bluuebunny/crossref_metadata_2025 huggingface dataset:
A Framework for Inclusive Graduate Medical Education Recruitment Strategies: Meeting the ACGME Standard for a Diverse and Inclusive Workforce
Authors: Gonzaga Alda Maria R. , Appiah-Pippim James , Onumah Chavon M. , Yialamas Maria A.
Published: November 2019

To help address health care disparities and promote higher-quality, culturally sensitive care in the United States, the Accreditation Council for Graduate Medical Education and other governing bodies propose cultivating a more diverse physician workforce. In addition, improved training and patient outcomes have been demonstrated for diverse care teams. However, prioritizing graduate medical education (GME) diversity and inclusion efforts can be challenging and unidimensional diversity initiatives typically result in failure.

Little literature exists regarding actionable steps to promote diversity in GME. Building on existing literature and the authors’ experiences at different institutions, the authors propose a 5-point inclusive recruitment framework for diversifying GME training programs. This article details each of the 5 steps of the framework, which begins with strong institutional support by setting diversity as a priority. Forming a cycle, the other 4 steps are seeking out candidates, implementing inclusive recruitment practices, investing in trainee success, and building the pipeline. Practical strategies for each step and recommendations for measurable outcomes for continued support for this work are provided. The proposed framework may better equip colleagues and leaders in academic medicine to prioritize and effectively promote diversity and inclusion in GME at their respective institutions.
Keratinocyte Carcinoma Mortality in the United States as Reported in Death Certificates, 2011–2017
Authors: Misitzis Angelica , Beatson Meghan , Weinstock Martin A.
Published: November 2019

BACKROUND

Keratinocyte carcinoma (KC) mortality is relatively modest and its measures are subject to considerable error. Deaths due to KC have been decreasing through 2000 and were relatively stable until 2010.

OBJECTIVE

To estimate the KC mortality rates (MRs) from 2011 to 2017 in USA based on death certificates.

METHODS

A population-based analysis of Center of Disease Control and Prevention data. Main outcomes and measures were the age-adjusted (US 2000 standard population) MRs.

RESULTS

Overall, KC MRs increased significantly (b = 0.04, p < .01). For the period studied, KC MR was 1.24 per 100,000 persons per year (0.62 for sun-exposed sites, 0.38 for genital and 0.23 for perianal sites). At sun-exposed genital and perianal anatomic sites, KC MRs have been increasing in whites, but not in blacks.

CONCLUSION

There was a 17% decrease in the KC MRs until 2000, followed by an increase of 44% through 2017. The accuracy of KC MRs is uncertain. If indeed the increase in mortality is verified, causes may include an increase in KC incidence, an increase of immunosuppressed populations, and changes in the cause of death documentation.
A Systematic Review of Clinical Outcomes Associated With Intrahospital Transitions
Authors: Bristol Alycia A. , Schneider Catherine E. , Lin Shih-Yin , Brody Abraham A.
Published: November 2019

Previous transitional care research has focused on transitions occurring between community and hospital settings. Little is known regarding intrahospital transitions and how they affect care quality. A systematic review was therefore conducted to synthesize the literature regarding clinical outcomes associated with intrahospital transitions. Literature published between January 2003 and December 2018 and indexed in Medline/PubMed, CINAHL, and PsychINFO were reviewed using PRISMA guidelines. Articles were limited to English language and peer-reviewed. Articles were excluded if they focused on transitions occurring from or to the hospital, discharge/discharge planning, or postdischarge follow-up. Data abstraction included study characteristics, sample characteristics, and reported clinical outcomes. Fourteen studies met inclusion criteria, primarily using cross-sectional, cohort, or retrospective chart review quantitative designs. Data were analyzed and synthesized based on outcomes reported. Major outcomes emerging from the articles included delirium, hospital length of stay, mortality, and adverse events. Delirium, hospital length of stay, and morbidity and mortality rates were associated with delayed transfers and transfers to inappropriate units. In addition, increased fall risk and infection rates were associated with higher rates of transfer. Intrahospital transitions represent critical periods of time where the quality of care being provided may be diminished, negatively affecting patient safety and outcomes.
Educational characteristics and content of postgraduate nurse practitioner residency/fellowship programs
Authors: Kesten Karen S. , El-Banna Majeda M. , Blakely Jessica
Published: November 2019

Background:

Nurse practitioner (NP) residency/fellowship programs are an emerging industry across the country.

Purpose:

This study aimed to conduct an in-depth exploration about postgraduate NP residency/fellowship programs in the United States and to gain an understanding of program characteristics, educational content, and implementation methods to assist NPs to transition to practice.

Methods:

This exploratory study used a quantitative design to conduct an online survey of program directors of NP residency/fellowship programs to collect data about program characteristics to assist graduates to transition to practice. Descriptive statistics were calculated for continuous variables, whereas frequency and percentage were calculated for categorical variables.

Results:

Nurse practitioner residency/fellowship programs lack consistency in standards for educational content and delivery methods. Only 26% of the programs were accredited, and the programs were not consistently based on nationally recognized competencies. Ninety percent of the programs relied on didactic and clinical supervision delivery methods. More than 90% of the residents/fellows cared for adults older than 65 years of age and managed chronic diseases. Family Nurse Practitioner was the most commonly cited population track offered (73%). Nurse practitioner residency/fellowship programs are sparsely offered in the most rural states with underserved populations.

