bluuebunny/crossref_metadata_2025 huggingface dataset:
Jonathan Goldberg
Authors: Frank Marcie
Published: January 2020

Astonishingly prolific, literary theorist Jonathan Goldberg has published fourteen books, and edited or coedited five more. Goldberg took his PhD in 1968 from Columbia University with a dissertation on John Donne’s Devotions, supervised by Edward Tayler. Widely recognized as a meticulous scholar and a writer of dazzling and playful prose, Goldberg has published on all the major authors of the English Renaissance. His early work provided models of how to use the most significant paradigms of post-structuralist literary theory in the study of Renaissance literature. He helped to inaugurate queer Renaissance studies in the 1990s with Sodometries: Renaissance Texts, Modern Sexualities (1992) and Queering the Renaissance (1994). Along with Eve Kosofsky Sedgwick, Michael Moon, and Judith Butler, Goldberg played a vital role in disseminating queer theory as a scholar, a coeditor of Series Q at Duke University Press, and as a teacher. Goldberg’s thinking has always been centripetal and transversal. He has worked across numerous study areas, including Renaissance and contemporary, English and American, homo and hetero, gay and queer, men and women, and gay and lesbian. He traverses both geography and temporality, analyzing the discourses of sodomy in the Old and New Worlds, and bringing Shakespeare’s Tempest together with its reception in 20th-century Caribbean writing. He has written about Renaissance and 20th-century women writers alongside their male counterparts as well as on their own. He has worked across media, analyzing the paintings of Tintoretto, the opera of Beethoven, and the films of Hitchcock, Fassbinder, and Todd Haynes. He has upheld the same rigorous standards of scholarship in everything he has published. Goldberg has served the profession of literary studies beyond the boundaries of the early modern period, in no small part by calling them into question. In its coherence, his oeuvre marks out the territory upon which literary interpretation stakes its claims to intellectual value beyond period specialization and for the rest of the humanities. Now Distinguished Arts and Sciences Professor Emeritus at Emory University, previously Goldberg was Sir William Osler Professor of English at The Johns Hopkins University (1986–2006), where he also served as senior editor at ELH (2002–2006). He also taught at Duke University (1995–1998), Brown University (1985–1986), and Temple University (1968–1985). In addition to his own scholarship, Goldberg edited a posthumous collection of Eve Kosofsky Sedgwick’s writing, The Weather in Proust (2011), and coedited a collection of essays, This Distracted Globe: Worldmaking in Early Modern Literature (2016), and has edited Milton (1991).
Ristoro d’Arezzo
Authors: Lützelschwab Ralf
Published: January 2020

The scarce information we have about the life of Ristoro d’Arezzo is obtained from his only surviving work, La composizione del mondo colle sue cascioni. According to the explicit, it was finished in 1282. Ristoro (Restoro in the local phonetic form used at Arezzo) was born in Arezzo at an unknown date in the first decades of the 13th century, when the city was a stimulating intellectual center. He was an adult in 1239, when he viewed a total eclipse of the sun. There has been much speculation about his intellectual and professional background. Based on recent research, it is highly improbable that he was either a professed monk or a Dominican architect. His text is full of analogies taken from the arts of painting, mosaic, goldsmithing, and metallurgy, presenting the world as a huge mosaic waiting to be decoded. It is difficult, however, to try to identify Ristoro with contemporary local artists sharing the same name. To date, none of these ascriptions can be sufficiently proven.
Native Peoples of Brazil
Authors: Langfur Hal
Published: January 2020

This article connects two realms often considered separately, sometimes even antithetically: the historiography of Brazilian indigenous peoples and that of the Lusophone Atlantic world. While the first would seem to point toward the South American interior, the second presumably faces from the seaboard eastward. This difference in orientations has led many scholars of these realms to pursue their research with little reference to each other. Those who sought to understand Portuguese America’s transatlantic connections long ignored the colony’s diverse native populations, except as an initial, quickly vanishing element of the colonial encounter. Historians of indigenous Brazil, for their part, concentrated on establishing the legitimacy of their field of study, largely relegated to anthropology until the 1990s. The degree to which they might draw insights from the burgeoning scholarship on Atlantic history was a secondary concern. Moreover, although the Atlantic paradigm occupies a growing place in the broader historiography of colonial Brazil, it does so in the face of some ambivalence. Skeptics question whether Atlantic history simply re-inscribes a traditional privileging of European over indigenous peoples. Others note that Atlantic historiography too often marginalizes the South Atlantic. Consequently, the authors whose works are assembled here, representing a young but increasingly vibrant field of Brazilian indigenous history, seldom frame their research in Atlantic terms. Nevertheless, one can identify in their studies a de facto historiography of Brazilian native peoples as both dispossessed victims of and resilient agents in a consolidating South Atlantic world. The timing and nature of the changes indigenous peoples suffered, resisted, evaded, refashioned, or embraced differed markedly as they became actors in this larger world. As elsewhere in the Americas, outcomes depended on native social, political, and cultural constitution; the geography, ecology, and natural resources of diverse domains; relations maintained with neighboring groups; distinctive trade and labor regimes; imperial policies, projects, fears, and fantasies; and the religious and racial preconceptions and malleability of the colonizers. It is no surprise, then, that the books and articles comprising this bibliography constitute a complex and varied whole. After initial sections on general works and early primary sources, the organizational scheme is first broadly regional (Coastal Contact and Exchange, Highlands, Amazon Basin) then thematic (Warfare, Resistance, Diplomacy; Slavery; Evangelization and Mission Life) with considerable overlap. Thus a study of coastal peoples might well address the theme of warfare, while a slavery study might emphasize Amazonian peoples. The reader is therefore advised to consult both regional and thematic sections.
Relevance Theory
Authors: Allott Nicholas
Published: January 2020

