bluuebunny/crossref_metadata_2025_split huggingface dataset:
Relative Efficiencies of Simple and Complex Substitution Models in Estimating Divergence Times in Phylogenomics
Authors: Tao Qiqing , Barba-Montoya Jose , Huuki Louise A , Durnan Mary Kathleen , Kumar Sudhir 
Published: February 2020

AbstractThe conventional wisdom in molecular evolution is to apply parameter-rich models of nucleotide and amino acid substitutions for estimating divergence times. However, the actual extent of the difference between time estimates produced by highly complex models compared with those from simple models is yet to be quantified for contemporary data sets that frequently contain sequences from many species and genes. In a reanalysis of many large multispecies alignments from diverse groups of taxa, we found that the use of the simplest models can produce divergence time estimates and credibility intervals similar to those obtained from the complex models applied in the original studies. This result is surprising because the use of simple models underestimates sequence divergence for all the data sets analyzed. We found three fundamental reasons for the observed robustness of time estimates to model complexity in many practical data sets. First, the estimates of branch lengths and node-to-tip distances under the simplest model show an approximately linear relationship with those produced by using the most complex models applied on data sets with many sequences. Second, relaxed clock methods automatically adjust rates on branches that experience considerable underestimation of sequence divergences, resulting in time estimates that are similar to those from complex models. And, third, the inclusion of even a few good calibrations in an analysis can reduce the difference in time estimates from simple and complex models. The robustness of time estimates to model complexity in these empirical data analyses is encouraging, because all phylogenomics studies use statistical models that are oversimplified descriptions of actual evolutionary substitution processes.
Locally acting transcription factors regulate p53-dependent cis-regulatory element activity
Authors: Catizone Allison N , Uzunbas Gizem Karsli , Celadova Petra , Kuang Sylvia , Bose Daniel , Sammons Morgan A 
Published: February 2020

Abstract
The master tumor suppressor p53 controls transcription of a wide-ranging gene network involved in apoptosis, cell cycle arrest, DNA damage repair, and senescence. Recent studies revealed pervasive binding of p53 to cis-regulatory elements (CREs), which are non-coding segments of DNA that spatially and temporally control transcription through the combinatorial binding of local transcription factors. Although the role of p53 as a strong trans-activator of gene expression is well known, the co-regulatory factors and local sequences acting at p53-bound CREs are comparatively understudied. We designed and executed a massively parallel reporter assay (MPRA) to investigate the effect of transcription factor binding motifs and local sequence context on p53-bound CRE activity. Our data indicate that p53-bound CREs are both positively and negatively affected by alterations in local sequence context and changes to co-regulatory TF motifs. Our data suggest p53 has the flexibility to cooperate with a variety of transcription factors in order to regulate CRE activity. By utilizing different sets of co-factors across CREs, we hypothesize that global p53 activity is guarded against loss of any one regulatory partner, allowing for dynamic and redundant control of p53-mediated transcription.
Mutation signatures specific to DNA alkylating agents in yeast and cancers
Authors: Saini Natalie , Sterling Joan F , Sakofsky Cynthia J , Giacobone Camille K , Klimczak Leszek J , Burkholder Adam B , Malc Ewa P , Mieczkowski Piotr A , Gordenin Dmitry A 
Published: February 2020

AbstractAlkylation is one of the most ubiquitous forms of DNA lesions. However, the motif preferences and substrates for the activity of the major types of alkylating agents defined by their nucleophilic substitution reactions (SN1 and SN2) are still unclear. Utilizing yeast strains engineered for large-scale production of single-stranded DNA (ssDNA), we probed the substrate specificity, mutation spectra and signatures associated with DNA alkylating agents. We determined that SN1-type agents preferably mutagenize double-stranded DNA (dsDNA), and the mutation signature characteristic of the activity of SN1-type agents was conserved across yeast, mice and human cancers. Conversely, SN2-type agents preferably mutagenize ssDNA in yeast. Moreover, the spectra and signatures derived from yeast were detectable in lung cancers, head and neck cancers and tumors from patients exposed to SN2-type alkylating chemicals. The estimates of mutation loads associated with the SN2-type alkylation signature were higher in lung tumors from smokers than never-smokers, pointing toward the mutagenic activity of the SN2-type alkylating carcinogens in cigarettes. In summary, our analysis of mutations in yeast strains treated with alkylating agents, as well as in whole-exome and whole-genome-sequenced tumors identified signatures highly specific to alkylation mutagenesis and indicate the pervasive nature of alkylation-induced mutagenesis in cancers.
Theater in the 20th Century
Authors: McCormick Stacie 
Published: February 2020