Implications for practice:

This study provides data and insight into the emerging industry of postgraduate NP residency/training programs for educators and employers. In addition, it informs regulators and decision makers about the quality and consistency of programs and the impact of programs on the care delivered by new graduate NPs.
Neurosyphilis complicated with pial arteriovenous fistula
Authors: Xu Lingmei , Han Fugang
Published: November 2019

Introduction:

Neurosyphilis is a chronic, infectious disease of the central nervous system. Pial arteriovenous fistulae (PAVF) are rare vascular malformations. Both can cause vascular damage, but it is quite rare for both to present at the same time.

Patient concerns:

Here we present a 66-year-old man with affective disorder, hypomnesia, and recent convulsions. Magnetic resonance imaging revealed cerebral swelling, hyperintensity in the cortex/subcortex, and multiple lacunar cerebral infarctions. Computed tomography angiography revealed the presence of a pial arteriovenous fistula.

Diagnoses:

Based on laboratory tests and imaging, diagnoses of neurosyphilis and pial arteriovenous fistula were made.

Interventions:

Antisyphilis therapy was provided.

Outcomes:

Symptoms improved and antisyphilis treatment continued as an outpatient. No intracranial hemorrhage was seen 6 months later.

Conclusion:

Treponema pallidum infection may be related to the formation of PAVF, and may also promote the progression of it; however, further work is required to confirm this.
Phlegmonous gastritis in a patient with mixed-phenotype acute leukemia in the neutropenia phase during chemotherapy
Authors: Shi Dayu , He Jinde , Lv Meng , Liu Rui , Zhao Ting , Jiang Qian
Published: November 2019

Rationale:

Phlegmonous gastritis is a rare bacterial infection of the gastric wall with high mortality. However, diagnosis of phlegmonous gastritis is difficult and standard treatment remains unestablished.

Patient concerns:

We report a 33-year-old male patient with mixed-phenotype acute leukemia who developed acute phlegmonous gastritis during the neutropenia phase on induction chemotherapy and was successfully treated.

Diagnoses:

The patient was diagnosed with phlegmonous gastritis, which might be caused by Stenotrophomonas maltophilia on the basis of clinical manifestation, physical examination, enhanced computed tomography scan, histological finding, and microorganism culture of biopsied specimen in endoscopy.

Interventions:

The patient was treated with gastrointestinal decompression and broad-spectrum antibiotics.

Outcomes:

He recovered from phlegmonous gastritis and received the 2nd cycle of chemotherapy with no complaint of abdominal discomfort.

Lessons:

Early recognition and proper management including broad-spectrum antibiotics are key approaches to phlegmonous gastritis.
The transjugular approach is a safe and effective alternative for performing portal vein embolization
Authors: Jiang Ming-Shan , Luo Xue-Feng , wang Zhu , Li Xiao
Published: November 2019

To evaluate the safety and efficacy of the novel technique, transjugular portal vein embolization (TPVE).

A single-center retrospective review of 18 patients (12 males and 6 females; mean age, 62 years) who underwent TPVE between January 2012 and January 2013 was conducted. The technical success rate, future liver remnant (FLR) volume, total liver volume (TLV) and FLR/TLV ratio after PVE were analyzed. Liver function, including total bilirubin (TB), aspartate aminotransferase (AST), alanine aminotransferase (ALT) and International Normalized Ratio (INR), was assessed before and after PVE. Any complications of TPVE and liver resection after TPVE were recorded.

TPVE was performed on 18 patients before right hepatic resection for both primary and secondary hepatic malignancies (10 hepatocellular carcinomas, 4 cases of colorectal liver metastasis, and 4 cholangiocarcinomas). Technical success was achieved in 100% of patients (18 of 18). The mean FRL significantly increased to 580 ± 155 mL (P < .001) after PVE. The mean FLR/TLV ratio (%) significantly increased to 34 ± 4 (P < .001) after PVE. One patient suffered septicemia after TPVE. A small number patients experienced mild to moderate abdominal pain during TPVE. No other major complications occurred after TPVE in our study. The patient who developed septicemia died 3 days after the surgery as a result of this complication and subsequent multiple organ dysfunction syndrome (MODS).

Transjugular portal vein embolization is a safe, efficacious, and promising novel technique to induce hypertrophy of the FLR.
Absicoccus porci gen. nov., sp. nov., a member of the family Erysipelotrichaceae isolated from pig faeces
Authors: Shin Yeseul , Paek Jayoung , Kim Hongik , Kook Joong-Ki , Kim Joong-Su , Kim Si Hyun , Chang Young-Hyo
Published: November 2019

An obligately anaerobic, Gram-stain-positive and coccus-shaped bacterium, designated strain YH-panp20T, was isolated from pig faeces. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the isolate belongs to the family

Erysipelotrichaceae

, and is most closely related to

Catenisphaera adipataccumulans

KCTC 15517T (93.5 % sequence similarity), followed by

Faecalitalea cylindroides

KCTC 5815T (92.2 %),

Faecalicoccus acidiformans

KCTC 15521T (90.2 %) and

Holdemanella biformis

KCTC 5969T (89.6 %). Average nucleotide identity values between YH-panp20T and its closest relatives were lower than 71 %. The G+C content of the isolate was 38.4 mol%, and its cell-wall peptidoglycan was found to be of A1γ type and contained meso-diaminopimelic acid. The predominant fatty acids were C18 : 1
cis 9, C18 : 0 DMA and C16 : 0. The major end-products of glucose fermentation were lactate, acetate and formate. Therefore, based on the phenotypic, phylogenetic and chemotaxonomic properties, a novel genus and species, Absicoccus porci gen. nov., sp. nov., is proposed for isolate YH-panp20T (=KCTC 15747T=JCM 32769T).
Vibrio sinensis sp. nov. and Vibrio viridaestus sp. nov., two marine bacteria isolated from the East China Sea
Authors: Li Yuying , Liang Jinchang , Liu Ronghua , Xue Chun-Xu , Zhou Shun , He Xinxin , Li Bei , Wang Xiaolei , Zhang Xiao-Hua
Published: November 2019