Relevance·theory, one of the leading research programs in pragmatics, aims to provide a psychologically realistic, explicit account of communication. It makes foundational claims about both cognition in general and utterances and how they are processed in particular. The former is the cognitive principle of relevance: cognition tends to seek maximal relevance, where an input to a cognitive process is more relevant the more positive effects it has on the mind’s representations of the world, and less relevant the greater the effort required to derive them. On this view, we have a built-in tendency to seek the greatest possible payoff for the least possible effort. Of course, there is no guarantee that an input to a cognitive process will be relevant. But communication is special. Speakers want to be understood, and they therefore tailor their utterances to their audience. Relevance theory claims that this raises a defeasible expectation that the utterance will be “optimally relevant”; that is, that it is both relevant enough to be worth processing and as relevant as the speaker is willing and able to make it. (This is the communicative principle of relevance.) It further claims that this mandates the relevance-theoretic comprehension heuristic: a fast and frugal procedure dedicated to processing utterances. Relevance theory claims that what a speaker communicates falls into two classes: explicatures, which are defined as propositions that are developments of the logical form of the sentence uttered; and other propositions conveyed, which are implicatures. A further fundamental assumption of relevance theory is that linguistically encoded meaning radically underdetermines the content that a speaker intends to convey. Much research has focused on investigating this linguistic underdetermination and on developing accounts of the interpretation of particular linguistic items and types of utterances. Specific areas of research include lexical pragmatics; figurative speech, including metaphor and irony; the interpretation of discourse connectives and linguistic items that have non-truth-conditional meaning; and the interpretation of logical linguistic items such as and, if . . . then, and negation. Turning briefly to the history of the field: relevance theory is grounded both in the philosopher Paul Grice’s work on meaning and conversation, and the conceptual and methodological advances of the cognitive revolution in linguistics and psychology. It was initially developed by Dan Sperber and Deirdre Wilson in the late 1970s and 1980s; both continue to be active in developing the theory. Other key contributors include Diane Blakemore, who introduced the notion of procedural meaning, and Robyn Carston, who is best known for her work on the semantics/pragmatics interface and linguistic underdeterminacy. Relevance theory has contributed considerably to the burgeoning fields of experimental and developmental pragmatics, and it is in dialogue with philosophy of language.
Alcohol use and mental health symptoms in female firefighter recruits
Authors: Gulliver S B , Zimering R T , Dobani F , Pennington M L , Morissette S B , Kamholz B W , Knight J A , Keane T M , Kimbrel N A , Carpenter T P , Meyer E C
Published: January 2020

Background

Limited research suggests that female firefighters report problem drinking at higher rates than the general population.

Aims

To identify longitudinal drinking patterns in female firefighters, make comparisons to male firefighters and examine problem drinking in relation to post-traumatic stress disorder (PTSD) and depression.

Methods

Study participants included 33 female and 289 male firefighter recruits, who were assessed over their first 3 years of fire service.

Results

Female firefighters consumed increasing numbers of drinks per week, with a median of 0.90 drinks per week at baseline, and 1.27 drinks in year 3. Female firefighters reported binge drinking at high rates, with nearly half binging at least once per year across all time points (44–74%). The percentage that reported binge drinking three or more times per month doubled over the course of the study (from 9% to 18%). Overall, males reported higher rates of binge drinking and a greater number of drinks per week; however, binge drinking rates among females increased over time and became comparable to rates of binge drinking among males. A greater percentage of female than male firefighters met the criteria for problem drinking by year 1. Problem drinking was associated with screening positive for PTSD at year 1 and depression at year 2, but not with occupational injury.

Conclusions

Over time, female firefighters reported increasing amounts of drinking, more frequent binge drinking and more negative consequences from drinking. These findings along with existing literature indicate female firefighters change their drinking in the direction of their male counterparts.
What Do Partisan Donors Want?
Authors: Broockman David , Malhotra Neil
Published: January 2020

Influential theories indicate concern that campaign donors exert outsized political influence. However, little data have documented what donors actually want from government, and existing research has devoted less attention to donors’ views on individual issues. Findings from an original survey of US donors, including an oversample of the largest donors, and a concurrently fielded mass survey document significant heterogeneity by party and policy domain in how donors’ and citizens’ views diverge. We find that Republican donors are much more conservative than Republican citizens on economic issues, whereas their views are similar on social issues. By contrast, Democratic donors are much more liberal than Democratic citizens on social issues, whereas their views are more similar on economic issues. Both parties’ donors, but especially Democratic donors, are more pro-globalism than their citizen counterparts. We replicate these patterns in an independent dataset. Our findings have important implications for the study of American politics.
Obesity prevention in early care and education: a comparison of licensing regulations across Canadian provinces and territories
Authors: Vercammen Kelsey A , Frelier Johannah M , Poole Mary Kathryn , Kenney Erica L
Published: January 2020

Background

Early care and education (ECE) settings represent an important point of intervention for childhood obesity prevention efforts. The objective of this paper was to compare ECE licensing regulations for each Canadian province/territory to evidence-based, obesity prevention standards.

