bluuebunny/crossref_metadata_2025 huggingface dataset:
COMPARISON OF PROJECTION-RESOLVED OPTICAL COHERENCE TOMOGRAPHY ANGIOGRAPHY-BASED METRICS FOR THE EARLY DETECTION OF RETINAL MICROVASCULAR IMPAIRMENTS IN DIABETES MELLITUS
Authors: Zhu Tie Pei , Li En Hui , Li Jin Yu , Dai Xi Zhe , Zhang Hui Na , Chen Bin Bin , Ye Pan Pan , Su Zhao An , Ye Juan
Published: October 2019

Purpose:

To determine the ability of nonperfusion, vessel density, and morphologic measurements using projection-resolved optical coherence tomography angiography to detect early retinal microvasculature impairments in diabetes mellitus.

Methods:

A retrospective review was performed on Type 2 diabetes mellitus patients with no diabetic retinopathy (DR) or mild nonproliferative DR and age-matched controls imaged with optical coherence tomography angiography. Foveal avascular zone-related metrics and extrafoveal avascular area were measured in optical coherence tomography angiography images. Vessel density and fractal dimension were calculated with and without a skeletonization process. The vessel diameter index and vessel tortuosity were computed. The area under the receiver operating characteristic curve (AUC) estimated diagnostic performances.

Results:

Dilated capillary diameter was observed in the deep capillary plexus in the diabetic groups. Vessel density and fractal dimension of skeletonized deep capillary plexus significantly and progressively decreased in the no DR and mild nonproliferative DR groups compared with controls. Superficial extrafoveal avascular area, vessel density, and fractal dimension of the skeletonized deep capillary plexus had the highest diagnostic performance to differentiate mild nonproliferative DR from control eyes, with AUCs of 0.885, 0.876, and 0.876, respectively.

Conclusion:

Vessel density and fractal dimension from the skeletonized deep capillary network may be the most sensitive for detecting early retinal capillary loss in diabetes mellitus.
FLAT IRREGULAR PIGMENT EPITHELIUM DETACHMENT IN CENTRAL SEROUS CHORIORETINOPATHY
Authors: Hwang Hyeseong , Kim Jin YOUNG , Kim Kyung TAE , Chae Ju BYUNG , Kim Dong YOON
Published: October 2019

Purpose:

To investigate the differences in natural course, intravitreal bevacizumab injection (IVB) responsiveness, and optical coherence tomography angiography findings according to the type of pigment epithelial detachment (PED) in patients with central serous chorioretinopathy (CSC).

Methods:

A retrospective review of angiographically proven CSC patients was conducted. Pigment epithelium detachment was classified as flat irregular or focal. To identify the natural course of CSC, we had observed whether subretinal fluid was improved without any treatment until symptom duration was >3 months. When CSC symptom duration was >3 months, IVB injection was performed. Symptom duration, central subfield thickness, subfoveal choroidal thickness, presence of subretinal fluid, natural course, optical coherence tomography angiography findings, and IVB responsiveness were compared between the PED types.

Results:

One hundred eyes were included (64 flat irregular PED vs. 34 focal PED). Flat irregular PED had a longer symptom duration than focal PED (7.20 ± 11.52 vs. 3.69 ± 3.98 months, P = 0.03). In untreated cases, the rate of complete resolution of subretinal fluid was significantly lower in flat irregular PED than in focal PED (34.78% vs. 65.22%, P = 0.017). In contrast to the natural course, responsiveness to IVB was significantly better in flat irregular PED (72.41% vs. 31.58%, P = 0.005). Optical coherence tomography angiography revealed more CNV in flat irregular PED (42.90% vs. 10.00%, P = 0.014). Subfoveal choroidal thickness in flat irregular PED was significantly thicker.

Conclusion:

In CSC patients with flat irregular PED, the natural course was poor, but treatment response to IVB was favorable. Flat irregular PED patients showed longer symptom duration and thicker subfoveal choroidal thickness than those with focal PED. Optical coherence tomography angiography revealed more choroidal neovascularization in flat irregular PED. These findings suggest that CSC with flat irregular PED could be considered a form of pachychoroid neovasculopathy.
MITOGEN-ACTIVATED PROTEIN INHIBITORS: FULL-FIELD ELECTRORETINOGRAM DEMONSTRATING GENERALIZED RETINAL DYSFUNCTION
Authors: van Lint Michel , Ebraert Herlinde , Van Aken Elisabeth H.
Published: October 2019

Purpose:

To report a patient with generalized retinal toxicity to mitogen-activated protein inhibitors.

Methods:

Retrospective case report.

Results:

Full-field electroretinogram findings indicate a generalized toxicity to the use of the mitogen-activated protein inhibitor trametinib. There was an improved response and resolution of serous detachments after decreasing the dose.

Conclusion:

Mitogen-activated protein inhibitors may affect global retinal function, as opposed to the serous detachments that are concentrated in the posterior pole. This may be of importance in further understanding the underlying pathologic mechanisms.
Nurse practitioners and barriers to diabetic foot treatment
Authors: Anderson Michelle , Arvidson Cathy
Published: October 2019

Background:

Even with full practice authority, nurse practitioners (NPs) face limitations in care and treatment options. An example of this is current federal law prohibiting NPs from ordering diabetic shoes.

Purpose:

This study reviewed the background of this problem, potential impacts on patient health and NP practice, and viable solutions for consideration.