Two Gram-staining-negative, facultatively anaerobic, motile, short clavate and flagellated marine bacteria, designated strains BEI233T and LJC006T, were isolated from the East China Sea. On the basis of the results of 16S rRNA gene sequencing and multilocus sequence analysis, BEI233T and LJC006T should be assigned to the genus

Vibrio

. The closest phylogenetic relatives of BEI233T are

Vibrio scophthalmi

LMG 19158T (98.7 % 16S rRNA gene sequence pairwise similarity),

Vibrio ichthyoenteri

DSM 14397T (98.5 %),

Vibrio renipiscarius

KCTC 42287T (97.7 %),

Vibrio aestuarianus

ATCC 35048T (97.3 %) and

Vibrio thalassae

MD16T (96.5 %), whereas for LJC006T they were

Vibrio furnissii

CAIM 518T (97.1 %),

Vibrio fluvialis

LMG 7894T (97.0%),

Vibrio tritonius

JCM 16456T (96.9 %) and

Vibrio xuii

LMG 21346T (96.1 %). The growth of BEI233T occurred at 10–37 °C, pH 5.0–8.0 and with 1–7 % (w/v) NaCl, while the growth of LJC006T occurred at 10–37 °C, pH 6.0–9.0, and 0–8 % (w/v) NaCl. The predominant fatty acids (>10 %) were summed feature 3 (C16 : 1ω7c or/and C16 : 1ω6c), C16 : 0 and summed feature 8 (C18 : 1ω7c or/and C18 : 1ω6c), with different proportions. The DNA G+C contents of BEI233T and LJC006T are 42.41 mol% and 41.88 mol%, respectively. On the basis of the results of polyphasic analysis, BEI233T and LJC006T are considered to represent novel species of the genus Vibrio, for which the names Vibrio sinensis sp. nov. and Vibrio viridaestus sp. nov. are proposed. The type strains are BEI233T (=JCM 32692T=KCTC 62618T) and LJC006T (=JCM 32693T=KCTC 62620T), respectively.
Flavobacterium psychrotolerans sp. nov., a psychrotolerant bacterium isolated from Renlongba glacier on the Tibetan Plateau
Authors: Yang Lei-Lei , Liu Qing , Liu Hong-Can , Zhou Yu-Guang , Xin Yu-Hua
Published: November 2019

One aerobic, Gram-stain-negative, rod-shaped bacterium, designated strain RB1R5T, was isolated from Renlongba glacier in Tibet Autonomous Region, China. Growth was observed at 4–25 °C and pH 7.0–8.0. Phylogenetic analysis based on 16S rRNA gene sequences revealed that strain RB1R5T belongs to the genus

Flavobacterium

, and its closest relatives are

Flavobacterium luteum

IMCC26026T and

Flavobacterium psychroterrae

CCM 8827T with 97.75 and 97.42% gene sequence similarities, respectively. The average nucleotide identity and DNA–DNA hybridization values between strain RB1R5T and its closest relative

Flavobacterium luteum

IMCC26026T were 78.02 and 21.8 %, respectively. The major cellular fatty acids were anteiso-C15 : 0 and summed feature 3 (comprising C16:1ω7c/C16:1ω6c). The sole menaquinone was MK-6. The major phospholipid was phosphatidylethanolamine. On the basis of phenotypic, phylogenetic and chemotaxonomic characterizations, strain RB1R5T represents a novel species of the genus

Flavobacterium

, for which the name Flavobacterium psychrotolerans sp. nov. is proposed. The type strain is RB1R5T (=CGMCC 1.23024T=NBRC 113060T).
Protocol for an observational study evaluating new approaches to modelling diagnostic information from large administrative hospital datasets
Authors: Cowling Thomas E , Cromwell David A , Sharples Linda D , van der Meulen Jan
Published: November 2019

Introduction

The Charlson and Elixhauser indices define sets of conditions used to adjust for patients’ comorbidities in administrative hospital data. A strength of these indices is the parsimony that results from including only 19 and 30 conditions respectively, but the conditions included may not be the ones most relevant to a specific outcome and population. Our objectives are to: (1) test an approach to developing parsimonious indices for the specific outcome and populations being studied, while comparing performance to the Charlson and Elixhauser indices; and (2) evaluate several approaches that involve models with more diagnosis-related terms and aim to improve prediction performance by capturing more of the information in large datasets.