Methods

Two authors reviewed existing ECE regulations for each province/territory and examined whether the regulatory text supported standards for nutrition (n = 11), physical activity (n = 5) and screen time (n = 4). Provinces/territories were evaluated on the strength of regulatory language for each standard (i.e. fully, partially, or not addressed) and a total comprehensiveness score (maximum score of 20). ECE centres and homes were examined separately.

Results

The majority of provinces/territories required providers to follow Canada’s Food Guide, but few had regulations for specific foods or beverages. Most provinces/territories included standards related to written menus and drinking water, but the strength of these standards was weak. Many provinces/territories required physical activity and outdoor opportunities to be provided daily, but few included a time requirement. Only two provinces included any screen time standards. Total comprehensiveness scores averaged 5.7 for centres and 5.4 for homes.

Conclusions

Canadian provinces/territories have insufficient obesity prevention regulations in ECE settings, highlighting a potential point of intervention to prevent obesity.
Use of Artificial Nipples Among Brazilian Infants and Associated Factors
Authors: Miranda Cristianny , de Sousa Taciana Maia , do Carmo Ariene Silva , Pereira Simone Cardoso Lisboa , Notaro Karine Antunes Marques , dos Santos Luana Caroline
Published: January 2020

Transversal study conducted in a Human Milk Bank to evaluate the factors associated with the use of artificial nipples (pacifier and/or nursing bottle) among Brazilian infants. Analyses were performed using the χ2 test and logistic regression analysis. A total of 6017 nursing mothers were evaluated and the use of artificial nipples was reported by 31.3%. The chance of using artificial nipples was higher among infants whose mothers attended antenatal care in private hospitals [odds ratio (OR): 1.61, 95% confidence interval (CI) 1.21–2.14], born in maternities without the Baby-Friendly Hospital Initiative (BFHI) (OR: 18.38, 95% CI 13.50–25.04) and those with adequate birth weight (OR: 2.83, 95% CI 1.99–4.03). A lower chance of using artificial nipples was observed among infants whose mothers had previous breastfeeding experience (OR: 0.76, 95% CI 0.61–0.95), received guidance on breastfeeding during antenatal care (OR: 0.80, 95% CI 0.65–0.98), practiced exclusive breastfeeding (OR: 0.36, 95% CI 0.28–0.45), breastfeeding on demand (OR: 0.66, 95% CI 0.52–0.85) and residents of inland cities/towns (OR: 0.38, 95% CI 0.20–0.72). The findings highlight the importance of breastfeeding guidance during antenatal care and the role of BFHI in clarifying risks associated with artificial nipple use.
A Conserved Helix in the C-Terminal Region of Watermelon Silver Mottle Virus Nonstructural Protein S Is Imperative For Protein Stability Affecting Self-Interaction, RNA Silencing Suppression, and Pathogenicity
Authors: Huang Chung-Hao , Foo Mung-Hsia , Raja Joseph A. J. , Tan Yue-Rong , Lin Tzu-Tung , Lin Shih-Shun , Yeh Shyi-Dong
Published: January 2020

In orthotospovirus, the nonstructural protein S (NSs) is the RNA-silencing suppressor (RSS) and pathogenicity determinant. Here, we demonstrate that a putative α-helix, designated H8, spanning amino acids 338 to 369 of the C-terminal region of the NSs protein, is crucial for self-interaction of watermelon silver mottle virus NSs protein and that the H8 affects RSS function. Co-immunoprecipitation, yeast two-hybrid, and bimolecular fluorescence complementation analyses revealed that the triple point mutation (TPM) of H8 amino acids Y338A, H350A, and F353A resulted in NSs protein self-interaction dysfunction. Transient expression of H8-deleted (ΔH8) and TPM NSs proteins in Nicotiana benthamiana plants by agroinfitration indicated that these proteins have weaker RSS activity and are far less stable than wild-type (WT) NSs. However, an electrophoretic mobility assay revealed that small interfering RNA (siRNA) binding ability of TPM NSs protein is not compromised. The pathogenicity assay of WT NSs protein expressed by the attenuated turnip mosaic virus vector restored severe symptoms in recombinant-infected N. benthamiana plants but not for ΔH8 or TPM proteins. Taken together, we conclude that the H8 helix in the C-terminal region of NSs protein is crucial for stabilizing NSs protein through self-interaction to maintain normal functions of RSS and pathogenicity, but not for NSs-siRNA binding activity.
Observational human studies in allergic diseases: design concepts and highlights of recent National Institute of Allergy and Infectious Diseases-funded research
Authors: Rudman Spergel Amanda K. , Togias Alkis
Published: January 2020

Purpose of review

To present and discuss key design concepts for optimizing the impact of observational studies in the field of allergy and to highlight recent findings from NIAID-funded research networks.

