bluuebunny/crossref_metadata_2025_split huggingface dataset:
Accuracy of Three-Dimensional Soft Tissue Prediction in Orthognathic Cases Using Dolphin Three-Dimensional Software
Authors: Elshebiny Tarek , Morcos Sherif , Mohammad Abdulaziz , Quereshy Faisal , Valiathan Manish 
Published: October 2018

Introduction:
Orthodontists and surgeons have been looking for more accurate methods to plan and predict surgical outcomes in patients with skeletal discrepancies.

Methods:
The sample consisted of 20 subjects from the surgical clinic of a graduate orthodontic program who had been treated with Le Fort I maxillary movement, bisagittal split osteotomy, with or without genioplasty. All subjects had to have preoperative (T0) and at least 6 months postoperative (T1) cone-beam computed tomographies that were imported to Dolphin three-dimensional (3D) software version 11.9 in digital imaging and communications in medicine format. Three-dimensional voxel-based superimposition on the cranial base was performed for T0 and T1 to accurately measure the skeletal surgical movements. A virtual orthognathic surgery was performed on T0 to mimic the actual skeletal osteotomies using the treatment simulation tool in Dolphin 3D. A prediction 3D soft tissue image (Tp) was generated based on the Dolphin virtual skeletal planning. The differences between Tp and T1 for all patients were measured using linear and angular measurements visualized by surface mapping.

Results:
Significant differences were found between Tp and T1 in Nasolabial angle, Soft tissue A point, and Subalar area.

Conclusions:
The soft tissue prediction accuracy after double jaw surgery using Dolphin 3D is limited in some areas, especially upper lip and base of the nose.
Initial evaluation of the efficacy and safety of in-hospital expandable hemostatic minisponge use in penetrating trauma
Authors: Warriner Zachary , Lam Lydia , Matsushima Kazuhide , Benjamin Elizabeth , Strumwasser Aaron , Demetriades Demetrios , Inaba Kenji 
Published: October 2018

BACKGROUND
Hemorrhage remains the leading cause of preventable death after trauma. The XSTAT expandable minisponge hemostatic device was developed for the control of severe, life-threatening bleeding from junctional wounds not amenable to tourniquet application. This is an initial report of the clinical use of this novel method of hemorrhage control for civilian penetrating injury.

METHODS
A review of trauma admissions at a high-volume Level I trauma center was performed from July 2016 to November 2017. All patients sustaining penetrating trauma with active hemorrhage were evaluated for XSTAT use. Ten device deployments occurred during this time. Each deployment was reviewed in detail, capturing patient and injury data, efficacy of hemorrhage control, and evaluation of any potential device or treatment related complications.

RESULTS
Six thousand three hundred sixty-three trauma admissions were reviewed with 22.1% sustaining a penetrating mechanism of injury. XSTAT was deployed in 10 (0.7%) penetrating trauma admissions with a mean age of 38.3 (range, 16–59) years, systolic blood pressure (SBP) of 126.7 (range, 74–194) mm Hg, Glasgow Coma Scale (GCS) score of 14.5 (range, 13–15), and New Injury Severity Score (NISS) of 9.5 (range, 1–27). Eight patients had an identifiable arterial injury; the remainder had vein or soft tissue bleeding. Overall, half were junctional injuries. XSTAT was able to stop bleeding in nine of ten patients on the first deployment, with the remaining patient requiring one repeat injection. Dwell times ranged from 1 hour to 40 hours (median, 15 hours). There were no technical device failures or embolic complications. Retained sponges were identified in two patients on initial postremoval x-rays following wound exploration for definitive hemorrhage control and sponge removal. No patient died during the study period.

CONCLUSION
XSTAT use appears safe. It is rapid, reliable, and provides a high degree of hemorrhage control on first deployment. Sponge removal should always be followed by radiographic clearance. For patients with hemorrhage from cavitary wounds not amenable to tourniquet placement, this device was effective. Further study is warranted as XSTAT use becomes more widespread.

LEVEL OF EVIDENCE
Therapeutic study, level V.
Clinic Nonattendance Is a Risk Factor for Poor Kidney Transplant Outcomes
Authors: Richardson Cathy , Williams Aimee , McCready Jill , Khalil Khalid , Evison Felicity , Sharif Adnan 
Published: October 2018

Background
The aim of this study was to analyze the impact of clinic nonattendance within the first year after kidney transplantation on graft-related outcomes.