Methods:

This was a descriptive study of NPs in a northwestern state with full practice authority. An anonymous online survey was used. There were 54 total NP respondents.

Results:

The potential negative patient outcomes associated with restricted NP ability to prescribe diabetic footwear were supported through the literature review and the survey, including increased foot complications and acuity, translating to increased costs. Of the NPs queried, 80% felt inability to prescribe diabetic footwear was limiting to their practice, and 92% felt this affected patient outcomes. Federal legislative changes with support of bipartisan bills allowing NPs to prescribe diabetic footwear could facilitate timeliness and access to care while reducing costs.

Implications for practice:

Legislation affecting NP scope of practice is an important issue with implications related to patient outcomes. Nurse practitioners should continue to support legislation at the federal level to pass bills allowing for NPs to certify orders for diabetic shoes.
Magnesium Requirements in Children
Authors: Cao Sisi , Hodges Joanna K. , McCabe Linda D. , Weaver Connie M.
Published: October 2019

Magnesium (Mg), a cofactor in 300 enzymes, is essential for energy transfer and adequate vitamin D status and plays an important structural role with 60% of bodily reserves residing in bone. The Food and Nutrition Board recommendations for dietary intake of Mg, the Dietary Reference Intakes, have not been updated since 1997. Current recommendations for children were set based on an intake producing positive Mg balance. Population-based studies showed that the average intakes in children are suboptimal relative to the current recommendation. Newer evidence suggests Mg requirement should be related to body size. Other potential modifying factors of Mg requirements include calcium and sodium intake and chronic disease state. Future research is needed to refine public health recommendations for Mg and to establish the new Dietary Reference Intakes category of Chronic Disease Risk Reduction level for Mg, especially for children.
Immediate Breast Reconstruction in The Netherlands and the United States: A Proof-of-Concept to Internationally Compare Quality of Care Using Cancer Registry Data
Authors: Kamali Parisa , van Bommel Annelotte , Becherer Babette , Cooter Rodney , Mureau Marc A. M. , Pusic Andrea , Siesling Sabine , van der Hulst René R. J. W. , Lin Samuel J. , Rakhorst Hinne
Published: October 2019

Background:

Studies based on large-volume databases have made significant contributions to research on breast cancer surgery. To date, no comparison between large-volume databases has been made internationally. This is the first proof-of-concept study exploring the feasibility of combining two existing operational databases of The Netherlands and the United States, focusing on breast cancer care and immediate breast reconstruction specifically.313/291

Methods:

The National Breast Cancer Organization The Netherlands Breast Cancer Audit (NBCA) (2011 to 2015) and the U.S. Surveillance, Epidemiology, and End Results (SEER) database (2010 to 2013) were compared on structure and content. Data variables were grouped into general, treatment-specific, cancer-specific, and follow-up variables and were matched. As proof-of-concept, mastectomy and immediate breast reconstruction rates in patients diagnosed with invasive breast cancer or ductal carcinoma in situ were analyzed.

Results:

The NBCA included 115 variables and SEER included 112. The NBCA included significantly more treatment-specific variables (n = 46 versus 6), whereas the SEER database included more cancer-specific variables (n = 74 versus 26). In patients diagnosed with breast cancer or ductal carcinoma in situ, immediate breast reconstruction was performed in 19.3 percent and 24.0 percent of the breast cancer cohort and 44.0 percent and 35.3 percent of the ductal carcinoma in situ cohort in the NBCA and SEER, respectively. Immediate breast reconstruction rates increased significantly over time in both data sets.

Conclusions:

This study provides a first overview of available registry data on breast cancer care in The Netherlands and the United States, and revealed limited data on treatment in the United States. Comparison of treatment patterns of immediate breast reconstruction showed interesting differences. The authors advocate the urgency for an international database with alignment of (treatment) variables to improve quality of breast cancer care for patients across the globe.
Abdominoplasty in the Overweight and Obese Population: Outcomes and Patient Satisfaction
Authors: Hammond Dennis C. , Chandler Ashley R. , Baca Marissa E. , Li Yu Kit , Lynn Jeremy V.
Published: October 2019

Background:

Abdominoplasty is a safe, efficacious body contouring procedure commonly performed on patients after massive weight loss or pregnancy, or because of general aging. However, complication rates and patient satisfaction levels remain largely unexplored for the overweight and obese patient population. The purpose of this study was twofold: to determine the complication rate and to gauge the psychological impact of abdominoplasty in the overweight or obese patient.

Methods:

A retrospective review was conducted of consecutive overweight and obese patients undergoing abdominoplasty or panniculectomy over a 12-year period from January of 2004 to December of 2016. Patient medical records were reviewed to identify patient demographics and comorbidities, operative details, and postoperative course. A patient survey was used to assess satisfaction, personal experience with complications, and the recovery process.

Results:

Forty-six total patients underwent abdominoplasty or panniculectomy during the 12-year period and met the criterion of body mass index greater than or equal to 25 kg/m2. The average patient body mass index was 32.0 kg/m2, with the majority of the patients categorized as overweight. The average abdominal resection weight was 4834.9 g. Major complications, defined as complications requiring return to the operating room, occurred in four patients (8.7 percent). Minor complications, defined as complications that could be handled in an office setting, occurred in 18 patients (39.1 percent). Thirty-six patients (78.3 percent) responded to the survey. The overwhelming majority of patients who responded to the survey [n = 35 (97.2 percent)] stated that they were satisfied with the final outcome and would choose to have the procedure again.