Recent findings

We discuss three concepts. First, the benefit of prospective, longitudinal observational studies exemplified by recent findings on the seasonal nature of all rhinitis phenotypes in children with asthma and the protective effects of high house dust allergen content during the first year of life on the development of asthma at age 7 years. Second, the benefit of detailed (deep) phenotyping exemplified by the identification of a MALT1 gene variant as a strong genetic link to peanut allergy and the determination that atopic dermatitis with food allergy constitutes a distinct cutaneous endotype, compared with atopic dermatitis alone. Third, the benefit of hypothesis-generating research combined with prospective design and deep phenotyping as exemplified by the unveiling of potential pathophysiologic pathways leading to asthma exacerbations in children, after a ‘cold’.

Observational studies can be highly impactful if designed well. Longitudinal study design, deep phenotyping, and hypothesis-generating research are three major design concepts that should be considered in the development of these studies.
Elucidating the mechanisms of action of parecoxib in the MG-63 osteosarcoma cell line
Authors: Lemos Sílvia , Sampaio-Marques Belém , Ludovico Paula , Gaivão Isabel , Palmeira Carlos , Martins Gabriela , Peixoto Francisco , Pinto-Leite Rosário , Oliveira Paula
Published: January 2020

Different types of tumors often present an overexpression of cyclooxygenase-2. The aim of this study was to evaluate the effects of parecoxib (NSAID, cyclooxygenase-2 selective inhibitor) in the behavior of the human osteosarcoma MG-63 cell line, concerning several biological features. Cells were exposed to several concentrations of parecoxib for 48 hours. Cell viability/proliferation, cyclooxygenase-2 expression, morphologic alterations, membrane integrity, cell cycle evaluation, cell death and genotoxicity were evaluated. When compared with untreated cells, parecoxib led to a marked decrease in cell viability/proliferation, in COX-2 expression and changes in cell morphology, in a concentration-dependent manner. Cell recuperation was observed after incubation with drug-free medium. Parecoxib exposure increased lactate dehydrogenase release, an arrest of the cell cycle at S-phase and G2/M-phase, as well as growth of the sub-G0/G1-fraction and increased DNA damage. Parecoxib led to a slight increase of necrosis regulated cell death in treated cells, and an increase of autophagic vacuoles, in a concentration-dependent manner. In this study, parecoxib showed antitumor effects in the MG-63 human osteosarcoma cells. The potential mechanism was inhibiting cell proliferation and promoting necrosis. These results further suggested that parecoxib might be a potential candidate for in-vivo studies.
Development and Validation of an UHPLC-MS/MS Assay for the Therapeutic Monitoring of Brivaracetam Plasma Concentrations in Patients with Epilepsy
Authors: Mohamed Susan , Riva Roberto , Contin Manuela
Published: January 2020

Background:

Brivaracetam is an antiepileptic drug used as an add-on therapy for partial-onset seizures in subjects aged 4 years and older. Owing to potential drug interactions and intersubject variability in plasma concentrations, therapeutic monitoring for brivaracetam may be useful. The aim of this study was to develop a simplified method for measuring brivaracetam plasma concentrations applicable to therapeutic drug monitoring in epilepsy.

Methods:

An ultra high-pressure liquid chromatography–tandem mass spectrometry method was developed and validated according to current guidelines for bioanalytical methods. Sample preparation (100 µL) involved only a simple precipitation step by acetonitrile. Brivaracetam-d7 was used as internal standard. The chromatographic analysis was performed by a Synergi Fusion column using 0.1% formic acid in water/acetonitrile as a binary gradient mobile phase, at a flow rate of 0.3 mL/min. Both brivaracetam and the internal standard eluted at 1.01 minutes. This method was applied to measure trough and 1-hour postmorning dose brivaracetam plasma concentrations of 11 patients with epilepsy.

Results:

The method was validated over a concentration range of 0.10–10 mcg/mL. The mean recovery was 95%. Both intra- and inter-assay imprecision and inaccuracy were <15% for all quality control samples. The lower limit of quantitation and detection was 0.10 and 0.05 mcg/mL, respectively. No interferences or carry-over was observed. Median (25%–75% quartiles) trough and 1-hour postdosing brivaracetam plasma concentrations were 0.61 mcg/mL (0.47–0.83 mcg/mL) and 1.55 mcg/mL (1.24–2.12 mcg/mL), respectively, at a median dose of 80 mg/d (50–150 mg/d). Large, up to 8-fold, intrasubject fluctuations of brivaracetam concentrations between trough and 1-hour postdosing were observed.

Conclusions:

The present assay is faster and simpler than previously published analytical reports for brivaracetam in human plasma and is suitable for therapeutic drug monitoring.
Is it possible to investigate menopausal age? A comparative cross-sectional study of five cohorts between 1968 and 2017 from the Population Study of Women in Gothenburg, Sweden
Authors: Rödström Kerstin , Weman Lilian , Sandin Linda , Hange Dominique , Björkelund Cecilia
Published: January 2020

Objective:

The aim of this study was to examine if the previously found trend of increasing menopausal age is continuing, taking into consideration hormonal use and surgical menopause in both 38- and 50-year-old women of today.

Methods:

Cohort comparisons of five generations of population-based samples of 38- and 50-year-old women from the Prospective Population Study of Women in Gothenburg with start in 1968/1969, and with follow-ups in 1980/1981, 1992/1993, 2004/2005, and 2016/2017. Across the time periods newly recruited women as well as earlier participants were included. Use of hormonal contraceptives, estrogen plus progestogen therapy (EPT), and time for menopause was registered. Changes between different generations of 38- and 50-year-old women from 1968/1969 until today were studied. The overall sample size across the time periods was 1,873 individuals.