Methods and analysis

This is a modelling study using a linked national dataset of administrative hospital records and death records. The study populations are patients admitted to hospital for acute myocardial infarction, hip fracture, or major surgery for colorectal cancer in England between 1 January 2015 and 31 December 2017. The outcome is death within 365 days of the date of admission (acute myocardial infarction and hip fracture) or procedure (colorectal surgery). In the ‘First analysis’, prognostic indices will be developed based on the presence/absence of individual ICD-10 codes in patients’ medical histories. Logistic regression will be used to estimate associations with a full set of sociodemographic and diagnostic predictors from which reduced models (with fewer diagnostic predictors) will be produced using a step-down approach. In the ‘Second analysis’, models will also account for the timing that each ICD-10 code was last recorded and allow for non-linear relationships and interactions between conditions and the timings of records. Validation will include an overall measure of performance (scaled Brier score) and measures of discrimination (c-statistic) and calibration (such as the Integrated Calibration Index) in bootstrap or cross-validation samples. Sensitivity analyses will include varying the length of medical history analysed, using a comparator that combines the Charlson and Elixhauser sets of conditions, and aggregating ICD-10 codes into clinical groups.
Transcription imparts architecture, function, and logic to enhancer units
Authors: Tippens Nathaniel D , Liang Jin , Leung King Y , Ozer Abdullah , Booth James G , Lis John T , Yu Haiyuan
Published: November 2019

Distal enhancers remain one of the least understood regulatory elements with pivotal roles in development and disease. We used massively parallel reporter assays to perform functional comparisons of two leading enhancer models and find that gene-distal transcription start sites (TSSs) are robust predictors of enhancer activity with higher resolution and specificity than histone modifications. We show that active enhancer units are precisely delineated by active TSSs, validate that these boundaries are sufficient to capture enhancer function, and confirm that core promoter sequences are required for this activity. Finally, we assay pairs of adjacent units and find that their cumulative activity is best predicted by the strongest unit within the pair. Synthetic fusions of enhancer units demonstrate that adjacency imposes winner-takes-all logic, revealing a simple design for a maximum-activity filter of enhancer unit outputs. Together, our results define fundamental enhancer units and a principle of non-cooperativity between adjacent units.
Analysis of genomic-length HBV sequences to determine genotype and subgenotype reference sequences
Authors: McNaughton Anna L , Revill Peter , Littlejohn Margaret , Matthews Philippa C , Ansari M Azim
Published: November 2019

Hepatitis B virus (HBV) is a diverse, partially double-stranded DNA virus, with 9 genotypes (A-I), and a putative 10th genotype (J), thus far characterised. Given the broadening interest in HBV sequencing, there is an increasing requirement for a consistent, unified approach to HBV genotype and subgenotype classification. We set out to generate an updated resource of reference sequences using the diversity of all genomic-length HBV sequences available in public databases. We collated and aligned genomic-length HBV sequences from public databases and used maximum-likelihood phylogenetic analysis to identify genotype clusters. Within each genotype, we examined the phylogenetic support for currently defined subgenotypes, as well as identifying well-supported clades and deriving reference sequences for them. An alignment of these reference sequences and maximum-likelihood phylogenetic trees of the sequences are provided to simplify classification. Based on the phylogenies generated, we present a comprehensive set of HBV reference sequences at the genotype and subgenotype level.
A process-based metacommunity framework linking local and regional scale community ecology
Authors: Thompson Patrick L. , Guzman Laura Melissa , De Meester Luc , Horváth Zsófia , Ptacnik Robert , Vanschoenwinkel Bram , Viana Duarte S. , Chase Jonathan M.
Published: November 2019

The metacommunity concept has the potential to integrate local and regional dynamics within a general community ecology framework. To this end, the concept must move beyond the discrete archetypes that have largely defined it (e.g. neutral vs. species sorting) and better incorporate local scale species interactions and coexistence mechanisms. Here, we present a fundamental reconception of the framework that explicitly links local coexistence theory to the spatial processes inherent to metacommunity theory, allowing for a continuous range of competitive community dynamics. These dynamics emerge from the three underlying processes that shape ecological communities: 1) density-independent responses to abiotic conditions, 2) density-dependent biotic interactions, and 3) dispersal. Stochasticity is incorporated in the demographic realization of each of these processes. We formalize this framework using a simulation model that explores a wide range of competitive metacommunity dynamics by varying the strength of the underlying processes. Using this model and framework, we show how existing theories, including the traditional metacommunity archetypes, are linked by this common set of processes. We then use the model to generate new hypotheses about how the three processes combine to interactively shape diversity, functioning, and stability within metacommunities.

Statement of authorship

This project was conceived at the sTURN working group, of which all authors are members. PLT developed the framework and model with input from all authors. PLT wrote the model code. PLT and LMG performed the simulations. PLT produced the figures and wrote the first draft with input from LMG and JMC. All authors provided feedback and edits on several versions of the manuscript.

Data accessibility

All code for running the simulation model and producing the figures is archived on Zenodo -https://doi.org/10.5281/zenodo.3833035.
Estimating and interpreting nonlinear receptive fields of sensory responses with deep neural network models
Authors: Keshishian Menoua , Akbari Hassan , Khalighinejad Bahar , Herrero Jose , Mehta Ashesh D. , Mesgarani Nima
Published: November 2019