Conclusion:

Abdominoplasty and panniculectomy in overweight and obese patients are associated with an elevated complication rate, yet patient satisfaction is overwhelmingly high, suggesting the viability of body contouring procedures in this patient population.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, IV.
A Prospective, Multicenter, Randomized, Evaluator-Blinded, Split-Hand Study to Evaluate the Effectiveness and Safety of Large-Gel-Particle Hyaluronic Acid with Lidocaine for the Correction of Volume Deficits in the Dorsal Hand
Authors: Moradi Amir , Allen Shawn , Bank David , Marmur Ellen , Fagien Steven , Glaser Dee Anna , Maguire Courtney , Cohen Joel L.
Published: October 2019

Background:

Hand rejuvenation has become increasingly popular, but there are few reports published on the use of hyaluronic acid gels for correction of volume deficits in the dorsal hand.

Methods:

This study evaluated the efficacy and safety of large-gel-particle hyaluronic acid with lidocaine, a 20-mg/ml hyaluronic acid gel with 0.3% lidocaine, compared to no treatment for the correction of volume deficits in the dorsal hand. This was a prospective, multicenter, split-hand study in 90 subjects who received treatment with product in one hand. The primary efficacy endpoint was based on a 1 point of improvement with treatment versus no treatment according to the Merz Hand Grading Scale at week 12. Other assessments included Central Independent Photographic Reviewers evaluations of hand photographs, Global Aesthetic Improvement Scale, subject satisfaction, and safety.

Results:

The mean injection volume was 2.1 ml at the first treatment. Subjects demonstrated significantly higher response rates with treatment compared to no treatment at week 12 (85.9 percent versus 21.2 percent) and at weeks 16, 20, and 24 (p < 0.0001). Photographic Reviewers assessments showed consistently greater improvements in the treated hands compared with the untreated hands from week 12 to week 24. Most subjects and investigators (≥92.8 percent) reported improvements in Global Aesthetic Improvement Scale score across all time points with treatment. Treatment-related adverse events were reported in seven subjects (7.9 percent). Most of these were mild, and none were serious.

Conclusion:

Hyaluronic acid with lidocaine is safe, effective, and well tolerated for the correction of volume deficits in the dorsal hand.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, II.
International and Geographic Trends in Gender Authorship within Plastic Surgery
Authors: Bucknor Alexandra , Peymani Abbas , Kamali Parisa , Epstein Sherise , Chen Austin D. , Bletsis Patrick , Chattha Anmol , Mathijssen Irene , Rakhorst Hinne , Lin Samuel J.
Published: October 2019

Background:

Professional advancement in academic plastic surgery may depend on scholarly activity. The authors evaluate gender-based publishing characteristics in three international plastic surgery journals.

Methods:

A retrospective review of all articles published in 2016 in the following journals was undertaken: Plastic and Reconstructive Surgery, Journal of Plastic, Reconstructive and Aesthetic Surgery, European Journal of Plastic Surgery, Annals of Surgery, and New England Journal of Medicine. Data were collected on lead author gender (first or senior author) and differences in author gender proportions, by journal, by article topic, and by geographic location were evaluated.

Results:

Overall, 2610 articles were retrieved: 34.1 percent were from plastic surgery journals, 12.8 percent were from the Annals of Surgery, and 53.1 percent were from the New England Journal of Medicine. There was a lower proportion of female lead authors among plastic surgery journals compared with the Annals of Surgery and the New England Journal of Medicine (31 percent versus 39 percent versus 39 percent; p = 0.001). There were no differences in female lead author geographic location in the Annals of Surgery or the New England Journal of Medicine; within the plastic surgery journals, there were differences (p = 0.005), including a lower proportion arising from East Asia (15 percent) and a higher proportion arising from Canada (48 percent). Within plastic surgery, Plastic and Reconstructive Surgery had the lowest proportion of female lead author (p < 0.001). The proportion of female lead author varied by article topic (p < 0.001) and was notably higher in breast (45.6 percent) and lower in head and neck/craniofacial-orientated articles (25.0 percent).

Conclusions:

There are gender disparities in three mainstream plastic surgery journals—Plastic and Reconstructive Surgery, the Journal of Plastic, Reconstructive and Aesthetic Surgery, the European Journal of Plastic Surgery—and there are lower proportions of lead female authorship compared with the Annals of Surgery and the New England Journal of Medicine. Further research should focus on understanding any geographic disparities that may exist.
Management of Pilonidal Sinus Disease with the Aesthetically Shaped Parasacral Perforator Flap: Multicenter Evaluation of 228 Patients
Authors: Chaput Benoit , Herlin Christian , Jacques Jérémie , Berthier Charline , Meresse Thomas , Bekara Farid , Sinna Raphael , Boissière Florian , Bertheuil Nicolas , Grolleau Jean-Louis
Published: October 2019

Background:

The management of pilonidal sinus disease is still not standardized. Currently, the two main procedures are a lay-open excision procedure with secondary healing or coverage with local flaps. The authors present their experience with a one-stage excision-coverage with an innovative parasacral artery perforator flap propeller designed to respect the aesthetic unity of the buttocks.

Methods:

Study patients were managed with this procedure in the Toulouse, Montpellier, and Rennes university hospitals between 2012 and 2018. Data were collected on clinical and surgical details, immediate and late postoperative complications, and long-term recurrence. Aesthetic satisfaction was evaluated with a self-evaluation questionnaire.