Results:

The prevalence of oral contraceptives in 38-year-old women was about 10% in 1968/1969, increasing from 16% in 2004/2005 to almost 22% in 2016/2017. From 2004/2005 the use of hormonal intrauterine contraceptive method (the Levonorgestrel-releasing intrauterine system [LNG-IUS]) increased from about 11% to 14% in 2016/2017. The same pattern was found in 50-year-old women using LNG-IUS, increasing from 6% to 15.5% between 2004/2005 and 2016/2017. The total hormonal use, including LNG-IUS, oral contraceptives, and EPT, was 28% in 50-year-old women in 2016/2017. The total proportion of hormone use in 50-year-old women increased over the years and together with surgical menopause it reached over 37% in the 2016/2017 survey.

Conclusions:

This study has shown an increase in the hormonal use, in both 38- and 50-year-old women, making it difficult to determine when the actual menopause occurs. Thus, the previously found increasing secular trend in menopausal age will be more complicated to assess in female generations of today and tomorrow.
Evaluation and Treatment Patterns of New Low Back Pain Episodes for Elderly Adults in the United States, 2011–2014
Authors: Ly Dan P.
Published: January 2020

Introduction:

New low back pain (LBP) is a common outpatient complaint. Little is known about how care is delivered over the course of a year to patients who develop new LBP and whether such care patterns are guideline-concordant.

Methods:

This retrospective analysis included Medicare claims of 162,238 opioid-naïve beneficiaries with new LBP from January 1, 2011, through December 31, 2014. Simple rates of modality use [computed tomography and magnetic resonance imaging (advanced imaging), physical therapy (PT), opioid and nonopioid medications] and percentiles (5th percentile, 25th percentile, median, 75th percentile, and 95th percentile) were reported.

Results:

Within the first year, 29.4% [95% confidence interval (CI), 29.1–29.8] of patients with ≥2 visits for new LBP received advanced imaging, and 48.4% (95% CI, 47.7–49.0) of these patients received advanced imaging within 6 weeks of the first visit; 17.3% (95% CI, 17.1–17.6) of patients with ≥2 visits received PT; 42.2% (95% CI, 41.8–42.5) of patients with ≥2 visits received non–steroidal anti-inflammatory drugs (NSAIDs), 16.9% (95% CI, 16.6–17.1) received a muscle relaxant, and 26.2% (95% CI, 25.9–26.6) received tramadol; 32.3% (95% CI, 31.9–32.6) of patients with ≥2 visits received opioids; 52.4% (95% CI, 51.7–53.0) of these patients had not received a prescription NSAID, and 82.2% (95% CI, 81.7–82.7) of these patients had not received PT.

Conclusions:

Many patients who develop new LBP receive guideline nonconcordant care such as early advanced imaging and opioids before other modalities like PT and prescription NSAIDs.
Cancer-associated fibroblasts in cholangiocarcinoma
Authors: Vaquero Javier , Aoudjehane Lynda , Fouassier Laura
Published: January 2020

Purpose of review

To give a state-of-art knowledge regarding cancer-associated fibroblasts (CAF) in cholangiocarcinoma (CCA) based both on direct evidence and studies on other desmoplastic cancers. High contingency of CAF characterizes CCA, a tumor with a biliary epithelial phenotype that can emerge anywhere in the biliary tree. Current treatments are very limited, the surgical resection being the only effective treatment but restricted to a minority of patients, whereas the remaining patients undergo palliative chemotherapy regimens. In cancer, CAF shape the tumor microenvironment, drive cancer growth and progression, and contribute to drug resistance. All these functions are accomplished through an interplay network between CAF and surrounding cells including tumor and other stromal cells, i.e. immune and endothelial cells.

Recent findings

Several studies have pointed out the existence of CAF sub-populations carrying out several and opposite functions, cancer-promoting or cancer-restraining as shown in pancreatic cancer, another prototypic desmoplastic tumor in which heterogeneity of CAF is well demonstrated.

New CAF functions are now emerging in pancreatic and breast cancers like the modulation of immune responses or tumor metabolism, opening new area for treatments.
Environmental mixtures and children's health: identifying appropriate statistical approaches
Authors: Tanner Eva , Lee Alison , Colicino Elena
Published: January 2020

Purpose of review

Biomonitoring studies have shown that children are constantly exposed to complex patterns of chemical and nonchemical exposures. Here, we briefly summarize the rationale for studying multiple exposures, also called mixture, in relation to child health and key statistical approaches that can be used. We discuss advantages over traditional methods, limitations and appropriateness of the context.

Recent findings

New approaches allow pediatric researchers to answer increasingly complex questions related to environmental mixtures. We present methods to identify the most relevant exposures among a high-multitude of variables, via shrinkage and variable selection techniques, and identify the overall mixture effect, via Weighted Quantile Sum and Bayesian Kernel Machine regressions. We then describe novel extensions that handle high-dimensional exposure data and allow identification of critical exposure windows.