Sensory processing by neural circuits includes numerous nonlinear transformations that are critical to perception. Our understanding of these nonlinear mechanisms, however, is hindered by the lack of a comprehensive and interpretable computational framework that can model and explain nonlinear signal transformations. Here, we propose a data-driven framework based on deep neural network regression models that can directly learn any nonlinear stimulus-response mapping. A key component of this approach is an analysis method that reformulates the exact function of the trained neural network as a collection of stimulus-dependent linear functions. This locally linear receptive field interpretation of the network function enables straightforward comparison with conventional receptive field models and uncovers nonlinear encoding properties. We demonstrate the efficacy of this framework by predicting the neural responses recorded invasively from the auditory cortex of neurosurgical patients as they listened to speech. Our method significantly improves the prediction accuracy of auditory cortical responses particularly in nonprimary areas. Moreover, interpreting the functions learned by neural networks uncovered three distinct types of nonlinear transformations of speech that varied considerably in primary and nonprimary auditory regions. By combining two desired properties of a computational sensory-response model; the ability to capture arbitrary stimulus-response mappings and maintaining model interpretability, this data-driven method can lead to better neurophysiological models of the sensory processing.
Neurocomputational mechanisms underlying immoral decisions benefiting self or others
Authors: Qu Chen , Hu Yang , Tang Zixuan , Derrington Edmund , Dreher Jean-Claude
Published: November 2019

Immoral behavior often consists of weighing transgression of a moral norm against maximizing personal profits. One important question is to understand why immoral behaviors vary based on who receives specific benefits and what are the neurocomputational mechanisms underlying such moral flexibility. Here, we used model-based fMRI to investigate how immoral behaviors change when benefiting oneself or someone else. Participants were presented with offers requiring a tradeoff between a moral cost (i.e., profiting a morally bad cause) and a benefit for either oneself or a charity. Participants were more willing to obtain ill-gotten profits for themselves than for a charity, driven by a devaluation of the moral cost when deciding for their own interests. The subjective value of an immoral offer, computed as a linear summation of the weighed monetary gain and moral cost, recruited the ventromedial prefrontal cortex regardless of beneficiaries. Moreover, paralleling the behavioral findings, this region enhanced its functional coupling with mentalizing-related regions while deciding whether to gain morally-tainted profits for oneself vs. charity. Finally, individual differences in moral preference differentially modulated choice-specific signals in the dorsolateral prefrontal cortex according to who benefited from the decisions. These findings provide insights for understanding the neurobiological basis of moral flexibility.
Dissemination of linezolid-resistance through sex pheromone plasmid transfer in Enterococcs faecalis
Authors: Zou Jiaqi , Tang Zhaobing , Yan Jia , Liu Hang , Chen Yingzhu , Zhang Dawei , Zhao Jinxin , Tang Yu , Zhang Jing , Xia Yun
Published: November 2019

Despite recent recognition of the ATP-binding cassette protein OptrA as an important mediator of linezolid-resistance in Enterococcus faecalis worldwide, the mechanisms of optrA gene acquisition and transfer remain poorly understood. In this study, we performed comprehensive molecular and phenotypic profiling of 44 optrA-carrying E. faecalis clinical isolates with linezolid-resistance. Pulse-field gel electrophoresis and DNA hybridization revealed the presence of optrA in the plasmid in 26 (59%) isolates and in the chromosome in 18 (41%) isolates. Conjugation experiments showed a successful transfer of optrA in 88.5% (23/26) of isolates carrying optrA in plasmids while no transfer occurred in any isolates carrying optrA in the chromosome (0/18). All 23 transconjugants exhibited in vitro resistance to linezolid and several other antibiotics, and were confirmed to contain optrA and other resistance genes. Plasmid typing demonstrated a predominance (18/23 or 78%) of rep9–type plasmids (pCF10 prototype) known to be the best studied sex pheromone responsive plasmids. Full plasmid genome sequencing of one isolate revealed the presence of drug resistance genes (optrA and fexA) and multiple sex pheromone response genes in the same plasmid, which represents the first sex pheromone responsive plasmid carrying optrA from a clinical isolate. PCR-based genotyping revealed the presence of three key sex pheromone response genes (prgA, prgB and prgC) in almost all 23 optrA-carrying isolates tested. Finally, functional studies of these isolates by clumping induction assay detected different degrees of clumping in most of the 23 isolates. Our analysis strongly suggests that optrA-mediated linezolid-resistance can be widely disseminated through sex pheromone plasmid transfer.
Nicotine e-cigarette vapor inhalation effects on nicotine & cotinine plasma levels and somatic withdrawal signs in adult male Wistar rats
Authors: Montanari Christian , Kelley Leslie K , Kerr Tony M , Cole Maury , Gilpin Nicholas W.
Published: November 2019

Rationale

Non-contingent chronic nicotine exposure procedures have evolved rapidly in recent years, culminating in Electronic Nicotine Delivery Systems (ENDS or e-cigarettes) to deliver vaporized drugs to rodents in standard housing chambers.

Objectives

The aim of the current work was to use ENDS to test concentration-dependent effects of nicotine e-cigarette vapor inhalation on blood-nicotine concentrations, blood-cotinine concentrations, and somatic withdrawal signs over time in rats.

Methods

Male Wistar rats were exposed to vapor containing various concentrations of nicotine (20, 40, 80 mg/mL) for 11 days through ENDS, and blood concentrations of nicotine and cotinine, the major proximate metabolite of nicotine, as well as spontaneous and precipitated somatic withdrawal signs were measured over time (across days of exposure and over hours after termination of vapor exposure).

Results

Exposing male Wistar rats to non-contingent nicotine vapor inhalation through ENDS produces somatic withdrawal symptoms and measurable blood-nicotine and blood-cotinine levels that change according to 1) concentration of nicotine in vape solution, 2) number of days of nicotine vapor exposure, 3) time since termination of nicotine vapor exposure, and 4) relative to the withdrawal signs, whether withdrawal was spontaneous or precipitated (by mecamylamine).