Black theater in the 20th century comprises a wide array of dramatic productions by black Americans growing out of the legacies of minstrel-era performance of the 19th century. As a result, black theater has largely been driven by the desire to present depictions of black life that were not overdetermined by the white gaze. A dynamic corpus of literary, dramatic, and expressive art, black theater of the 20th century has been foundational to the development of black theater as it is known today. This period was also concerned with questions central to black theater such as: What should black plays be about? Where should black theaters be located? Who can write a black play? What is a black play? Various theater companies, playwrights, and artistic movements have forged responses to such questions with each deepening the textures of black theater. In a significant and early articulation of what black theater should be, W.E.B. Du Bois, writing in the July 1926 issue of The Crisis, established the governing mantra for the Harlem-based theater company the Krigwa Players and black theater more broadly. He states that it should be should be “About us by us . . . for us . . . [and] near us.” Voices such as Alain Locke and Theophilus Lewis would deepen these conversations with their own perspectives on the purpose of black theater with Locke advocating for a lessened emphasis on social issues and Lewis expressing the need to appeal to working-class black Americans whose support for black theater was unwavering. Moreover, theater companies; artistic and social movements; and the work of playwrights such as Zora Neale Hurston, Langston Hughes, Lorraine Hansberry, James Baldwin, August Wilson, George C. Wolfe, Adrienne Kennedy, and Suzan-Lori Parks would go on to develop a critical body of work that makes up black theater of the 20th century. Black theater of the 20th century is intrinsically tied to black performance histories of storytelling, improvisation, “signifyin’,” humor, and masking. This dramatic work has contributed greatly to the project of self-authorship and expression that sits at the heart of black literature. This entry traverses the many contours of 20th-century black theater moving from broader explorations of anthologies and theater histories to close analyses of playwrights and finally to emergent thematic examinations that signal future directions for the study of 20th-century black theater.
Forverts/Forward
Authors: Rojanski Rachel 
Published: February 2020

Forverts (the Jewish Daily Forward or The Forward) was a Yiddish-language newspaper based in New York City that appeared as a daily for eighty-six years. It was the largest and most influential Jewish newspaper in the world, the most widely read socialist daily in the United States, and the foreign language newspaper with the largest distribution in the United States. Launched on 22 April 1897, Forverts was founded by a group of Yiddish-speaking members of the Socialist Labor Party (SLP). Abraham Cahan (b. 1860–d. 1951) was appointed its first editor. He left after a few months but returned in 1902 to lead the paper for some forty-eight years, until his death. Although Forverts was a Socialist paper, its readership encompassed the broad masses of eastern European Jewish immigrants in early-20th-century America, regardless of their political orientation. As many scholars have argued, Forverts played an important role in the Americanization of its readers, providing them with useful information about their new country and helping them integrate into American life. But it was an immigrant paper in a much deeper sense, too. By adapting ideological ideas and cultural trends from eastern Europe to the American reality, Forverts became instrumental in developing a new kind of secular Jewish identity. Its editorial policy was to preserve a socialist and nonreligious tone, to use simple Yiddish, to publish a range of articles—some more serious, others light—and to serve as a platform for both high-quality and popular literature (shund). As a result, Forverts contributed a great deal to the development of Yiddish literature, and many great Yiddish writers, including Isaac Bashevis Singer, published in its pages. The paper’s advice column—“a bintl brief” (a bundle of letters)—was especially popular. It regularly printed readers’ questions about important aspects of everyday life together with the editor’s responses reflecting his views on Jewish society and family life in America. No less important was the women’s page, which encouraged women to participate in the job market alongside their family roles. On the political front, Forverts supported the labor movement, participated in Jewish political debates during World War I, and fought immigration restrictions. In its early days, the paper featured anti-Zionist views, though this changed after the Balfour Declaration (1917) and Cahan’s trip to Palestine (1925). Demographic changes following immigration restrictions in the 1920s caused a gradual decline in its distribution. The paper continued as a daily until 1983, when it became a weekly. In 1990 an English-language weekly joined the Yiddish newspaper. Since early 2019, both the Yiddish and the English editions are entirely digital.
Posterior Column Osteotomy of the Lumbar Spine: 2-Dimensional Operative Video
Authors: Duan Ping Guo , Mehra Ratnesh N , Wang Minghao , Chou Dean 
Published: February 2020