Methods
Our retrospective analysis included all patients receiving their transplant (2007-2017) and receiving their long-term follow up at our center. Clinic nonattendance was extracted from electronic patient records and informatics systems, with highest clinic nonattenders stratified at the 75th percentile.

Results
Data were analyzed for 916 kidney allograft recipients, with median follow up 1168 days (interquartile range, 455-2073 days). Median number of missed transplant clinic visits in the first year was 5 (interquartile range, 3-7) and nonattenders were defined above the 75th percentile. Nonattenders versus attenders were more likely to be black, ABO-incompatible, repeat kidney transplant recipients but less likely to have pretransplantation diabetes. Nonattenders versus attenders had longer hospital stays after their transplant surgery in days (14.4 vs 12.2 respectively, P = 0.007), higher rate of delayed graft function (21.3% vs 12.8% respectively, P = 0.005), higher risk for 1-year rejection (12.5% vs 7.8% respectively, P = 0.044), worse 1-year estimated glomerular filtration rate in mL/min (47.0 vs 54.1, respectively, P = 0.002) and increased risk for death-censored graft loss by median follow (17.5% vs 12.0%, respectively, P = 0.013). In a Cox regression model, kidney transplant recipients defined as clinic nonattenders within the first postoperative year demonstrated a significantly increased rate of death-censored graft loss (hazard ratio, 1.983; 95% confidence interval, 1.061-3.707; P = 0.032).

Conclusions
Kidney transplant recipients in the top quartile for nonattendance require additional support and supervision to help attenuate long-term risks to their graft function and survival.
Genome-wide gene expression profiling reveals that cuticle alterations and P450 detoxification are associated with pyrethroid resistance in Anopheles arabiensis populations from Ethiopia
Authors: Simma Eba Alemayehu , Dermauw Wannes , Balabanidou Vasileia , Snoeck Simon , Bryon Astrid , Clark Richard M. , Yewhalaw Delenasaw , Vontas John , Duchateau Luc , Van Leeuwen Thomas 
Published: October 2018

AbstractBACKGROUNDVector control is the main intervention in malaria control and elimination strategies. However, the development of insecticide resistance is one of the major challenges for controlling malaria vectors. Anopheles arabiensis populations in Ethiopia showed resistance against both DDT and the pyrethroid deltamethrin. Although a L1014F target-site resistance mutation was present in the voltage gated sodium channel of investigated populations, the levels of resistance and biochemical studies indicated the presence of additional resistance mechanisms. In this study, we used genome-wide transcriptome profiling by RNAseq to assess differentially expressed genes between three deltamethrin and DDT resistant An. arabiensis field populations (Tolay, Asendabo, Chewaka) and two susceptible strains (Sekoru and Mozambique).RESULTSBoth RNAseq analysis and RT-qPCR showed that a glutathione-S-transferase, gstd3, and a cytochrome P450 monooxygenase, cyp6p4, were significantly overexpressed in the group of resistant populations compared to the susceptible strains, suggesting that the enzymes they encode play a key role in metabolic resistance against deltamethrin or DDT. Furthermore, a gene ontology enrichment analysis showed that expression changes of cuticle related genes were strongly associated with insecticide resistance, although this did not translate in increased thickness of the procuticle.CONCLUSIONOur transcriptome sequencing of deltamethrin/DDT resistant An. arabiensis populations from Ethiopia suggests non-target site resistance mechanisms and pave the way for further investigation of the role of cuticle composition in resistance.
Transient Replication in Specialized Cells Favors Conjugative Transfer of a Selfish DNA Element
Authors: Delavat François , Moritz Roxane , van der Meer Jan Roelof 
Published: October 2018

AbstractBacterial evolution is driven to a large extent by horizontal gene transfer (HGT) – the processes that distribute genetic material between species rather than by vertical descent. HGT is mostly mediated by an assortment of different selfish DNA elements, several of which have been characterized in great molecular detail. In contrast, very little is known on adaptive features optimizing horizontal fitness. By using single DNA molecule detection and time-lapse microscopy, we analyze here the fate of an integrative and conjugative element (ICE) in individual cells of the bacteriumPseudomonas putida. We uncover how the ICE excises and irregularly replicates, exclusively in a sub-set of specialized host cells. As postulated, ICE replication is dependent on its origin of transfer and its DNA relaxase. Rather than being required for ICE maintenance, however, we find that ICE replication serves more effective conjugation to recipient cells, providing selectable benefit to its horizontal transfer.
Dynamic Hh signaling can generate temporal information during tissue patterning
Authors: García-Morales Diana , Navarro Tomás , Iannini Antonella , Míguez David G. , Casares Fernando 
Published: October 2018

