bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prospective feasibility and safety assessment of surgical biopsy for patients with newly diagnosed diffuse intrinsic pontine glioma
Authors: Gupta Nalin , Goumnerova Liliana C , Manley Peter , Chi Susan N , Neuberg Donna , Puligandla Maneka , Fangusaro Jason , Goldman Stewart , Tomita Tadanori , Alden Tord , DiPatri Arthur , Rubin Joshua B , Gauvain Karen , Limbrick David , Leonard Jeffrey , Geyer J Russel , Leary Sarah , Browd Samuel , Wang Zhihong , Sood Sandeep , Bendel Anne , Nagib Mahmoud , Gardner Sharon , Karajannis Matthias A , Harter David , Ayyanar Kanyalakshmi , Gump William , Bowers Daniel C , Weprin Bradley , MacDonald Tobey J , Aguilera Dolly , Brahma Barunashish , Robison Nathan J , Kiehna Erin , Krieger Mark , Sandler Eric , Aldana Philipp , Khatib Ziad , Ragheb John , Bhatia Sanjiv , Mueller Sabine , Banerjee Anu , Bredlau Amy-Lee , Gururangan Sri , Fuchs Herbert , Cohen Kenneth J , Jallo George , Dorris Kathleen , Handler Michael , Comito Melanie , Dias Mark , Nazemi Kellie , Baird Lissa , Murray Jeff , Lindeman Neal , Hornick Jason L , Malkin Hayley , Sinai Claire , Greenspan Lianne , Wright Karen D , Prados Michael , Bandopadhayay Pratiti , Ligon Keith L , Kieran Mark W 
Published: May 2018

Abstract

Background
Diagnosis of diffuse intrinsic pontine glioma (DIPG) has relied on imaging studies, since the appearance is pathognomonic, and surgical risk was felt to be high and unlikely to affect therapy. The DIPG Biology and Treatment Study (DIPG-BATS) reported here incorporated a surgical biopsy at presentation and stratified subjects to receive FDA-approved agents chosen on the basis of specific biologic targets.

Methods
Subjects were eligible for the trial if the clinical features and imaging appearance of a newly diagnosed tumor were consistent with a DIPG. Surgical biopsies were performed after enrollment and prior to definitive treatment. All subjects were treated with conventional external beam radiotherapy with bevacizumab, and then stratified to receive bevacizumab with erlotinib or temozolomide, both agents, or neither agent, based on O6-methylguanine-DNA methyltransferase status and epidermal growth factor receptor expression. Whole-genome sequencing and RNA sequencing were performed but not used for treatment assignment.

Results
Fifty-three patients were enrolled at 23 institutions, and 50 underwent biopsy. The median age was 6.4 years, with 24 male and 29 female subjects. Surgical biopsies were performed with a specified technique and no deaths were attributed to the procedure. Two subjects experienced grade 3 toxicities during the procedure (apnea, n = 1; hypertension, n = 1). One subject experienced a neurologic deficit (left hemiparesis) that did not fully recover. Of the 50 tumors biopsied, 46 provided sufficient tissue to perform the study assays (92%, two-stage exact binomial 90% CI: 83%–97%).

Conclusions
Surgical biopsy of DIPGs is technically feasible, associated with acceptable risks, and can provide biologic data that can inform treatment decisions.
Use of a Contralateral Nasoseptal Flap for Sino-Orbital Fistula Closure
Authors: Hararah Mohammad K. , Mattingly Jameson K. , Ramakrishnan Vijay R. 
Published: May 2018

Abstract
Sino-orbital fistulas can occur after orbital exenteration. Chronic nonhealing fistulas lead to bothersome symptoms including malodorous discharge, hypernasal speech, crusting, wound breakdown, or inability to wear an ocular prosthesis. Reconstruction can be difficult due to the complexity of the defects and the multitude of treatments patients often undergo for the management of the primary disease. Prior radiation, lack of available local tissue, or compromised blood supply are some of the issues that make successful fistula closure problematic. This report describes a method for autologous vascularized tissue coverage using a contralateral nasoseptal flap to successfully close a sino-orbital fistula.
Cas9/CRISPR genome editing to demonstrate the contribution of Cyp51A Gly138Ser to azole resistance in Aspergillus fumigatus
Authors: Umeyama Takashi , Hayashi Yuta , Shimosaka Hisaki , Inukai Tatsuya , Yamagoe Satoshi , Takatsuka Shogo , Hoshino Yasutaka , Nagi Minoru , Nakamura Shigeki , Kamei Katsuhiko , Ogawa Kenji , Miyazaki Yoshitsugu 
Published: May 2018