Abstract
The posterior column osteotomy (PCO) is a tool for correction in spinal deformity. It allows for the induction of lordosis and coronal plane correction. It can be performed at multiple levels to loosen and mobilize the spine. Although the PCO does not provide as much correction as a 3-column osteotomy, it can be done in less operative time and with less morbidity. Performing a PCO involves the resection of posterior bony elements, including entire facet complexes, the ligamentum flavum, and at least part of the lamina. The ligamentum flavum laterally is also resected, and the exiting nerve roots are skeletonized bilaterally. Compression of the osteotomy can cause foraminal stenosis, and it is important to ensure that the exiting nerve roots are adequately decompressed to avoid potential postoperative radiculopathy. The authors present an illustration of the technique with saw bones, a clinical case describing the use of PCOs, and an intraoperative video of a PCO performed at L5-S1.
The patient consented to the surgical procedure and video/image recording for possible publication purposes prior to the operation being performed.
Kadanoff-Baym Approach to Entropy Production in O(N) Theory with Next-to-Leading Order Self-Energy
Authors: Nishiyama Akihiro , Ohnishi Akira 
Published: February 2020

Abstract
We investigate entropy production in the O(N) scalar theory using the Kadanoff-Baym equation. We show that one of the candidate expressions of the kinetic entropy satisfies the H-theorem in the first order of the gradient expansion with the next-to-leading-order self-energy of the 1/N expansion in the symmetric phase, and that entropy production occurs as the Green's function evolves with nonzero collision term contributions. Entropy production stops at local thermal equilibrium where the collision term contribution vanishes and the maximal entropy state is realized. We numerically examine these features of entropy production in thermalization processes in 1+1 dimensions for a couple of homogeneous cases, where the thermalization can proceed only with the off-shell effects. We find that the entropy production rate γ is larger for smaller N and is found to follow γ ∝ (1/N)ν where δ ≳ 2 at strong coupling measured in the unit of bare mass (m), ⋋= 40 m2.
The positive association between employment and self-reported mental health in the USA: a robust application of marginalized zero-inflated negative binomial regression (MZINB)
Authors: Eric Chinaeke , Melanie Gwynn , Yuan Hong , Jiajia Zhang , Bankole Olatosi 
Published: February 2020

AbstractBackgroundFew studies have assessed the impact of employment on mental health among chronically ill patients. This study investigated the association between employment and self-reported mental unhealthy days among US adults.MethodsFor this cross-sectional cohort study, we pooled 2011–2017 Behavioral Risk Factor Surveillance System (BRFSS) survey data. We examined the association between employment and mental health in nine self-reported chronic conditions using marginalized zero-inflated negative binomial regression (MZINB). All analyses were conducted using SAS statistical software 9.4.ResultsRespondents (weighted n = 245 319 917) were mostly white (77.16%), aged 18–64 (78.31%) and employed (57.08%). Approximately 10% of respondents reported one chronic condition. Expected relative risk of mental unhealthy days was highest for employed respondents living with arthritis (RR = 1.70, 95% CI = [1.66, 1.74]), COPD (RR = 1.45, 95% CI = [1.41, 1.49]) and stroke (RR = 1.31, 95% CI = [1.25, 1.36]) compared to unemployed respondents. Employed males had 25% lower risk of self-reported mental unhealthy days compared to females.ConclusionsResults show the interactive effects of employment on self-reported mental health. Employment may significantly impact on self-reported mental health among patients suffering from chronic conditions than those without chronic conditions.
Identification of the urine and serum metabolomics signature of gout
Authors: Huang Yefei , Xiao Min , Ou Jiayong , Lv Qing , Wei Qiujing , Chen Zena , Wu Jialing , Tu Liudan , Jiang Yutong , Zhang Xi , Qi Jun , Qiu Minli , Cao Shuangyan , Gu Jieruo 
Published: February 2020