Results:

The authors operated on 228 consecutive patients for pilonidal sinus disease with an aesthetically shaped parasacral artery perforator flap. The median patient age was 23.5 years, the median operative time was 46 minutes, the median flap length was 9.3 cm (range, 6.5 to 14 cm), and the median flap width was 4.1 cm (range, 4 to 6.5 cm). There were five distal necroses but no complete flap necrosis. There were six postoperative hematomas, 11 infections, and 18 wound dehiscences. The median follow-up period was 27.9 months. Median hospital length of stay was 4.2 days. Three recurrences of pilonidal sinus disease and six instances of hidradenitis suppurativa were detected. Approximately 82 percent of the women and more than 85 percent of the men were “satisfied” or “very satisfied” with the aesthetic outcome, without significant differences between the sexes (p = 0.901).

Conclusions:

The aesthetically shaped parasacral artery perforator flap combines very satisfactory results regarding recurrence and postoperative recovery with cosmetic outcome. This procedure is technically more demanding than other flap procedures, although it is accessible to numerous surgeons as the first-line treatment for pilonidal sinus disease after initial learning.

CLINICAL QUESTION/LEVEL OF EVIDENCE:

Therapeutic, IV.
Ballistic and Penetrating Injuries of the Chest
Authors: Truesdell William , Gore Ashwani , Primakov Denis , Lieberman Howard , Jankowska Danuta , Joshi Gayatri , Goyal Nikhil
Published: October 2019

Ballistic injuries are a major cause of morbidity and mortality in the United States. Unstable patients have high mortality, and only a small subset arrive at the hospital alive. Many patients undergo emergent surgery upon arrival, but a small subset undergo imaging with plain film, computed tomography, and echocardiography. We present a pictorial essay of ballistic and penetrating injuries and their complications with a focus on lung, cardiac, and vascular injury.
Fourteen Years After Delayed Replantation of an Avulsed Permanent Tooth: Clinical Features and Outcomes
Authors: Lou Qun , Zhu Yaqin , Wang Xudong
Published: October 2019

This article reports a clinical case of a boy who underwent an avulsion of the upper right central incisor at 8 years old. The avulsed tooth was kept in the socket for 11 years after replantation. The clinical and radiographic findings after 14 years revealed a complete root resorption, but alveolar bone volume is adequate for future implantation from the recent tomography scans view, even in labial area where alveolar bone morphology is poor.
Functional single-cell genomics of human cytomegalovirus infection
Authors: Hein Marco Y. , Weissman Jonathan S.
Published: October 2019

The complex life cycle of herpesviruses is orchestrated by the interplay of host factors and hundreds of viral genes. Understanding how they work together and how perturbations of viral and host factors impact infection represents both a fundamental problem in virology and the basis for designing antiviral interventions. Here, we use CRISPR screening to comprehensively define the functional contribution of each viral and host factor to human cytomegalovirus (HCMV) infection in primary cells. We then record the transcriptomes of tens of thousands of single cells, and monitor how genetic perturbation of critical host and viral factors alters the timing, course, and progression of infection. We find that normally, the large majority of cells follow a stereotypical transcriptional trajectory. Perturbing critical host factors does not change this trajectory per se, but can either stall, delay or accelerate progression along the trajectory, allowing us to pinpoint systematically the stage of infection at which each host factor acts. Conversely, perturbation of viral factors can create distinct, abortive trajectories. Our results reveal a dichotomy between the roles of host and viral factors and more generally provide a road map for functional dissection of host-pathogen interactions.
Choosing Your Battles: Which Resistance Genes Warrant Global Action?
Authors: Zhang An-Ni , Li Li-Guan , Yin Xiaole , Dai Chengzhen L , Groussin Mathieu , Poyet Mathilde , Topp Edward , Gillings Michael R , Hanage William P , Tiedje James M , Alm Eric J , Zhang Tong
Published: October 2019

The increasing accumulation of antibiotic resistance genes (ARGs) in pathogens poses a severe threat to the treatment of bacterial infections. However, not all ARGs do not pose the same threats to human health. Here, we present a framework to rank the risk of ARGs based on three factors: “anthropogenic enrichment”, “mobility”, and “host pathogenicity”. The framework is informed by all available bacterial genomes (55,000), plasmids (16,000), integrons (3,000), and 850 metagenomes covering diverse global eco-habitats. The framework prioritizes 3% of all known ARGs in Rank I (the most at risk of dissemination amongst pathogens) and 0.3% of ARGs in Rank II (high potential emergence of new resistance in pathogens). We further validated the framework using a list of 38 ARG families previously identified as high risk by the World Health Organization and published literature, and found that 36 of them were properly identified as top risk (Rank I) in our approach. Furthermore, we identified 43 unreported Rank I ARG families that should be prioritized for public health interventions. Within the same gene family, homologous genes pose different risks, host range, and ecological distributions, indicating the need for high resolution surveillance into their sequence variants. Finally, to help strategize the policy interventions, we studied the impact of industrialization on high risk ARGs in 1,120 human gut microbiome metagenomes of 36 diverse global populations. Our findings suggest that current policies on controlling the clinical antimicrobial consumptions could effectively control Rank I, while greater antibiotic stewardship in veterinary settings could help control Rank II. Overall, our framework offered a straightforward evaluation of the risk posed by ARGs, and prioritized a shortlist of current and emerging threats for global action to fight ARGs.
Repeated hypoglycemia blunts the responsiveness of glucose-inhibited GHRH neurons by remodeling neural inputs and disrupting mitochondrial structure and function
Authors: Bayne M , Alvarsson A , Devarakonda K , Li R , Jimenez-Gonzalez M , Conner K. , Varghese M , Serasinghe M N , Chipuk J E , Hof P R , Stanley S A
Published: October 2019