AbstractAzole resistance in Aspergillus fumigatus is predominantly associated with increased expression of Cyp51A (lanosterol 14α-demethylase), the target enzyme of azole antifungal agents, or with single-nucleotide polymorphisms (SNPs) in cyp51A. Although several SNPs that may be linked to low susceptibility in azole-resistant isolates have previously been reported, few studies have been conducted to conclusively demonstrate the contribution of SNPs to decreased azole susceptibility. An A. fumigatus strain was isolated from the sputum of a 74-year-old male receiving long-term voriconazole treatment for chronic progressive pulmonary aspergillosis. Etest antifungal susceptibility testing showed low susceptibility to voriconazole, itraconazole, and posaconazole. Nucleotide sequencing of cyp51A from this isolate revealed the mutations Gly138Ser (GGC→AGC) and Asn248Lys (AAT→AAA) compared with the cyp51A of azole-susceptible isolates. PCR-amplified DNA fragments containing cyp51A with or without the mutations of interest and a hygromycin marker were simultaneously introduced along with the Cas9 protein and in vitro-synthesized single-guide RNA into protoplasts of the azole-resistant/susceptible strains. Etest azole susceptibility testing of recombinant strains showed an increased susceptibility via the replacement of Ser138 by glycine. In contrast, azole susceptibility was slightly decreased when a Ser138 mutation was introduced into the azole-susceptible strain AfS35, indicating that the serine at position 138 of Cyp51A contributes to low susceptibility in the azole-resistant isolate. Genetic recombination, which has been hampered thus far in clinical isolates, can now be achieved using Cas9/CRISPR genome editing. This technique could be useful to investigate the contribution of other SNPs of cyp51A to azole resistance.
Clear, extended field-of-view single-molecule imaging by highly inclined swept illumination
Authors: Tang Jialei , Han Kyu Young 
Published: May 2018

AbstractHighly inclined and laminated optical sheet (HILO) illumination facilitates high-contrast single-molecule imaging inside cells with a single objective lens. However, the beam thickness is strongly coupled to the illumination area, limiting its usage. Here, we present highly inclined swept tile illumination microscopy (HIST). By sweeping a thin HILO beam with confocal slit detection, HIST provides a 2-fold thinner illumination and >40-fold larger imaging area than conventional HILO microscopy, enabling 3D single-molecule imaging with high signal-to-background ratio. We demonstrate single-molecule mRNA imaging with a few probes or a single probe in cultured cells and mouse brain tissues.
Spatiotemporally controlled Myosin relocalization and internal pressure cause biased cortical extension to generate sibling cell size asymmetry
Authors: Pham Tri Thanh , Monnard Arnaud , Helenius Jonne , Lund Erik , Lee Nicole , Müller Daniel J. , Cabernard Clemens 
Published: May 2018

AbstractMetazoan cells can generate unequal sized sibling cells during cell division. This form of asymmetric cell division depends on spindle geometry and Myosin distribution but the underlying mechanics are unclear. Here, we use atomic force microscopy and live cell imaging to elucidate the biophysical forces involved in the establishment of physical asymmetry in Drosophila neural stem cells. We show that the force driving initial apical membrane expansion is provided by hydrostatic pressure, peaking shortly after anaphase onset, and enabled by a relieve of actomyosin contractile tension on the apical cell cortex. The subsequent increase in contractile forces at the cleavage furrow, combined with the relocalization of basally located Myosin results in basal membrane extension and sustained apical expansion. We propose that spatiotemporally controlled actomyosin contractile tension and hydrostatic pressure enables stereotypic biased membrane expansion to generate sibling cell size asymmetry.
Dissecting the herpesvirus architecture by targeted proteolysis
Authors: Daniel Gina R. , Pegg Caitlin E. , Smith Gregory A. 
Published: May 2018