AbstractObjectiveGout is the most common inflammatory arthritis and the worldwide incidence is increasing. By revealing the metabolic alterations in serum and urine of gout patients, the first aim of our study was to discover novel molecular biomarkers allowing for early diagnosis. We also aimed to investigate the underlying pathogenic pathways.MethodsSerum and urine samples from gout patients (n = 30) and age-matched healthy controls (n = 30) were analysed by ultra-performance liquid chromatography–mass spectrometry (UPLC-MS) to screen the differential metabolites and construct a diagnostic model. Next, the model was verified and optimized in the second validation cohort (n = 100). The pathways were illustrated to understand the underlying pathogenesis of gout.ResultsIn general, serum metabolomics demonstrated a clearer distinction than urine metabolomics. In the discovery cohort, 40 differential serum metabolites were identified that could distinguish gout patients from healthy controls. Among them, eight serum metabolites were verified in the validation cohort. Through regression analysis, the final model consisted of three serum metabolites—pyroglutamic acid, 2-methylbutyryl carnitine and Phe-Phe—that presented optimal diagnostic power. The three proposed metabolites produced an area under the curve of 0.956 (95% CI 0.911, 1.000). Additionally, the proposed metabolic pathways were primarily involved in purine metabolism, branched-chain amino acids (BCAAs) metabolism, the tricarboxylic acid cycle, synthesis and degradation of ketone bodies, bile secretion and arachidonic acid metabolism.ConclusionThe metabolomics signatures could serve as an efficient tool for early diagnosis and provide novel insights into the pathogenesis of gout.
Privilege in the Delivery Room? Race, Class, and the Realization of Natural Birth Preferences, 2002–2013
Authors: Johnson Katherine M , Simon Richard M 
Published: February 2020

AbstractWe expand prior research on the sociology of birth by testing race and class effects on women’s capacity to realize their childbirth preferences in hospital settings. Drawing on data from the U.S. Listening to Mothers survey, we use Poisson regression and logistic regression to examine the extent to which women’s preferences are associated with actual experiences of medical intervention during perinatal care. We find that 1) less privileged women were significantly less likely to have certain interventions and had fewer interventions overall; but 2) less privileged women with natural birth preferences were significantly more likely to have certain medical interventions, compared to their race/class privileged counterparts. Thus, less privileged women simultaneously receive less and more childbirth interventions—both of which appear to be out of sync with their birthing preferences. Our results support previous research which has found race and social class inequities in medical treatment, which we interpret here as “privilege in the delivery room.”
Transportation robot battery power forecasting based on bidirectional deep-learning method
Authors: Thurow Kerstin , Chen Chao , Junginger Steffen , Stoll Norbert , Liu Hui 
Published: February 2020

Abstract
This paper proposes a data-driven hybrid model for forecasting the battery power voltage of transportation robots by combining a wavelet method and a bidirectional deep-learning technique. In the proposed model, the on-board battery power data is measured and transmitted. A WPD (wavelet packet decomposition) algorithm is employed to decompose the original collected non-stationary series into several relatively more stable subseries. For each subseries, a deep learning–based predictor – bidirectional long short-term memory (BiLSTM) – is constructed to forecast the battery power voltage from one step to three steps ahead. Two experiments verify the effectiveness and generalization ability of the proposed hybrid forecasting model, which shows the highest forecasting accuracy. The obtained forecasting results can be used to decide whether the robot can complete the given task or needs to be recharged, providing effective support for the safe use of transportation robots.
Neutralizing Complement C5a Protects Mice with Pneumococcal Pulmonary Sepsis
Authors: Müller-Redetzky Holger , Kellermann Ute , Wienhold Sandra-Maria , Gutbier Birgitt , Lienau Jasmin , Hellwig Katharina , Reppe Katrin , Letsiou Eleftheria , Tschernig Thomas , Scholz Markus , Ahnert Peter , Maasch Christian , Hoehlig Kai , Klussmann Sven , Vater Axel , Firsching Theresa C. , Hoppe Judith , Suttorp Norbert , Witzenrath Martin 
Published: February 2020