Hypoglycemia is a frequent complication of diabetes, limiting therapy and increasing morbidity and mortality. With recurrent hypoglycemia, the counter-regulatory response (CRR) to decreased blood glucose is blunted, resulting in hypoglycemia unawareness. The mechanisms leading to these blunted effects remain incompletely understood. Here, we identify, with in situ hybridization, immunohistochemistry and the tissue clearing capability of iDisco, that GHRH neurons represent a unique population of arcuate nucleus neurons activated by glucose deprivationin vivo. Repeated glucose deprivation reduces GHRH neuron activation and remodels excitatory and inhibitory inputs to GHRH neurons. We show low glucose sensing is coupled to GHRH neuron depolarization, decreased ATP production and mitochondrial fusion. Repeated hypoglycemia attenuates these responses during low glucose. By maintaining mitochondrial length with the small molecule, mdivi-1, we preserved hypoglycemia sensitivityin vitroandin vivo. Our findings present possible mechanisms for the blunting of the CRR, broaden significantly our understanding of the structure of GHRH neurons and for the fist time, propose that mitochondrial dynamics play an important role in hypoglycemia unawareness. We conclude that interventions targeting mitochondrial fission in GHRH neurons may offer a new pathway to prevent hypoglycemia unawareness in diabetic patients.
Functional and structural properties of highly responsive somatosensory neurons in mouse barrel cortex
Authors: Barz C , Garderes PM , Ganea D , Reischauer S , Feldmeyer D , Haiss F
Published: October 2019

Sparse population activity is a hallmark of supra-granular sensory neurons in neocortex. The mechanisms underlying sparseness are not well understood because a direct link between the neurons activated in vivo and their cellular properties investigated in vitro has been missing. We used two-photon calcium imaging to identify a subset of neurons in layer L2/3 (L2/3) of mouse primary somatosensory cortex that are highly active following principal whisker vibrotactile stimulation. These high responders were then tagged using photoconvertible green fluorescent protein for subsequent targeting in the brain slice using intracellular patch-clamp recordings and biocytin staining. This approach allowed us to investigate the structural and functional properties of high responders that distinguish them from less active control cells. Compared to less responsive L2/3 neurons, high responders displayed increased levels of stimulus-evoked and spontaneous activity, elevated noise and spontaneous pair-wise correlations, and stronger coupling to the population response. Intrinsic excitability was reduced in high responders, while other electrophysiological and morphological parameters were unchanged. Thus, the choice of which neurons participate in stimulus encoding may largely be determined by network connectivity rather than by cellular structure and function.
Geographic variation in hemocyte diversity and phagocytic propensity shows a diffuse genomic signature in the green veined white butterfly
Authors: Keehnen Naomi L.P. , Fors Lisa , Järver Peter , Spetz Anna-Lena , Nylin Sören , Theopold Ulrich , Wheat Christopher W.
Published: October 2019

Insects rely on their innate immune system to successfully mediate complex interactions with their internal microbiota, as well as the microbes present in the environment. Given the variation in microbes across habitats, the challenges to respond to them is likely to result in local adaptation in the immune system. Here we focus upon phagocytosis, a mechanism by which pathogens and foreign particles are engulfed in order to be contained, killed and processed for antigen presentation. We investigated the phenotypic and genetic variation related to phagocytosis, in two allopatric populations of the butterflyPieris napi. We found that the populations differ in their hemocyte composition, and overall phagocytic capability, driven by the increased phagocytic propensity of each cell type. However, no evidence for divergence in phagocytosis-related genes was observed, though an enrichment of genes involved in glutamine metabolism was found, which have recently been linked to immune cell differentiation in mammals.
Encapsulation boosts islet-cell signature in differentiating human induced pluripotent stem cells via integrin signalling
Authors: Vethe Heidrun , Legøy Thomas Aga , Abadpour Shadab , Strand Berit L. , Scholz Hanne , Paulo Joao A. , Ræder Helge , Ghila Luiza , Chera Simona
Published: October 2019

Cell replacement therapies hold great therapeutic potential. Nevertheless, our knowledge of the mechanisms governing the developmental processes is limited, impeding the quality of differentiation protocols. Generating insulin-expressing cells in vitro is no exception, with the guided series of differentiation events producing heterogeneous cell populations that display mixed pancreatic islet phenotypes and immaturity. The achievement of terminal differentiation ultimately requires the in vivo transplantation of, usually, encapsulated cells. Here we show the impact of cell confinement on the pancreatic islet signature during the guided differentiation of alginate encapsulated human induced pluripotent stem cells (hiPSCs). Our results show that encapsulation improves differentiation by significantly reshaping the proteome landscape of the cells towards an islet-like signature. Pathway analysis is suggestive of integrins transducing the encapsulation effect into intracellular signalling cascades promoting differentiation. These analyses provide a molecular framework for understanding the confinement effects on hiPSCs differentiation while confirming its importance for this process.
Body weight at young adulthood and association with epigenetic aging and lifespan in the BXD murine family
Authors: Sandoval-Sierra Jose Vladimir , Helbing Alexandra H. B. , Williams Evan G. , Ashbrook David G. , Roy Suheeta , Williams Robert W. , Mozhui Khyobeni
Published: October 2019

