there are some recent exceptions to this. The primary reason for this paucity of research is the fact that this is a rare disease, and it is very difficult to acquire a sufficient sample size for statistical significance using traditional statistical approaches. Several larger trials have failed, probably due to using the broad general diagnostic criteria (the “Budapest” criteria) in a multifactorial/multi-mechanism disease. Responsive subsets can often be identified in these larger trials, but not sufficient to achieve statistically significant results in the general diagnostic grouping. This being the case the authors have necessarily included data from less compelling protocols, including trials such as case series and even in some instances case reports/empirical information. In the humanitarian spirit of treating our often desperate patients with this rare syndrome, without great evidence, we must take what data we can find (as in this work) and tailor a treatment regime for each patient.
Reshaping Global Trade: The Immediate and Long-Run Effects of Bank Failures
Authors: Xu Chenzi 
Published: March 2022

Abstract
I show that a disruption to the financial sector can reshape the patterns of global trade for decades. I study the first modern global banking crisis originating in London in 1866 and collect archival loan records that link multinational banks headquartered there to their lending abroad. Countries exposed to bank failures in London immediately exported significantly less and did not recover their lost growth relative to unexposed places. Their market shares within each destination also remained significantly lower for four decades. Decomposing the persistent market-share losses shows that they primarily stem from lack of extensive-margin growth, as the financing shock caused importers to source more from new trade partnerships. Exporters producing more substitutable goods, those with little access to alternative forms of credit, and those trading with more distant partners experienced more persistent losses, consistent with the existence of sunk costs and the importance of finance for intermediating trade.
Associations of the MUC5B promoter variant with timing of interstitial lung disease and rheumatoid arthritis onset
Authors: McDermott Gregory , Gill Ritu , Gagne Staci , Byrne Suzanne , Huang Weixing , Cui Jing , Prisco Lauren , Zaccardelli Alessandra , Martin Lily , Kronzer Vanessa L , Moll Matthew , Cho Michael H , Shadick Nancy , Dellaripa Paul F , Doyle Tracy , Sparks Jeffrey A 
Published: March 2022

Abstract

Objectives
To investigate the associations of the common MUC5B promoter variant with timing of RA-associated interstitial lung disease (RA-ILD) and RA onset.

Methods
We identified patients with RA meeting 2010 ACR/EULAR criteria and available genotype information in the Mass General Brigham Biobank, a multihospital biospecimen and clinical data collection research study. We determined RA-ILD presence by reviewing all RA patients who had CT imaging, lung biopsy or autopsy results. We determined the dates of RA and RA-ILD diagnoses by manual records review. We examined the associations of the MUC5B promoter variant (G&gt;T at rs35705950) with RA-ILD, RA-ILD occurring before or within 2 years of RA diagnosis and RA diagnosis at age &gt;55 years. We used multivariable logistic regression to estimate odds ratios (ORs) for each outcome by MUC5B promoter variant status, adjusting for potential confounders including genetic ancestry and smoking.

Results
We identified 1005 RA patients with available genotype data for rs35705950 (mean age 45 years, 79% female, 81% European ancestry). The MUC5B promoter variant was present in 155 (15.4%) and was associated with RA-ILD [multivariable OR 3.34 (95% CI 1.97, 5.60)], RA-ILD before or within 2 years of RA diagnosis [OR 4.01 (95% CI 1.78, 8.80)] and RA onset after age 55 years [OR 1.52 (95% CI 1.08, 2.12)].

Conclusions
The common MUC5B promoter variant was associated with RA-ILD onset earlier in the RA disease course and older age of RA onset. These findings suggest that the MUC5B promoter variant may impact RA-ILD risk early in the RA disease course, particularly in patients with older-onset RA.
How Does Human Capital Affect Investing? Evidence from University Endowments
Authors: Binfarè Matteo , Brown Gregory , Harris Robert , Lundblad Christian 
Published: March 2022

Abstract
We examine the links between human capital and endowment investing. Harnessing detailed information on university endowments, we find that higher asset allocations to alternative assets accompany higher levels of human capital in the endowment’s investment process. Moreover, high levels of human capital are linked to larger returns, even on a risk-adjusted basis. The improved investment outcomes arise because endowments (i) capture higher returns that can accompany alternative assets, (ii) select or have access to high performing managers, and (iii) minimize fees by accessing funds directly rather than through funds of funds. Our measures of human capital include expertise in alternatives on governing bodies, the presence of a chief investment officer, and the size of the investment staff. Finally, we conduct a novel survey of endowments and confirm that human capital is central in facilitating alternative investments.
The Bureaucratic Dissociation of Race in Policing: From State Racial Projects to Colorblind Ideologies
Authors: Gordon Daanika 
Published: March 2022

Abstract
Policing has long been implicated in state projects that construct race and racial inequality, yet many officers maintain that their work is colorblind. Burgeoning theories of racialized organizations offer a means of analyzing the processes that mediate such relationships between state racial projects and the ideologies of individuals. I suggest an extension of the racialized organizations framework that specifically considers the functions and forms of bureaucracies. Using a case study of policing in a segregated city, I describe a phenomenon of bureaucratic dissociation: bureaucratic arrangements facilitate racial governance, on the one hand, while obscuring the racial logics and consequences of daily work from officers, on the other. After detailing the incorporation of racial state interests into the police bureaucracy, I draw on over 500 hours of ethnographic observations of police work to explore the connections between bureaucratic structures and the racial ideologies of the police. I find widespread denial of racism in officers’ accounts of phenomena ranging from segregation to police shootings. Officers instead offer colorblind interpretations of social problems and narrate their work in relation to geographic and functional subdivisions, policies, and laws. These organizational accounts operate to legitimize police work in the face of its ongoing racial projects.
Resilience of Families Involved in Child Welfare: A Mixed-Methods Study
Authors: Helton Jesse J , Cooper-Sadlo Shannon C , House Nathaniel G , Adler Haley , Norton Lauren 
Published: March 2022

Abstract
Efforts to prevent child abuse and neglect have primarily focused on family deficits, including poverty and parental psychopathology. Models of resiliency, which are focused instead on family adaptation and strengths, offer an alternative to deficit-based practices. Although child-focused resilience studies are common in the field of child welfare, few focus on parents. The authors employed a mixed-methods study to understand how mothers involved in child welfare use resiliency strategies—including belief systems, organizational patterns, and open communication—to overcome adversities. Mothers (N = 129) at risk for child welfare involvement completed a quantitative survey, with 38 completing a follow-up qualitative phone interview. Both survey and interview asked a variety of questions on everyday adversities and coping. Two mothers were assessed as nonresilient. However, a majority of mothers exhibited resiliency, including consistent daily routines, peaceful homes, and family mealtimes. A strong aspirational belief system, not necessarily stemming from a faith tradition or community, provided both parents and children hope in times of trouble. Further, open communication with children about stressors was common. The authors’ results showed that resiliency strategies are being utilized by families typically defined as “at-risk,” and that child welfare professionals should consider focusing prevention efforts more on family strengths than on shortcomings.