ABSTRACTHerpesvirus particles have a complex architecture consisting of an icosahedral capsid that is surrounded by a lipid envelope. Connecting these two components is a layer of tegument that consists of varying amounts of twenty or more proteins. The arrangement of proteins within the tegument cannot easily be assessed and instead is inferred from tegument interactions identified in reductionist models. To better understand the tegument architecture, we have developed an approach to probe capsid-tegument interactions within extracellular viral particles by encoding tobacco etch virus (TEV) protease sites in viral structural proteins, along with distinct fluorescent tags in capsid and tegument components. In this study, TEV sites were engineered within the pUL36 large tegument protein: a critical structural element that is anchored directly on the capsid surface. Purified pseudorabies virus extracellular particles were permeabilized and TEV protease was added to selectively cleave the exposed pUL36 backbone. Interactions with the capsid were assessed in situ by monitoring the fate of the fluorescent signals following cleavage. Although several regions of pUL36 are proposed to bind capsids, pUL36 was found stably anchored to the capsid exclusively at its carboxyl terminus. Two additional tegument proteins, pUL37 and pUS3, were tethered to the capsid via pUL36 whereas the pUL16, pUL47, pUL48, and pUL49 tegument proteins were not stably bound to the capsid.IMPORTANCENeuroinvasive alphaherpesviruses produce diseases of clinical and economic significance in humans and veterinary animals, but are predominantly associated with less serious recurrent disease. Like all viruses, herpesviruses assemble a metastable particle that selectively dismantles during initial infection. This process is made more complex by the presence of a tegument layer that resides between the capsid surface and envelope. Components of the tegument are essential for particle assembly and also serve as critical effectors that promote infection upon entry into cells. How this dynamic network of protein interactions is arranged within virions is largely unknown. We present a molecular approach to dissect the tegument and with it, begin to tease apart the protein interactions that underlie this complex layer of the virion architecture.
Intestinal bacteria modulate the foraging behavior of the Oriental fruit flyBactrocera dorsalis(Diptera: Tephritidae)
Authors: Akami Mazarin , Andongma Awawing A. , Zhengzhong Chen , Nan Jiang , Khaeso Kanjana , Jurkevitch Edouard , Niu Chang-Ying , Yuval Boaz 
Published: May 2018

AbstractThe gut microbiome of insects directly or indirectly affects the metabolism, immune status, sensory perception and feeding behavior of its host. Here, we examine the hypothesis that in the Oriental fruit fly(Bactrocera dorsalis, Diptera: Tephritidae), the presence or absence of gut symbionts affects foraging behavior and nutrient ingestion. We offered protein starved flies, symbiotic or aposymbiotic, a choice between diets containing all amino acids or only the non-essential ones. The different diets were presented in a foraging arena as drops that varied in their size and density, creating an imbalanced foraging environment. Suppressing the microbiome resulted in significant changes of the foraging behavior of both male and female flies. Aposymbiotic flies responded faster to the diets offered in experimental arenas, spent more time feeding, ingested more drops of food, and were constrained to feed on time consuming patches (containing small drops of food), when these offered the full complement of amino acids. We discuss these results in the context of previous studies on the effect of the gut microbiome on host behavior, and suggest that these be extended to the life history dimension.Importance and significance of the studyThe gut bacteria of tephritid fruit flies provide nutritional benefits to their hosts, by making essential amino-acids readily available. Foraging for food is risky, as active flies are exposed to predators and incur a considerable investment of time and energy. Therefore, making beneficial compromises between the feeding time and nutrient ingestion is a question of survival for the flies. Our study demonstrates how gut bacteria drive this behavior by allowing symbiotic flies to forage optimally while acquiring essential nutrients. This finding adds a novel step to the nexus connecting the insect gut, its microbiome, the nervous system, chemoreception to individual patterns of foraging.
Skyhawk: An Artificial Neural Network-based discriminator for reviewing clinically significant genomic variants
Authors: Luo Ruibang , Lam Tak-Wah , Schatz Michael C. 
Published: May 2018

AbstractMotivationMany rare diseases and cancers are fundamentally diseases of the genome. In the past several years, genome sequencing has become one of the most important tools in clinical practice for rare disease diagnosis and targeted cancer therapy. However, variant interpretation remains the bottleneck as is not yet automated and may take a specialist several hours of work per patient. On average, one-fifth of this time is spent on visually confirming the authenticity of the candidate variants.ResultsWe developed Skyhawk, an artificial neural network-based discriminator that mimics the process of expert review on clinically significant genomics variants. Skyhawk runs in less than one minute to review ten thousand variants, and about 30 minutes to review all variants in a typical whole-genome sequencing sample. Among the false positive singletons identified by GATK HaplotypeCaller, UnifiedGenotyper and 16GT in the HG005 GIAB sample, 79.7% were rejected by Skyhawk. Worked on the Variants with Unknown Significance (VUS), Skyhawk marked most of the false positive variants for manual review and most of the true positive variants no need for review.AvailabilitySkyhawk is easy to use and freely available at https://github.com/aquaskyline/Skyhawk
Molecular architecture of theLegionellaDot/Icm type IV secretion system
Authors: Ghosal Debnath , Chang Yi-Wei , Jeong Kwang Cheol , Vogel Joseph P. , Jensen Grant J. 
Published: May 2018