DNA methylation (DNAm) is shaped by genetic and environmental factors and modulated by aging. Here, we examine interrelations between epigenetic aging, body weight (BW), and lifespan in 12 inbred mouse strains from the BXD panel that exhibit over two-fold variation in longevity. Genome-wide DNAm was assayed in 70 liver specimens from mice ranging in age from 6 to 25 months that were maintained on normal chow or high fat diet (HFD). We defined subsets of CpG regions associated with age, BW at young adulthood, and strain-by-diet dependent life expectancy. The age associated differentially methylated CpG regions (age-DMRs) featured distinct genomic characteristics, with DNAm gains over time occurring in sites with high CpG density and low average methylation. CpG regions associated with BW were enriched in introns and generally showed lower methylation in mice with higher BW, and inversely correlated with gene expression such that mRNA was higher in mice with higher BW. Lifespan-associated regions featured no distinct genomic characteristics but were linked to genes involved in lifespan regulation, including the telomerase reverse transcriptase gene,Tert, which showed lower methylation and higher gene expression in long-lived strains. An epigenetic clock defined from the age-DMRs conveyed accelerated aging in mice belonging to strains with shorter lifespans. Both higher BW at young adulthood and HFD were associated with accelerated epigenetic aging. Our results highlight the age-accelerating effect of heavier body weight. Furthermore, the study demonstrates that the measure of epigenetic aging derived from age-DMRs can predict strain and diet-induced differences in lifespan.
circZNF827 nucleates a transcription inhibitory complex to balance neuronal differentiation
Authors: Hollensen Anne Kruse , Thomsen Henriette Sylvain , Lloret-Llinares Marta , Kamstrup Andreas Bjerregaard , Jensen Jacob Malthe , Luckmann Majbritt , Birkmose Nanna , Palmfeldt Johan , Jensen Torben Heick , Hansen Thomas Birkballe , Damgaard Christian Kroun
Published: October 2019

Circular RNAs are important for many cellular processes but their mechanisms of action remain poorly understood. Here, we map circRNA inventories of mouse embryonic stem cells, neuronal progenitor cells and differentiated neurons and identify hundreds of highly expressed circRNAs. By screening several candidate circRNAs for a potential function in neuronal differentiation, we find that circZNF827 represses expression of key neuronal markers, suggesting that this molecule negatively regulates neuronal differentiation. Among 760 tested genes linked to known neuronal pathways, knockdown of circZNF827 deregulates expression of numerous genes including nerve growth factor receptor (NGFR), which becomes transcriptionally upregulated to enhance NGF signalling. We identify a circZNF827-nucleated transcription-repressive complex containing hnRNP-K/L proteins and show that knockdown of these factors strongly augments NGFR regulation. Finally, we show that ZNF827 protein is part of the mRNP complex, suggesting a functional co-evolution of a circRNA and the protein encoded by its linear pre-mRNA host.
Alcohol induces mitochondrial fragmentation and stress responses to maintain normal muscle function in Caenorhabditis elegans
Authors: Oh Kelly H. , Kim Hongkyun
Published: October 2019

Abstracts

Chronic excessive ethanol consumption produces distinct toxic and adverse effects on different tissues. In skeletal muscle ethanol causes alcoholic myopathy characterized by myofiber atrophy and loss of muscle strength. Alcoholic myopathy is more prevalent than all inherited muscle diseases combined. Current evidence indicates that ethanol directly impairs muscle organization and function. However, the underlying mechanism by which ethanol causes its toxicity to muscle is poorly understood. Here, we show that the nematode C. elegans recapitulates key aspects of alcoholic myopathy when exposed to ethanol. As in mammals, ethanol exposure impairs muscle strength and organization and induces the expression of protective genes, including oxidative stress response. In addition, ethanol exposure causes a fragmentation of mitochondrial networks aligned with myofibril lattices. This ethanol-induced mitochondrial fragmentation is dependent on mitochondrial fission factor DRP-1 (dynamin-like protein 1), and its receptor proteins on the mitochondrial outer membrane. Our data indicate that this fragmentation contributes to activation of mitochondrial unfolded protein response (UPR). We also found that robust perpetual mitochondrial UPR activation effectively counters muscle weakness caused by ethanol exposure. Our results strongly suggest that modulation of mitochondrial stress responses provides a mechanism to ameliorate alcohol toxicity and damage to muscle.

Significance

Chronic alcohol abuse causes the damage and toxicity to peripheral tissues, including muscle. Alcohol perturbs the structure and function of striated skeletal and cardiac muscles. These toxic effects of alcohol on striated muscles negatively impact morbidity and mortality to alcohol misusers. Here, we demonstrate that the nematode C. elegans also exhibits key features of alcoholic myopathy when exposed to ethanol. Ethanol exposure impairs muscle organization and strength, and induces the expression of genes that cope with alcohol toxicity. Particularly, we find that ethanol toxicity is centered on mitochondria, the power plants of the cell. As an adaptive protective response to mitochondrial dysfunction, ethanol-exposed cells induce global transcriptional reprogramming to restore normal mitochondrial function. Upregulation of this transcriptional reprogramming in C. elegans effectively blocks ethanol-induced muscle weakness, a key feature of alcoholic myopathy. Thus, the modulation of mitochondrial stress responses is a potentially promising therapeutic strategy to ameliorate alcohol toxicity to muscle.
Microglial depletion with CSF1R inhibitor during chronic phase of experimental traumatic brain injury reduces neurodegeneration and neurological deficits
Authors: Henry Rebecca J. , Ritzel Rodney M. , Barrett James P. , Doran Sarah J. , Jiao Yun , Leach Jennie B. , Szeto Gregory L. , Stoica Bogdan A. , Faden Alan I. , Loane David J.
Published: October 2019