Abstract

Background
Community-acquired pneumonia and associated sepsis cause high mortality despite antibiotic treatment. Uncontrolled inflammatory host responses contribute to the unfavorable outcome by driving lung and extrapulmonary organ failure. The complement fragment C5a holds significant proinflammatory functions and is associated with tissue damage in various inflammatory conditions. The authors hypothesized that C5a concentrations are increased in pneumonia and C5a neutralization promotes barrier stabilization in the lung and is protective in pneumococcal pulmonary sepsis.

Methods
The authors investigated regulation of C5a in pneumonia in a prospective patient cohort and in experimental pneumonia. Two complementary models of murine pneumococcal pneumonia were applied. Female mice were treated with NOX-D19, a C5a-neutralizing l-RNA-aptamer. Lung, liver, and kidney injury and the inflammatory response were assessed by measuring pulmonary permeability (primary outcome), pulmonary and blood leukocytes, cytokine concentrations in lung and blood, and bacterial load in lung, spleen, and blood, and performing histologic analyses of tissue damage, apoptosis, and fibrin deposition (n = 5 to 13).

Results
In hospitalized patients with pneumonia (n = 395), higher serum C5a concentrations were observed compared to healthy subjects (n = 24; 6.3 nmol/l [3.9 to 10.0] vs. 4.5 nmol/l [3.8 to 6.6], median [25 to 75% interquartile range]; difference: 1.4 [95% CI, 0.1 to 2.9]; P = 0.029). Neutralization of C5a in mice resulted in lower pulmonary permeability in pneumococcal pneumonia (1.38 ± 0.89 vs. 3.29 ± 2.34, mean ± SD; difference: 1.90 [95% CI, 0.15 to 3.66]; P = 0.035; n = 10 or 11) or combined severe pneumonia and mechanical ventilation (2.56 ± 1.17 vs. 7.31 ± 5.22; difference: 4.76 [95% CI, 1.22 to 8.30]; P = 0.011; n = 9 or 10). Further, C5a neutralization led to lower blood granulocyte colony-stimulating factor concentrations and protected against sepsis-associated liver injury.

Conclusions
Systemic C5a is elevated in pneumonia patients. Neutralizing C5a protected against lung and liver injury in pneumococcal pneumonia in mice. Early neutralization of C5a might be a promising adjunctive treatment strategy to improve outcome in community-acquired pneumonia.

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Beyond antibiotics for pulmonary nontuberculous mycobacterial disease
Authors: Waterer Grant 
Published: February 2020

Purpose of review
Pulmonary nontuberculous mycobacterial disease (NTM) remains a significant clinical challenge with suboptimal therapy. This review focuses on recent understandings around the pathogenesis of NTM disease and nonantibiotic therapeutic approaches that are being pursued.

Recent findings
The absence of animal models that truly replicate human disease remains a major problem for NTM research with most findings coming from tuberculosis or tuberculosis-like studies. Recent research reiterates the known key roles of interferon gamma (IFNγ), tumor necrosis factor, interleukin-12 and granulocyte-macrophage colony stimulation factor (GM-CSF) in immunity to NTM. Autoantibodies to some of these factors may be important. Recent nonantibiotic research has focused on either boosting the immune response to NTM (e.g. with IFNγ or GM-CSF) or using other compounds to kill these pathogens (e.g. inhaled NO, gallium, etc.).

Summary
Our poor understanding of the immune deficit leading to NTM disease continues to hinder the development of highly effective therapies. New approaches are promising but need significant validation before being considered viable therapeutic options.