Conclusions

The data presented here provide parameters that can be used as a reasonable starting point for future work that employs ENDS to deliver non-contingent nicotine vapor in rats, although many parameters can and should be altered to match the specific goals of future work.
Antiretroviral APOBEC3 Cytidine Deaminases Alter HIV-1 Provirus Integration Site Profiles
Authors: Ajoge Hannah O. , Renner Tyler M. , Bélanger Kasandra , Kohio Hinissan P. , Coleman Macon D. , Langlois Marc-André , Barr Stephen D.
Published: November 2019

APOBEC3 (A3) proteins are host-encoded deoxycytidine deaminases that provide an innate immune barrier to retroviral infection, notably against HIV-1. While the catalytic activity of these proteins can induce catastrophic hypermutation in proviral DNA leading to near-total restriction of infection, sublethal levels of deamination contribute to the genetic evolution of HIV-1. So far, little is known about how A3 might impact HIV-1 integrations into human chromosomal DNA. Using a deep sequencing approach, we analyzed the influence A3F and A3G on HIV-1 integration site selections. DNA editing was detected at the extremities of the long terminal repeat regions of the virus. Both catalytic active and non-catalytic A3 enzymes decreased insertions into gene coding sequences and increased integration sites into SINE elements, oncogenes and transcription-silencing non-B DNA features. Our data implicate A3 as host factors that influence HIV-1 integration site selection and promote insertions into genomic sites that are transcriptionally less active.

GRAPHICAL ABSTRACT

Schematic depicting the influence of APOBEC3 (A3) proteins on HIV integration site targeting.

Left, in the absence of A3, HIV has a strong preference for integrating into genes.Right, both catalytic active and non-catalytic A3 mutants decrease integration into genes and increase integration into SINE elements and in transcription-silencing non-B DNA features.
Matrix Inversion and Subset Selection (MISS): A novel pipeline for mapping of diverse cell types across the murine brain
Authors: Mezias Christopher , Torok Justin , Maia Pedro D. , Markley Eric , Raj Ashish
Published: November 2019

The advent of increasingly sophisticated imaging platforms has allowed for the visualization of the murine nervous system at single-cell resolution. However, current experimental approaches have not yet produced whole-brain maps of a comprehensive set of neuronal and nonneuronal types that approaches the cellular diversity of the mammalian cortex. Here we aim to fill in this gap in knowledge with an open-source computational pipeline, Matrix Inversion with Subset Selection (MISS), that can infer quantitatively validated distributions of diverse collections of neural cell types at 200μm resolution using a combination of single-cell RNAseq and in situ hybridization datasets. We rigorously demonstrate the accuracy of MISS against literature expectations. Importantly, we show that gene subset selection, a procedure by which we filter out low-information genes prior to performing deconvolution, is a critical pre-processing step that distinguishes MISS from its predecessors and facilitates the production of cell type maps with significantly higher accuracy. We also show that MISS is generalizable by generating high-quality cell type maps from a second, independently curated single-cell RNAseq dataset. Together, our results illustrate the viability of computational approaches for determining the spatial distributions of a wide variety of cell types from genetic data alone.
Nanopore sequencing of DNA concatemers reveals higher-order features of chromatin structure
Authors: Ulahannan Netha , Pendleton Matthew , Deshpande Aditya , Schwenk Stefan , Behr Julie M. , Dai Xiaoguang , Tyer Carly , Rughani Priyesh , Kudman Sarah , Adney Emily , Tian Huasong , Wilkes David , Mosquera Juan Miguel , Stoddart David , Turner Daniel J. , Juul Sissel , Harrington Eoghan , Imielinski Marcin
Published: November 2019

Higher-order chromatin structure arises from the combinatorial physical interactions of many genomic loci. To investigate this aspect of genome architecture we developed Pore-C, which couples chromatin conformation capture with Oxford Nanopore Technologies (ONT) long reads to directly sequence multi-way chromatin contacts without amplification. In GM12878, we demonstrate that the pairwise interaction patterns implicit in Pore-C multi-way contacts are consistent with gold standard Hi-C pairwise contact maps at the compartment, TAD, and loop scales. In addition, Pore-C also detects higher-order chromatin structure at 18.5-fold higher efficiency and greater fidelity than SPRITE, a previously published higher-order chromatin profiling technology. We demonstrate Pore-C’s ability to detect and visualize multi-locus hubs associated with histone locus bodies and active / inactive nuclear compartments in GM12878. In the breast cancer cell line HCC1954, Pore-C contacts enable the reconstruction of complex and aneuploid rearranged alleles spanning multiple megabases and chromosomes. Finally, we apply Pore-C to generate a chromosome scalede novoassembly of the HG002 genome. Our results establish Pore-C as the most simple and scalable assay for the genome-wide assessment of combinatorial chromatin interactions, with additional applications for cancer rearrangement reconstruction andde novogenome assembly.
Secondary environmental variation creates a shifting evolutionary watershed for the methyl-parathion hydrolase enzyme
Authors: Anderson Dave W. , Baier Florian , Yang Gloria , Tokuriki Nobuhiko
Published: November 2019