Recent advances in statistics and machine learning enable researchers to identify important mixture components, estimate joint mixture effects and pinpoint critical windows of exposure. Despite many advantages over single chemical approaches, measurement error and biases may be amplified in mixtures research, requiring careful study planning and design. Future research requires increased collaboration between epidemiologists, statisticians and data scientists, and further integration with causal inference methods.
Evaluating the Anatomical Traits of Lip on Three-Dimensional Computed Tomography Images
Authors: Babacan Serdar , Işiklar Sefa , Kafa Ilker Mustafa , Gökalp Gökhan
Published: January 2020

Background:

Lips and mouth are the most recognizable parts of the lower face. The morphometry of the facial organs is important for the balance of the face. Besides congenital anomalies occur on the lips, some kinds of deformities might be seen because of trauma or carcinoma. In this respect, lips are in the study of plastic surgery, maxillofacial surgery and orthodontics. Lip morphology also takes an important role in forensic facial reconstruction (facial approximation).

Materials and Methods:

Twenty parameters on the soft tissue and 12 parameters on the hard tissue were measured on three dimensional (3D) computed tomography (CT) images belonging 50 individuals (25 female, mean age 35.40 ± 9.97; 25 male, mean age 34.32 ± 11.06).

Results:

Statistical significance was observed on 4 parameters measured at soft tissue and 6 parameters measured in hard tissue. Statistical significance was not seen between the measurements taken bilaterally. Fourteen equations were developed in order to estimate the lip morphometry using the morphometric traits of hard tissue.

Conclusion:

We hope that the results of current study will be useful at surgery and forensic sciences.
Effect of Induced Membrane on Guided Bone Regeneration in an Experimental Calvarial Model
Authors: Altiparmak Nur , Akdeniz Sidika Sinem , Akcay Eda Yilmaz , Bayram Burak , Araz Kenan
Published: January 2020

Objective:

The aim of this study was to evaluate the effect of induced membrane on guided bone regeneration and to compare its effect with poly-tetra-flourur-ethylene (PTFE) membrane and collagen membrane.

Methods:

Sixteen white Vienna rabbits were used for experiments. Initially 1 defect was created on the parietal bone of all animals and cement was placed inside the defects. After 8 weeks, the bone cements were removed, without damaging the induced membrane formed in the defect cavity. And then 2 more defects were created. All defects were filled with xsenogenic graft materials and were covered with newly formed induced membrane, d-PTFE membrane and collagen membrane. Eight animals were sacrificed at 4th week and other 8 animals were sacrificed at 8th week and all bone specimens were histologically evaluated.

Results:

New bone formation and bone marrow ratios were significantly higher in induced membrane and d-PTFE membrane group compared to collagen membrane group (P < 0.05) at 4th week. Mature bone ratios were significantly higher in induced membrane and d-PTFE membrane group compared to collagen membrane group (P < 0.05) at 8th week. The best CD31 value was detected with d-PTFE membrane group at 4th week and with induced membrane at 8th week.

Conclusion:

Induced membrane can act as a strong barrier membrane and stimulate bone regeneration. Induced membrane technique can be accepted as a good alternative for the reconstruction of critical size defects in maxillofacial region.
Ornithinimicrobium cerasi sp. nov., isolated from the fruit of Cerasus pseudocerasus and emended description of the genus Ornithinimicrobium
Authors: Fang Xiao-Mei , Du Hui-Jing , Bai Jing-Lin , He Wen-Ni , Li Jun , Wang Hao , Su Jing , Liu Hong-Yu , Zhang Yu-Qin , Yu Li-yan
Published: January 2020

Strain CPCC 203383T, isolated from the surface-sterilized fruit of Cerasus pseudocerasus (Lindl.) G. Don, was taxonomically characterized based on a polyphasic investigation. It had the highest 16S rRNA gene sequence similarities with

Ornithinimicrobium pekingense

DSM 21552 (97.2 %) and

O. kibberense

DSM 17687T (97.2%). Phylogenetic analysis based on 16S rRNA gene sequences showed that the strain formed a distinct phyletic branch within the genus

Ornithinimicrobium

and the whole genome sequence data analyses supported that strain CPCC 203383T was phylogenetically related to the

Ornithinimicrobium

species. The isolate shared a range of phenotypic patterns reported for members of the genus

Ornithinimicrobium

, but also had a range of cultural, physiological and biochemical characteristics that separated it from related

Ornithinimicrobium

species. The menaquinone was MK-8(H4). The polar lipid profile consisted of diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylinositol (PI) and unidentified lipids (ULs). The major fatty acids (>5 %) were iso-C15 : 0, anteiso-C15 : 0, iso-C16:0, 9-methyl C16 : 0, iso-C17 : 0 and anteiso-C17 : 0. The cell wall peptidoglycan contains l-ornithine as diagnostic diamino acid and an interpeptide bridge consisting of L-Orn←L-Ala←Gly←D-Asp. The combined genotypic and phenotypic data indicated that the isolate represents a novel species of the genus Ornithinimicrobium, for which the name Ornithinimicrobium cerasi sp. nov. is proposed, with CPCC 203383T(=NBRC 113522T=KCTC 49200T) as the type strain. The DNA G+C composition is 72.3 mol%. The availability of new data allows for an emended description of the genus