AbstractLegionella pneumophilasurvives and replicates inside host cells by secreting ~300 effectors through the Dot/Icm type IVB secretion system (T4BSS). Understanding this machine’s structure is challenging because of its large number of components (27) and integration into all layers of the cell envelope. Previously we overcame this obstacle by imaging the Dot/Icm T4BSS in its native state within intact cells through electron cryotomography. Here we extend our observations by imaging a stabilized mutant that yielded a higher resolution map. We describe for the first time the presence of a well-ordered central channel that opens up into a windowed large (~32 nm wide) secretion chamber with an unusual 13-fold symmetry. We then dissect the complex by matching proteins to densities for many components, including all those with periplasmic domains. The placement of known and predicted structures of individual proteins into the map reveals the architecture of the T4BSS and provides a roadmap for further investigation of this amazing specialized secretion system.
Melissa: Bayesian clustering and imputation of single cell methylomes
Authors: Kapourani Chantriolnt-Andreas , Sanguinetti Guido 
Published: May 2018

AbstractMeasurements of DNA methylation at the single cell level are promising to revolutionise our understanding of epigenetic control of gene expression. Yet, intrinsic limitations of the technology result in very sparse coverage of CpG sites (around 5% to 20% coverage), effectively limiting the analysis repertoire to a semi-quantitative level. Here we introduce Melissa (MEthyLation Inference for Single cell Analysis), a Bayesian hierarchical method to quantify spatially-varying methylation profiles across genomic regions from single-cell bisulfite sequencing data (scBS-seq). Melissa clusters individual cells based on local methylation patterns, enabling the discovery of epigenetic differences and similarities among individual cells. The clustering also acts as an effective regularisation method for imputation of methylation on unassayed CpG sites, enabling transfer of information between individual cells. We show both on simulated and real data sets that Melissa provides accurate and biologically meaningful clusterings, and state-of-the-art imputation performance. An R implementation of Melissa is publicly available at https://github.com/andreaskapou/Melissa.
A non-canonical lysosome biogenesis pathway generates Golgi-associated lysosomes during epidermal differentiation
Authors: Mahanty Sarmistha , Dakappa Shruthi Shirur , Shariff Rezwan , Patel Saloni , Swamy Mruthyunjaya Mathapathi , Majumdar Amitabha , Setty Subba Rao Gangi 
Published: May 2018

AbstractKeratinocytes maintain epidermis integrity and function including physical and antimicrobial barrier through cellular differentiation. This process is predicted to be controlled by calcium ion gradient and nutritional stress. Keratinocytes undergo proteome changes during differentiation, which enhances the intracellular organelle digestion to sustain the stress conditions. However, the molecular mechanism between epidermal differentiation and organelle homeostasis is poorly understood. Here, we used primary neonatal human epidermal keratinocytes to study the link between cellular differentiation, signaling pathways and organelle turnover. Upon addition of calcium chloride (2 mM) to the culture medium, keratinocytes increased their cell size and the expression of differentiation markers. Moreover, differentiated keratinocytes showed enhanced lysosome biogenesis that was dependent on ATF6-arm of UPR signaling but independent of mTOR-MiT/TFE transcription factors. Furthermore, chemical inhibition of mTOR has increased keratinocyte differentiation and relocalized the MiT/TFE TFs to the lysosome membranes, indicating that autophagy activation promotes the epidermal differentiation. Interestingly, differentiation of keratinocytes resulted in dispersal of fragmented Golgi and lysosomes, and the later organelles showed colocalization with Golgi-tethering proteins, suggesting that these lysosomes possibly originated from Golgi, hence named as Golgi-associated lysosomes (GALs). Consistent to this prediction, inhibition of Golgi function using brefeldin A completely abolished the formation of GALs and the keratinocyte differentiation. Thus, ER stress regulates the biogenesis of GALs, which maintains keratinocyte differentiation and epidermal homeostasis.
Sensory neuron lineage mapping and manipulation in theDrosophila olfactorysystem
Authors: Chai Phing Chian , Cruchet Steeve , Wigger Leonore , Benton Richard 
Published: May 2018