Chronic neuroinflammation with sustained microglial activation occurs following moderate-to-severe traumatic brain injury (TBI) and is believed to contribute to subsequent neurodegeneration and neurological deficits. Microglia, the primary innate immune cells in brain, are dependent on colony stimulating factor 1 receptor (CSF1R) signaling for their survival. In this translational study, we examined the effects of delayed depletion and subsequent repopulation of microglia on chronic neurodegeneration and functional recovery up to three months posttrauma. A CSF1R inhibitor, PLX5622, was administered to injured adult male C57Bl/6 mice at one month after controlled cortical impact to remove chronically activated microglia, and the inihibitor was withdrawn 1 week later to allow microglial repopulation. Following TBI, the repopulated microglia displayed a ramified morphology, similar to that of sham control uninjured animals, whereas microglia in untreated injured animals showed the typical chronic posttraumatic hypertrophic morphology. PLX5622 treatment limited TBI-associated neuropathological changes at 3 months posttrauma; these included a smaller cortical lesion, reduced neuronal cell death in the injured cortex and ipsilateral hippocampus, and decreased NOX2-dependent reactive microgliosis. Furthermore, delayed depletion of microglia led to widespread changes in the cortical transcriptome, including alterations in gene pathways involved in neuroinflammation, oxidative stress, and neuroplasticity. PLX5622 treated animals showed significantly improved neurological recovery using a variety of complementary neurobehavioral evaluations. These included beam walk and rotorod tests for sensori-motor function, as well as Y-maze, novel object recognition, and Morris water maze tests to evaluate cognitive function. Together, our findings show that chronic phase removal of neurotoxic microglia using CSF1R inhibitors after experimental TBI can markedly reduce chronic neuroinflammation and neurodegeneration, as well as related long-term motor and cognitive deficits. Thus, CSF1R inhibition may provide a clinically feasible approach to limit posttraumatic neurodegeneration and neurological dysfunction following head injury.
A Petascale Automated Imaging Pipeline for Mapping Neuronal Circuits with High-throughput Transmission Electron Microscopy
Authors: Yin Wenjing , Brittain Derrick , Borseth Jay , Scott Marie E. , Williams Derric , Perkins Jed , Own Chris , Murfitt Matt , Torres Russel M. , Kapner Daniel , Bleckert Adam , Castelli Daniel , Reid David , Lee Wei-Chung Allen , Graham Brett J. , Takeno Marc , Bumbarger Dan J. , Farrell Colin , Reid R. Clay , da Costa Nuno Macarico
Published: October 2019

Serial-section electron microscopy is the method of choice for studying cellular structure and network connectivity in the brain. We have built a pipeline of parallel imaging using transmission electron automated microscopes (piTEAM) that scales this technology and enables the acquisition of petascale datasets containing local cortical microcircuits. The distributed platform is composed of multiple transmission electron microscopes that image, in parallel, different sections from the same block of tissue, all under control of a custom acquisition software (pyTEM) that implements 24/7 continuous autonomous imaging. The suitability of this architecture for large scale electron microscopy imaging was demonstrated by acquiring a volume of more than 1 mm3 of mouse neocortex spanning four different visual areas. Over 26,500 ultrathin tissue sections were imaged, yielding a dataset of more than 2 petabytes. Our current burst imaging rate is 500 Mpixel/s (image capture only) per microscope and net imaging rate is 100 Mpixel/s (including stage movement, image capture, quality control, and post processing). This brings the combined burst acquisition rate of the pipeline to 3 Gpixel/s and the net rate to 600 Mpixel/s with six microscopes running acquisition in parallel, which allowed imaging a cubic millimeter of mouse visual cortex at synaptic resolution in less than 6 months.
Sensitive detection of protein ubiquitylation using a protein-fragment complementation assay
Authors: Boulch Marie Le , Brossard Audrey , Dez Gaëlle Le , Rabut Gwenaël
Published: October 2019

Ubiquitylation is a reversible post-translational protein modification that regulates a multitude of cellular processes. Detection of ubiquitylated proteins is often challenging, because of their low abundance. Here, we present NUbiCA, a sensitive protein-fragment complementation assay to facilitate the monitoring of ubiquitylation events in cultured cells and model organisms. Using yeast as a model system, we demonstrate that NUbiCA enables to accurately monitor mono- and poly-ubiquitylation of proteins expressed at endogenous levels. We also show that it can be applied to decipher ubiquitin chain linkages. We used NUbiCA to investigate the ubiquitylation of the low abundance centromeric histone Cse4, and found that it is ubiquitylated during S-phase. Finally, we assembled a genome wide collection of yeast strains ready to investigate the ubiquitylation of proteins with this new assay. This resource will facilitate the analysis of local or transient ubiquitylation events that are difficult to detect with current methods.