Ornithinimicrobium

.
Differential dynamics and impacts of prophages and plasmids on the pangenome and virulence factor repertoires of Shiga toxin-producing Escherichia coli O145:H28
Authors: Nakamura Keiji , Murase Kazunori , Sato Mitsuhiko P. , Toyoda Atsushi , Itoh Takehiko , Mainil Jacques Georges , Piérard Denis , Yoshino Shuji , Kimata Keiko , Isobe Junko , Seto Kazuko , Etoh Yoshiki , Narimatsu Hiroshi , Saito Shioko , Yatsuyanagi Jun , Lee Kenichi , Iyoda Sunao , Ohnishi Makoto , Ooka Tadasuke , Gotoh Yasuhiro , Ogura Yoshitoshi , Hayashi Tetsuya
Published: January 2020

Phages and plasmids play important roles in bacterial evolution and diversification. Although many draft genomes have been generated, phage and plasmid genomes are usually fragmented, limiting our understanding of their dynamics. Here, we performed a systematic analysis of 239 draft genomes and 7 complete genomes of Shiga toxin (Stx)-producing

Escherichia coli

O145:H28, the major virulence factors of which are encoded by prophages (PPs) or plasmids. The results indicated that PPs are more stably maintained than plasmids. A set of ancestrally acquired PPs was well conserved, while various PPs, including Stx phages, were acquired by multiple sublineages. In contrast, gains and losses of a wide range of plasmids have frequently occurred across the O145:H28 lineage, and only the virulence plasmid was well conserved. The different dynamics of PPs and plasmids have differentially impacted the pangenome of O145:H28, with high proportions of PP- and plasmid-associated genes in the variably present and rare gene fractions, respectively. The dynamics of PPs and plasmids have also strongly impacted virulence gene repertoires, such as the highly variable distribution of stx genes and the high conservation of a set of type III secretion effectors, which probably represents the core effectors of O145:H28 and the genes on the virulence plasmid in the entire O145:H28 population. These results provide detailed insights into the dynamics of PPs and plasmids, and show the application of genomic analyses using a large set of draft genomes and appropriately selected complete genomes.
Tuberculosis in Liberia: high multidrug-resistance burden, transmission and diversity modelled by multiple importation events
Authors: López Mariana G. , Dogba John B. , Torres-Puente Manuela , Goig Galo A. , Moreno-Molina Miguel , Villamayor Luis M. , Cadmus Simeon , Comas Iñaki
Published: January 2020

Tuberculosis (TB) surveillance is scarce in most African countries, even though it is the continent with the greatest disease incidence according to the World Health Organization. Liberia is within the 30 countries with the highest TB burden, probably as a consequence of the long civil war and the recent Ebola outbreak, both crippling the health system and depreciating the TB prevention and control programmes. Due to difficulties working in the country, there is a lack of resistance surveys and bacillus characterization. Here, we use genome sequencing of

Mycobacterium

tuberculosis

clinical isolates to fill this gap. Our results highlight that the bacillus population structure is dominated by lineage 4 strains that harbour an outstanding genetic diversity, higher than in the rest of Africa as a whole. Coalescent analyses demonstrate that strains currently circulating in Liberia were introduced several times beginning in the early year 600 CE until very recently coinciding with migratory movements associated with the civil war and Ebola epidemics. A higher multidrug-resistant (MDR)-TB frequency (23.5 %) than current estimates was obtained together with non-catalogued drug-resistance mutations. Additionally, 39 % of strains were in genomic clusters revealing that ongoing transmission is a major contribution to the TB burden in the country. Our report emphasizes the importance of TB surveillance and control in African countries where bacillus diversity, MDR-TB prevalence and transmission are coalescing to jeopardize TB control programmes.
Improving Deconvolution Methods in Biology through Open Innovation Competitions: An Application to the Connectivity Map
Authors: Blasco Andrea , Natoli Ted , Endres Michael G. , Sergeev Rinat A. , Randazzo Steven , Paik Jin H. , Maximilian Macaluso N. J. , Narayan Rajiv , Lu Xiaodong , Peck David , Lakhani Karim R. , Subramanian Aravind
Published: January 2020

Do machine learning methods improve standard deconvolution techniques for gene expression data? This paper uses a unique new dataset combined with an open innovation competition to evaluate a wide range of gene-expression deconvolution approaches developed by 294 competitors from 20 countries. The objective of the competition was to separate the expression of individual genes from composite measures of gene pairs. Outcomes were evaluated using direct measurements of single genes from the same samples. Results indicate that the winning algorithm based on random forest regression outperformed the other methods in terms of accuracy and reproducibility. More traditional gaussian-mixture methods performed well and tended to be faster. The best deep learning approach yielded outcomes slightly inferior to the above methods. We anticipate researchers in the field will find the dataset and algorithms developed in this study to be a powerful research tool for benchmarking their deconvolution methods and a useful resource for multiple applications.
Impact of trait exaggeration on sex-biased gene expression and genome architecture in a water strider
Authors: Toubiana William , Armisén David , Dechaud Corentin , Arbore Roberto , Khila Abderrahman
Published: January 2020