AbstractNervous systems exhibit myriad cell types, but understanding how this diversity arises is hampered by the difficulty to visualize and genetically-interrogate specific lineages, especially at early developmental stages prior to expression of unique molecular markers. Here, we use a genetic immortalization method to analyze the development of sensory neuron lineages in theDrosophilaolfactory system, from their origin to terminal differentiation. We apply this approach to first define a fate map of all olfactory lineages and refine the model of temporal patterns of lineage divisions. Taking advantage of a selective marker for the lineage that gives rise to Or67d pheromone-sensing neurons and a genome-wide transcription factor RNAi screen, we identify the spatial and temporal requirements for Pointed, an ETS family member, in this developmental pathway. Transcriptomic analysis of wild-type and Pointed-depleted olfactory tissue reveals a universal requirement for this factor as a switch-like determinant of fates in these sensory lineages.
Redox fluctuations control the coupled cycling of iron and carbon in tropical forest soils
Authors: Bhattacharyya Amrita , Campbell Ashley N. , Tfaily Malak M. , Lin Yang , Silver Whendee L. , Nico Peter S. , Pett-Ridge Jennifer 
Published: May 2018

ABSTRACTOscillating redox conditions are the norm in tropical soils; driven by an ample supply of reductants, high moisture, microbial oxygen consumption, and finely textured clays that limit diffusion. Yet the net result of variable soil redox regimes on iron-organic matter (Fe-OM) associations in tropical soils owing to changing climate is poorly understood. Using a 44-day redox incubation experiment with humid tropical soils from Puerto Rico, we examined patterns of Fe and C transformation under four redox regimes: static anoxic, flux 4-day (4d oxic, 4d anoxic), flux 8-day (8d oxic, 4d anoxic) and static anoxic. Prolonged anoxia promoted reductive dissolution of Fe-oxides and an increase in short-range ordered (SRO) Fe oxides. Preferential dissolution of this less-crystalline Fe pool was evident immediately following a shift in bulk redox status (oxic to anoxic), and coincided with increased dissolved organic carbon, presumably due to acidification or direct release of OM from dissolving Fe(III) mineral phases. Average nominal oxidation state of water-soluble carbon was lowest under persistent anoxic conditions, suggesting more reduced OC is microbially preserved under reducing conditions. Anoxic soil compounds had high H/C values (similar to lignin-like metabolites) whereas oxic soil compounds had higher O/C values, akin to tannin- and cellulose-like components. Cumulative respiration derived from native soil organic carbon was highest in static oxic soils. These results highlight the volatility of mineral-OM interactions in tropical soils, and suggest that short-term impacts of shifting soil O2 availability control exchanges of C between mineral-sorbed and aqueous pools, implying that the periodicity of low-redox moments may control the fate of C in wet tropical soils.Toc Art
Counter-Landnahme? Labour disputes in the care-work field
Authors: Becker Karina , Dörre Klaus , Kutlu Yalcin 
Published: May 2018

Purpose
The thesis of our paper is that the industrial dispute articulates a counter-movement against the progressive capitalist Landnahme of care work. What is ostensibly a standard wage conflict proves, on closer scrutiny, to be a dispute that contains a transformative social dynamic. It cannot be conceived either as a traditional class struggle or as a movement against the market’s unreasonable demands. The paper aims to discuss these issues.

Design/methodology/approach
The authors draw on a qualitative survey in the social and childcare services (expert interviews, groups discussions, expert hearings) and two partial-studies on the renewal of trade unions in East and West Germany (54 expert and 46 employee interviews).

Findings
Professional pride along with confidence in their own professional skills collides with the market- and competition-driven devaluation of the work of entire groups of employees. Used correctly, a putative professional consciousness can transform into a source of resilience, protest and collective engagement, which the authors interpret as counter-Landnahme. A consciousness rooted in professionality develops into a subjective power resource, the activation of which simultaneously strengthens trade unions’ power to effectuate change.

Originality/value
In the case of the childcare workers, this movement is rooted in a newly awakened consciousness as skilled labourers. What at first appears as a wage conflict is in fact, upon closer inspection, a conflict loaded with transformative potential. After all, any greater social recognition of this occupational group will naturally, at least by tendency, prompt a discussion concerning the modes of financing public reproductive activities.