Summary statement

We describe a sensitive protein-fragment complementation assay to facilitate the monitoring of ubiquitylation events that take place in cultured cells or model organisms.
Sequence-Dependent Dynamics of Synthetic and Endogenous RSSs in V(D)J Recombination
Authors: Hirokawa Soichi , Chure Griffin , Belliveau Nathan M. , Lovely Geoffrey A. , Anaya Michael , Schatz David G. , Baltimore David , Phillips Rob
Published: October 2019

Developing lymphocytes in the immune system of jawed vertebrates assemble antigen-receptor genes by undergoing large-scale reorganization of spatially separated V, D, and J gene segments through a process known as V(D)J recombination. The RAG protein initiates this process by binding and cutting recombination signal sequences (RSSs) composed of conserved heptamer and nonamer sequences flanking less well-conserved 12- or 23-bp spacers. Little quantitative information is known about the contributions of individual RSS positions over the course of the RAG-RSS interaction. We employ a single-molecule method known as tethered particle motion to quantify the formation, stability, and cleavage of the RAG-12RSS-23RSS paired complex (PC) for numerous synthetic and endogenous 12RSSs. We thoroughly investigate the sequence space around a RSS by making 40 different single-bp changes and characterizing the reaction dynamics. We reveal that single-bp changes affect RAG function based on their position: loss of cleavage function (first three positions of the heptamer); reduced propensity for forming the PC (the nonamer and last four bp of the heptamer); or variable effects on PC formation (spacer). We find that the rare usage of some endogenous gene segments can be mapped directly to their adjacent 12RSSs to which RAG binds weakly. The 12RSS, however, cannot explain the high-frequency usage of other gene segments. Finally, we find that RSS nicking, while not required for PC formation, substantially stabilizes the PC. Our findings provide detailed insights into the contribution of individual RSS positions to steps of the RAG-RSS re-action that previously have been difficult to assess quantitatively.

V(D)J recombination is a genomic cut-and-paste process for generating diverse antigen-receptor repertoires. The RAG enzyme brings separate gene segments together by binding the neighboring sequences called RSSs, forming a paired complex (PC) before cutting the DNA. There are limited quantitative studies of the sequence-dependent dynamics of the crucial inter-mediate steps of PC formation and cleavage. Here, we quantify individual RAG-DNA dynamics for various RSSs. While RSSs of frequently-used segments do not comparatively enhance PC formation or cleavage, the rare use of some segments can be explained by their neighboring RSSs crippling PC formation and/or cleavage. Furthermore, PC lifetimes reveal DNA-nicking is not required for forming the PC, but PCs with nicks are more stable.
Transmembrane helix 6b links proton- and metal-release pathways to drive conformational change in an Nramp transition metal transporter
Authors: Bozzi Aaron T. , McCabe Anne L. , Barnett Benjamin C. , Gaudet Rachelle
Published: October 2019

The natural resistance-associated macrophage protein (Nramp) family encompasses transition metal and proton co-transporters found in organisms from bacteria to humans. Recent structures ofDeinococcus radiodurans(Dra)Nramp in multiple conformations revealed the intramolecular rearrangements required for alternating access. Here we demonstrate that two parallel cytoplasm-accessible networks of conserved hydrophilic residues in DraNramp—one lining the wide intracellular vestibule for metal release, the other forming a narrow proton-transport pathway—are essential for metal transport. We further show that mutagenic or post-translational modifications of transmembrane helix (TM) 6b, which structurally links these two pathways, impedes normal conformational cycling and metal transport. TM6b contains two highly conserved histidines, H232 and H237. Different mutagenic perturbations for H232, just below the metal-binding site along the proton-exit route, differentially affect DraNramp’s conformational state, suggesting H232 serves as a pivot point for conformational change. In contrast, any tested replacement for H237, lining the metal-exit route, locks the transporter in a transport-inactive outward-closed state. We conclude that these two histidines, and TM6b more broadly, help trigger the bulk rearrangement to the inward-open state upon metal binding and facilitate the return of the empty transporter to an outward-open state upon metal release.
Field decomposition of Bt-506 corn leaf and its effect on Collembola in the black soil region of Northeast China
Authors: Wang Baifeng , Wu Fengci , Yin Junqi , Zhang Ling , Song Xinyuan
Published: October 2019

The litters of Bt corn would go into the soil through straw returning and field ploughing after cultivation. To clarify whether the leaf litter decomposition rate and the non-target soil Collembola were influenced by the Bt protein or other litter properties in leaf litters of Bt corn in Northeast China, leaf litterbags of Bt-506, its near isoline Zheng 58 and a local type Zhengdan 958 were used in the field in Northeast China. The leaf decomposition rate, the leaf properties and the collembolan community in litterbags were investigated later. After seven months, only 43.5 ng/g Bt protein in Bt-506 leaf litter was left. All the investigated indices were not significantly different between Bt-506 and its near isoline Zheng 58. But when compared with local type Zhengdan 958, Bt-506 and its near isoline Zheng 58 contained lower non-structural carbohydrate content but higher total nitrogen content, and had lower litter decomposition rate and less abundance of Collembola. Collembolan abundance and litter decomposition rate were both significantly correlated with the non-structural carbohydrate and total nitrogen contents of the leaf litters. Field study results revealed Bt protein did not affect the leaf litter decomposition rate and the collembolan community in leaf litterbags in short term. The significant differences of these investigated indices among corn types were caused by the different non-structural carbohydrate and total nitrogen contents in leaf litter.