Exaggerated secondary sexual traits are widespread in nature and often evolve under strong directional sexual selection. Although heavily studied from both theoretical and empirical viewpoints, we have little understanding of how sexual selection influences sex-biased gene regulation during the development of sex-specific phenotypes, and how these changes are reflected in genomic architecture. This is primarily due to the lack of a representative genome and transcriptomes to study the development of secondary sexual traits. Here we present the genome and developmental transcriptomes, focused on the legs of the water striderMicrovelia longipes, a species where males exhibit strikingly long third legs used as weapons. The quality of the genome assembly is such that over 90% of the sequence is captured in 13 scaffolds. The most exaggerated legs in males were particularly enriched in sex-biased genes, indicating a specific signature of gene expression in association with sex-specific trait exaggeration. We also found that male-biased genes showed patterns of fast evolution compared to non-biased and female-biased genes, indicative of directional or relaxed purifying selection. Interestingly, we found that female-biased genes that are expressed in the third legs only, but not male-biased genes, were over-represented in the X chromosome compared to the autosomes. An enrichment analysis for sex-biased genes along the chromosomes revealed that they can arrange in large genomic regions or in small clusters of two to four consecutive genes. The number and expression of these enriched regions were often associated with the exaggerated legs of males, suggesting a pattern of common regulation through genomic proximity in association with trait exaggeration. Our findings shed light on how directional sexual selection drives sex-biased gene expression and genome architecture along the path to trait exaggeration and sexual dimorphism.
Short-term exposure to high-water temperature causes a shift in the microbiome of the common aquarium spongeLendenfeldia chondrodes
Authors: Vargas Sergio , Leiva Laura , Wörheide Gert
Published: January 2020

Marine sponges harbor diverse microbiomes that contribute to their energetic and metabolic needs. Although numerous studies on sponge microbial diversity exist, relatively few focused on sponge microbial community changes under different sources of environmental stress. In this study, we assess the impact of elevated seawater temperature on the microbiome of culturedLendenfeldia chondrodes, a coral reef sponge commonly found in marine aquaria.Lendenfeldia chondrodesexhibits high thermal tolerance showing no evidence of tissue damage or bleaching at 5 °C above control water temperature (26 °C). High-throughput sequencing of the bacterial 16S rRNA V4 region revealed a response of the microbiome ofL. chondrodesto short-term exposure to elevated seawater temperature. Shifts in abundance and richness of the dominant bacterial phyla found in the microbiome of this species, namely Proteobacteria, Cyanobacteria, Planctomycetes, and Bacteroidetes, characterized this response. The observed resilience ofL. chondrodesand the responsiveness of its microbiome to short-term increases in seawater temperature suggest that this holobiont may be capable of acclimating to anthropogenic-driven sublethal environmental stress via a re-accommodation of its associated bacterial community. This sheds a new light on the potential for resilience of some sponges to increasing surface seawater temperatures and associated projected regime shifts in coral reefs.
Behavioral evidence for memory replay of video episodes in macaque monkeys
Authors: Zuo Shuzhen , Wang Lei , Shin Junghan , Cai Yudian , Lee Sang Wan , Appiah Kofi , Zhou Yong-di , Kwok Sze Chai
Published: January 2020

Humans recall the past by replaying fragments of events temporally. Here, we demonstrate a similar effect in macaques. We trained six rhesus monkeys with a temporal-order judgement (TOJ) task and collected 5000 TOJ trials. In each trial, they watched a naturalistic video of about 10 s comprising two across-context clips, and after a 2-s delay, performed TOJ between two frames from the video. The monkeys apply a non-linear forward, time-compressed replay mechanism during the temporal-order judgement. In contrast with humans, such compression of replay is however not sophisticated enough to allow them to skip over irrelevant information by compressing the encoded video globally. We also reveal that the monkeys detect event contextual boundaries and such detection facilitates recall by an increased rate of information accumulation. Demonstration of a time-compressed, forward replay like pattern in the macaque monkeys provides insights into the evolution of episodic memory in our lineage.

Impact Statement

Macaque monkeys temporally compress past experiences and use a forward-replay mechanism during judgment of temporal-order between episodes.
A New Model of Genetic Variation and Evolution Evaluates Relative Impacts of Background Selections and Selective Sweeps
Authors: Gu Xun
Published: January 2020

Intra-population genetic variation and interspecies divergence in chromosome regions can be considerably affected by different local recombination rates. There are two models: (i) the selective sweeps that reduces the genetic diversity at linked sites and elevates the divergence rate; and (ii) the background selection that reduces the genetic diversity at linked sites and divergence rate. An intriguing question, yet highly controversial, is which one is dominant. In this paper, I develop a framework of generalize background selection, formulated by a diffusion model with two killing functions: the one associated with (negative) background selection is the rate to stop a fixation process of a mutation randomly, and the other associated with positive background selection (selective sweep) is the rate to stop a loss process of a mutation randomly. A simple relationship between the level of reduced diversity and the rate of divergence is derived, depending on the strength of generalized background selection (G) and the proportion of positive background selection (β). We analyzed the interspecies divergence and intra-population diversity in low-recombination regions of three organisms (fruitfly, soybean and human). Strikingly, all datasets demonstrated the dominance of (negative) background selection, and the positive background selection (selective sweeps) only has a small contribution (β∼10%). However, our analysis rejects the notion ofβ=0, namely, a complete negative background selection is unlikely. These findings may shed some lights on the long-term debates around Neutral Theory.