ABSTRACTThe differentiation of tissues and organs requires that cells exchange information in space and time. Spatial information is often conveyed by morphogens, molecules that disperse across receiving cells generating signaling gradients. Cells translate such concentration gradients into space-dependent patterns of gene expression and cellular behavior [1, 2]. But could morphogen gradients also convey developmental time? Here, investigating the developmental role of Hh on a component of theDrosophilavisual system, the ocellar retina, we discovered that ocellar cells use the non-linear gradient of Hh as a temporal cue, collectively performing the biological equivalent of a mathematical logarithmic transformation. In this way, a morphogen diffusing from a non-moving source is decoded as a wave of differentiating photoreceptors that travels at constant speed throughout the retinal epithelium.
Bacterial Hsp90 mediates the degradation of aggregation-prone Hsp70-Hsp40 substrates preferentially by HslUV proteolysis
Authors: Fauvet Bruno , Finka Andrija , Castanié-Cornet Marie-Pierre , Cirinesi Anne-Marie , Genevaux Pierre , Quadroni Manfredo , Goloubinoff Pierre 
Published: October 2018

AbstractWhereas in eukaryotic cells, the Hsp90s are profusely-studied molecular chaperones controlling protein homeostasis together with Hsp70s, in bacteria, the function of Hsp90 (HtpG) and its collaboration with Hsp70 (DnaK) remains unknown. To uncover physiological processes depending on HtpG and DnaK, we performed comparative quantitative proteomic analyses of insoluble and total protein fractions from unstressed wild typeE. coli, and from knockout mutantsΔdnaKdnaJ(ΔKJ),ΔhtpG(ΔG) andΔdnaKdnaJΔhtpG(ΔKJG) and compared their growth rates under heat-stress also withΔdnaKdnaJΔhslV. Whereas, expectedly, mutant ΔG showed no proteomic differences with wild-type, ΔKJ expressed more chaperones, proteases and ribosomes and dramatically less metabolic and respiratory enzymes. Unexpectedly, we found that ΔKJG showed higher levels of metabolic and respiratory enzymes and both ΔKJG andΔdnaKdnaJΔhslVgrew better at 37oC than ΔKJ. The results indicate that bacterial Hsp90 mediates the degradation of aggregation-prone Hsp70-Hsp40 substrates, preferably by the HslUV protease.Significance statement:The molecular chaperones Hsp70 and Hsp90 are among the most abundant and well-conserved proteins in all realms of life, forming together the core of the cellular proteostasis network. In eukaryotes, Hsp90 functions in collaboration with Hsp70; we studied this collaboration inE. coli, combining genetic studies with label-free quantitative proteomics in which both protein abundance and protein solubility were quantified. Bacteria lacking Hsp70 (DnaK) and its co-chaperone DnaJ (ΔdnaKdnaJ) grew slower and contained significantly less key metabolic and respiratory enzymes. Unexpectedly, an additional deletion of the Hsp90(htpG)gene partially restored the WT phenotype. Deletion of the HslV protease in the ΔdnaKdnaJ background also improved growth, suggesting that bacterial Hsp90 mediates the degradation of Hsp70 substrates, preferentially through HslV.At 37oCΔdnaKdnaJ E. colimutants grow slower than wild type cells. Quantitative proteomics shows that compared to wild type cells,ΔdnaKdnaJcells grown at 30oC contain significantly less key metabolic and respiratory enzymes. Unexpectedly, deletion of theHtpGgene in the ΔdnaKdnaJbackground ameliorates growth at 37oC and partially restores the cellular levels of some metabolic and respiratory enzymes.
State-dependent changes in olfactory cortical networks via cholinergic modulation
Authors: Wilson Donald A. , Juventin Maxime , Ilina Maria , Pizzo Alessandro , Teixeira Catia 
Published: October 2018