Enzymes can evolve new catalytic activity when their environments change to present them with novel substrates. Despite this seemingly straightforward relationship, factors other than the direct catalytic target can also impact enzyme adaptation. Here, we characterize the adaptive landscape separating an ancestral dihydrocoumarin hydrolase from a methyl parathion hydrolase descendant under eight different environments supplemented with alternative divalent metals. This variation shifts an evolutionary watershed, causing the outcome of adaptation to depend on the environment in which it occurs. The resultant landscapes also vary in terms both the number and the genotype(s) of “fitness peaks” as a result of genotype-by-environment (G×E) interactions and environment-dependent epistasis (G×G×E). This suggests that adaptive landscapes may be fluid and that molecular adaptation is highly contingent not only on obvious factors (such as catalytic targets) but also on less obvious secondary environmental factors that can direct it toward distinct outcomes.
A cell-free biosynthesis platform for modular construction of protein glycosylation pathways
Authors: Kightlinger Weston , Duncker Katherine E. , Ramesh Ashvita , Thames Ariel H. , Natarajan Aravind , Yang Allen , Stark Jessica C. , Lin Liang , Mrksich Milan , DeLisa Matthew P. , Jewett Michael C.
Published: November 2019

Glycosylation plays important roles in cellular function and endows protein therapeutics with beneficial properties. However, constructing biosynthetic pathways to study and engineer protein glycosylation remains a bottleneck. To address this limitation, we describe a modular, versatile cell-free platform for glycosylation pathway assembly by rapid in vitromixing and expression (GlycoPRIME). In GlycoPRIME, crude cell lysates are enriched with glycosyltransferases by cell-free protein synthesis and then glycosylation pathways are assembled in a mix-and-match fashion to elaborate a single glucose priming handle installed by an N-linked glycosyltransferase. We demonstrate GlycoPRIME by constructing 37 putative protein glycosylation pathways, creating 23 unique glycan motifs. We then use selected pathways to design a one-pot cell-free system to synthesize a vaccine protein with an α-galactose motif and engineered Escherichia coli strains to produce human antibody constant regions with minimal sialic acid motifs. We anticipate that our work will facilitate glycoscience and make possible new glycoengineering applications.
Complete genome sequence of Oryctes rhinoceros Nudivirus isolated from Coconut Rhinoceros Beetle in the Solomon Islands
Authors: Etebari Kayvan , Filipović Igor , Rašić Gordana , Devine Gregor J. , Tsatsia Helen , Furlong Michael J.
Published: November 2019

Oryctes Nudivirus (OrNV) has been an effective biocontrol agent against the insect pest Oryctes rhinoceros (Coleoptera: Scarabaeidae) for decades, but there is evidence that resistance could be evolving in some host populations. We detected OrNv infection in O. rhinoceros from the Solomon Islands and used Oxford Nanopore Technologies (ONT) long-read sequencing to determine the full length of the virus genomic sequence isolated from an individual belonging to a mitochondrial lineage (CRB-G) that was previously reported as resistant to OrNV. The complete circular genome of the virus consisted of 125,917 nucleotides, encoding 130 open reading frames (ORFs) for proteins in the range ~5 kDa (51aa) to ~140 kDa (1280aa). This Solomon Islands isolate has high (99.85%) nucleotide sequence identity to the previously sequenced isolate PV505 from Southern Luzon, Philippines, and has 138 amino acid modifications when compared with the originally described full genome sequence of the Ma07 strain from Malaysia.
A Unified Molecular Signature of Systemic Lupus Erythematosus Revealed by Integrated, Multi-Cohort Transcriptomic Analysis
Authors: Haynes Winston A. , Haddon D. James , Diep Vivian K. , Khatri Avani , Bongen Erika , Yiu Gloria , Balboni Imelda , Bolen Christopher R. , Mao Rong , Utz Paul J. , Khatri Purvesh
Published: November 2019

Systemic lupus erythematosus (SLE) is a complex autoimmune disease that follows an unpredictable disease course and affects multiple organs and tissues. We performed an integrated, multi-cohort analysis of 7,471 transcriptomic profiles from 40 independent studies to identify robust gene expression changes associated with SLE. We identified a 93-gene signature (SLE MetaSignature) that is differentially expressed in the blood of SLE patients compared to healthy volunteers; distinguishes SLE from other autoimmune, inflammatory, and infectious diseases; and persists across diverse tissues and cell types. The SLE MetaSignature correlated significantly with disease activity and other clinical measures of inflammation. We prospectively validated the SLE MetaSignature in an independent cohort of pediatric SLE patients using a microfluidic RT-qPCR array. We found that 14 of the 93 genes in the SLE MetaSignature were independent of interferon-induced and neutrophil-related transcriptional profiles that have previously been associated with SLE. Pathway analysis revealed dysregulation associated with nucleic acid biosynthesis and immunometabolism in SLE. We further refined a neutropoeisis signature and identified under-appreciated transcripts related to immune cells and oxidative stress. Our multi-cohort, transcriptomic analysis has uncovered under-appreciated genes and pathways associated with SLE pathogenesis, with the potential to advance clinical diagnosis, biomarker development, and targeted therapeutics for SLE.
The ‘Threat of Scream’ paradigm: A tool for studying sustained physiological and subjective anxiety
Authors: Beaurenaut Morgan , Tokarski Elliot , Dezecache Guillaume , Grèzes Julie
Published: November 2019