AbstractActivity in sensory cortical networks reflects both peripheral sensory input and intra‐ and inter-cortical network input. How sensory cortices balance these diverse inputs to provide relatively stable, accurate representations of the external world is not well understood. Furthermore, neuromodulation could alter the balance of these inputs in a state‐ and behavior-dependent manner. Here, we used optogenetic stimulation to directly assay the relative strength of bottom-up (olfactory bulb) and top-down (lateral entorhinal cortex) synaptic inputs to piriform cortex in freely moving rats. Optotrodes in the piriform cortex were used to test the relative strength of these two inputs, in separate animals, with extracellular, monosynaptic evoked potentials. The results suggest a rapid state-dependent shift in the balance of bottom-up and top-down inputs to PCX, with enhancement in the strength of lateral entorhinal cortex synaptic input and stability or depression of olfactory bulb synaptic input during slow-wave sleep compared to waking. The shift is in part due to a state-dependent change in cholinergic tone as assessed with fiber photometry of GCaMP6 fluorescence in basal forebrain ChAT+ neurons, and blockade of the state-dependent synaptic shift with cholinergic muscarinic receptor activation.
Glycerol phosphate acyltransferase 6 controls filamentous pathogen interactions and cell wall properties of the tomato and Nicotiana benthamiana leaf epidermis
Authors: Fawke Stuart , Torode Thomas A. , Gogleva Anna , Fich Eric A. , Sørensen Iben , Yunusov Temur , Rose Jocelyn K.C. , Schornack Sebastian 
Published: October 2018

ABSTRACTThe leaf epidermal wall is covered by a cuticle, composed of cutin and waxes, which protects against dehydration and constitutes a barrier against pathogen attack. Cutin monomers are formed by the transfer of 16- or 18-carbon fatty acids to glycerol by glycerol-3-phosphate acyltransferase (GPAT) enzymes, which facilitates their transport to the plant surface. Here we address the dual functionality of pathogen-inducible Glycerol phosphate acyltransferase 6 (GPAT6) in controlling pathogen entry and dehydration in leaves. Silencing of Nicotiana benthamiana NbGPAT6a increased leaf susceptibility to the oomycetes Phytophthora infestans and P. palmivora, whereas stable overexpression of NbGPAT6a-GFP rendered leaves more resistant to infection. A loss-of-function mutation of the orthologous gene in tomato (Solanum lycopersicum), SlGPAT6, similarly resulted in increased susceptibility of leaves to Phytophthora infection concomitant with altered intracellular infection structure morphology. Conversely, Botrytis cinerea disease symptoms were reduced. Modulation of GPAT6 expression predominantly altered the outer cell wall of leaf epidermal cells. The impaired cell wall-cuticle continuum of tomato gpat6-a mutants resulted in increased water loss and these plants had fewer stomata. Our work highlights a hitherto unknown role for GPAT6-generated cutin monomers in controlling epidermal cell properties that are integral to leaf-microbe interactions and limit dehydration.
Structural Organization of a Type III-A CRISPR Effector Subcomplex Determined by X-ray Crystallography and Cryo-EM
Authors: Dorsey Bryan W. , Huang Lei , Mondragón Alfonso 
Published: October 2018

AbstractClustered regularly interspaced short palindromic repeats (CRISPR) and their associated Cas proteins provide an immune-like response in many prokaryotes against extraneous nucleic acids. CRISPR-Cas systems are classified into different classes and types. Class 1 CRISPR-Cas systems form multi-protein effector complexes that includes a guide RNA (crRNA) used to identify the target for destruction. Here we present crystal structures of Staphylococcus epidermidis Type III-A CRISPR subunits Csm2 and Csm3 and a 5.2 Å resolution single-particle cryo-electron microscopy (cryo-EM) reconstruction of an effector subcomplex including the crRNA. The structures help to clarify the quaternary architecture of Type III-A effector complexes, as well as to provide details on crRNA binding, target RNA binding and cleavage, and intermolecular interactions essential for effector complex assembly. The structures allow a better understanding of the organization of Type III-A CRISPR effector complexes as well as highlighting the overall similarities and differences with other Class 1 effector complexes.
Feeding behavior of Costa Rican velvet worms: food hiding, parental feeding investment and ontogenetic diet shift (Onychophora: Peripatidae)
Authors: Barquero-González José Pablo , Vega-Hidalgo Álvaro , Monge-Nájera Julián 
Published: October 2018

AbstractWe report, for the first time in onychophorans, food hiding, parental feeding investment and an ontogenetic diet shift two weeks after birth: from the parent’s adhesive used to capture prey, to the prey itself.
Transcriptome profiling of pathogen-specific CD4 T cells identifies T-cell-intrinsic caspase-1 as an important regulator of Th17 differentiation
Authors: Gao Yajing , Deason Krystin , Jain Aakanksha , Irizarry-Caro Ricardo A , Dozmorov Igor , Rauch Isabella , Wakeland Edward K , Pasare Chandrashekhar 
Published: October 2018

One sentence summaryOur study revealed that DCs shape distinct pathogen-specific CD4 T cell transcriptome and from which, we discovered an unexpected role for T-cell-intrinsic caspase-1 in promoting Th17 differentiation.ABSTRACTDendritic cells (DCs) are critical for priming and differentiation of pathogen-specific CD4 T cells. However, to what extent innate cues from DCs dictate transcriptional changes in T cells leading to effector heterogeneity remains elusive. Here we have used anin vitroapproach to prime naïve CD4 T cells by DCs stimulated with distinct pathogens. We have found that such pathogen-primed CD4 T cells express unique transcriptional profiles dictated by the nature of the priming pathogen. In contrast to cytokine-polarized Th17 cells that display signatures of terminal differentiation, pathogen-primed Th17 cells maintain a high degree of heterogeneity and plasticity. Further analysis identified caspase-1 as one of the genes upregulated only in pathogen-primed Th17 cells but not in cytokine-polarized Th17 cells. T-cell-intrinsic caspase-1, independent of its function in inflammasome, is critical for inducing optimal pathogen-driven Th17 responses. More importantly, T cells lacking caspase-1 fail to induce colitis following transfer into RAG-deficient mice, further demonstrating the importance of caspase-1 for the development of pathogenic Th17 cellsin vivo. This study underlines the importance of DC-mediated priming in identifying novel regulators of T cell differentiation.
Actomyosin-driven force patterning controls endocytosis at the immune synapse
Authors: Kumari Anita , Sáez Pablo J. , Maurin Mathieu , Lankar Danielle , San Roman Mabel , Voituriez Raphael , Hennig Katharina , Boura Vanessa F. , Karlsson Mikael C.I. , Balland Martial , Lennon Dumenil Ana-Maria , Pierobon Paolo 
Published: October 2018

AbstractAn important channel of cell-to-cell communication is direct contact. The immune synapse is a paradigmatic example of such type of interaction: it forms upon engagement of antigen receptors in lymphocytes by antigen-presenting cells and allows the local exchange of molecules [1]. Although [2], how forces organize and mechanics has been shown to play an important role in this process impact on synapse function is unknown. We found that mechanical forces are spatio-temporally patterned at the immune synapse: global contractile forces are observed at the synapse periphery and local point-like forces are detected at its centre. The global contractile forces result from a pulsatile centripetal actomyosin flow that leads to formation of F-actin protrusions from which the central point like forces emerge. Noticeably, these force-producing actin protrusions constitute the main site of antigen extraction and endocytosis. Accordingly, deletion of the myosin IIA gene leads to impaired B cell responses. The interplay between global and local forces governed by the actomyosin cytoskeleton therefore controls the endocytic function of the immune synapse and might constitute a more general mechanism in the physical regulation of cell-cell interactions.
Characterisation of deubiquitylating enzymes in the cellular response to high-LET ionising radiation and complex DNA damage
Authors: Carter Rachel J. , Nickson Catherine M. , Thompson James M. , Kacperek Andrzej , Hill Mark A. , Parsons Jason L. 
Published: October 2018

AbstractPurposeIonising radiation, particular high linear energy transfer (LET) radiation, can induce complex DNA damage (CDD) where two or more DNA lesions are induced in close proximity which contributes significantly to the cell killing effects. However knowledge of the enzymes and mechanisms involved in co-ordinating the recognition and processing of CDD in cellular DNA are currently lacking.Methods and MaterialsAn siRNA screen of deubiquitylation enzymes was conducted in HeLa cells irradiated with high-LET -particles or protons, versus low-LET protons and x-rays, and cell survival monitored by clonogenic assays. Candidates whose depletion led to decreased cell survival specifically in response to high-LET radiation were validated in both HeLa and oropharyngeal squamous cell carcinoma (UMSCC74A) cells, and the association with CDD repair was confirmed by using an enzyme modified neutral comet assay.ResultsDepletion of USP6 decreased cell survival specifically following high-LET α-particles and protons, but not by low-LET protons or x-rays. USP6 depletion caused cell cycle arrest and a deficiency in CDD repair mediated through instability of poly(ADP-ribose) polymerase-1 (PARP-1). This phenotype was mimicked using the PARP inhibitor olaparib.ConclusionUSP6 controls cell survival in response to high-LET radiation by stabilising PARP-1 protein levels which is essential for CDD repair. We also describe synergy between CDD induced by high-LET protons and PARP inhibition in effective cancer cell killing.