Progress in understanding the emergence of pathological anxiety depends on the availability of paradigms effective in inducing anxiety in a simple, consistent and sustained way. Much progress has been made using the Threat-of-Shock paradigm (TOS), which generates anxiety through the delivery of unpredictable electric shocks to participants. However, TOS may be problematic when testing vulnerable populations. Moreover, it is not clear whether anxiety can be sustained throughout experiments of long duration. Here, we bring support for an alternative approach called the Threat-of-Scream paradigm (TOSc), in which the tactile delivery of shocks is replaced by the auditory delivery of distress screams. We report on an one-hour long study (plus its replication) in which participants were exposed to blocks before which they were told that they could hear aversive screams at any time (threat blocks), vs. blocks before which they were told that no scream will be heard (safe blocks). Both the experiment and its replication showed higher subjective reports of anxiety, higher skin conductance level, and positive correlation between the two measures, in threat compared to safe blocks. Anxiety measures were sustained throughout the experiments, suggesting little emotional and physiological habituation. Our results suggest that the delivery of low intensity distress screams can be an efficient, stable and cheap methodology to assess the impact of sustained anxiety on a diversity of cognitive functions and populations. We therefore believe the TOSc will become an essential part of the psychological toolkit, particularly so for researchers interested in the emergence of pathological anxiety.
Study on the influence of G82S RAGE polymorphism on RAGE-Amyloid interaction in AD pathology
Authors: C Rani Cathrine. , Lukose Bincy , Rani P.
Published: November 2019

Receptor for advanced glycation end products (RAGE) has been implicated in the pathophysiology of AD due to its ability to bind amyloid-beta and mediate inflammatory response. G82S RAGE polymorphism is associated with AD but the molecular mechanism for this association is not understood. Our previous in silico study indicated a higher binding affinity for mutated G82S RAGE, which could be caused due to changes in N linked glycosylation at residue N81. To confirm this hypothesis, in the present study molecular dynamics (MD) simulations were used to simulate the wild type (WT) and G82S glycosylated structures of RAGE to identify the global structural changes and to find the binding efficiency with Aβ42 peptide. Binding pocket analysis of the MD trajectory showed that cavity/binding pocket in mutant G82S glycosylated RAGE variants is more exposed and accessible to external ligands compared to WT RAGE, which can enhance the affinity of RAGE for Aβ. To validate the above concept, an in vitro binding study was carried using SHSY5Y cell line expressing recombinant WT and mutated RAGE variant individually to which HiLyte Fluor labeled Aβ42 was incubated at different concentrations. Saturated binding kinetics method was adopted to determine the Kd values for Aβ42 binding to RAGE. The Kd value for Aβ42-WT and Aβ42-mutant RAGE binding were 92±40 nM (95% CI-52 to 152nM; R2-0.92) and 45±20 nM (95% CI −29 to 64nM; R2-0.93), respectively. The Kd value of <100nM observed for both variants implicates RAGE as a high-affinity receptor for Aβ42 and mutant RAGE has higher affinity compared to WT. The alteration in binding affinity is responsible for activation of the inflammatory pathway as implicated by enhanced expression of TNFα and IL6 in mutant RAGE expressing cell line which gives a mechanistic view for the G82S RAGE association with AD.
High density cultivation for efficient sesquiterpenoid biosynthesis inSynechocystissp. PCC 6803
Authors: Dienst Dennis , Wichmann Julian , Mantovani Oliver , Rodrigues João , Lindberg Pia
Published: November 2019

Cyanobacteria and microalgae are attractive phototrophic host systems for climate-friendly production of fuels and other high-value chemicals. The biosynthesis of an increasing diversity of industrially relevant compounds such as terpenoids has been demonstrated in recent years. To develop economically feasible and sustainable process designs, major challenges still remain regarding intracellular carbon partitioning, specific metabolic pathway activities and efficient cultivation strategies. Here, we present a technical study on comparative characteristics of sesquiterpene and sesquiterpene alcohol accumulation in engineered strains ofSynechocystissp. PCC 6803 (substrain GT-U) under different growth conditions and cell densities. This study particularly focuses on the basic applicability of a commercial High Density Cultivation platform in the presence of a dodecane overlay, which serves as a standardin-situextractant and sink for various hydrophobic biochemicals. Significantly, the presented data demonstrate high volumetric productivities of (E)-α-bisabolene under high-density conditions that are more than two orders of magnitude higher than previously reported for cyanobacteria. Operating in a two-step semi-batch mode over a period of eight days, average final volumetric titers of 179.4 ± 20.7 mg * L−1were detected. Likewise, the sesquiterpene alcohols (-)-patchoulol and (-)-α-bisabolol accumulated to many times higher levels in high density cultivation than under standard batch conditions, with final titers of 17.3 ± 1.85 mg * L−1and 96.3 ± 2.2 mg * L−1, respectively. In contrast, specific product accumulation (mg * L−1* OD750−1) was compromised particularly for bisabolene in the high density system during phases of high biomass accumulation rates. Volumetric productivities were high during linear growth at high densities, distinctly outperforming standard batch systems. While the presented data highlight the benefits of high-density strategies for highly efficient phototrophic terpenoid production, they further point at the presence of major metabolic bottlenecks for engineered terpenoid biosynthesis and the requirement for systematic and/or targeted strategies to sustainably redirect inherent carbon fluxes in cyanobacteria. Together, our data provide additional insights into growth- and density-related effects on the efficiency of product accumulation, introducing low-scale High Density Cultivation as a rapid and efficient platform for screening of heterologous terpenoid production in cyanobacteria.