bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modified V-Y Myocutaneous Flap With Vascular Pedicle for the Repair of Maxillofacial Skin Defects
Authors: Lu Ruohuang , Xiao Zhiqiang , Li Zan , Guo Xincheng 
Published: July 2020

Objective:It is challenging to repair postoperative defect caused by skin tumor resection on the maxillofacial, which not only affects appearance but also impairs functions. To better repair skin defect on the maxillofacial, the application value of V-Y vascular myocutaneous flap was introduced in our study.Methods:Between June 2011 and December 2018, 16 patients with maxillofacial skin tumors who received extensive resection were enrolled in our study. The defect on the maxillofacial was repaired by V-Y vascular myocutaneous flap. The follow-up period lasted for 12 to 24 months.Results:All 16 cases of myocutaneous flaps survived with 1 case of partial venous congestion and 1 case of partial distal necrosis. No recurrence occurred during follow-up. The color and texture of myocutaneous flaps like those of the surrounding skin.Conclusion:Featured with better freeness, larger repair range and aesthetic effect of “kite” flaps, V-Y vascular myocutaneous flap can repair the superior border of zygomatic arch pedicled with facial artery and repair 1.5 cm above the superior border of zygomatic arch pedicled with transverse facial artery for elderly patients in Asia.
Short-Term Efficacy and Safety of Different Mechanical Hemodynamic Support Devices for Cardiogenic Shock or High-Risk Pci: a Network Meta-Analysis of Thirty-Seven Trials
Authors: Duan Jingwei , Shi Yuanchao , Luo Gongming , Peng Yu , Duan Baomin , Zhang Zheng 
Published: July 2020

ABSTRACT

Background:
With more advanced mechanical hemodynamic support for patients with cardiogenic shock (CS) or high-risk percutaneous coronary intervention (HS-PCI), the morality rate is now significantly lower than before. While previous studies showed that intra-aortic balloon pumping (IABP) did not reduce the risk of mortality in patients with CS compared to conservative treatment, the efficacy in other mechanical circulatory support (MCS) trials was inconsistent.

Objective:
We conducted this network meta-analysis to assess the short-term efficacy and safety of different intervention measures for patients with CS or who underwent HS-PCI.

Methods:
Four online databases were searched. From the initial 1,550 articles, we screened 38 studies (an extra 14 studies from references) into this analysis, including a total of 11,270 patients from five interventions (pharmacotherapy, IABP, pMCS, ECMO alone, and ECMO+IABP).

Result:
The short-term efficacy was determined by 30-day or in-hospital mortality. ECMO+IABP significantly reduced mortality compared with pMCS and ECMO alone (OR = 1.85, 95% CrI [1.03–3.26]; OR = 1.89, 95% CrI [1.19–3.01], respectively). ECMO+IABP did not show reduced mortality when compared with pharmacotherapy and IABP (OR = 1.73, 95% CrI [0.97–3.82]; OR = 1.67, 95% CrI [0.98–2.89], respectively). The rank probability, however, supported that ECMO+IABP might be a more suitable intervention in improving mortality for patients with CS or who underwent HS-PCI. Regarding bleeding, compared with other invasive intervention measures, IABP showed a trend of reduced bleeding (with pMCS OR = 3.86, 95% CrI [1.53–10.66]; with ECMO alone OR = 3.74, 95% CrI [1.13–13.78]; with ECMO+IABP OR = 4.80, 95% CrI [1.61–18.53]). No difference was found in stroke, myocardial infarction, limb ischemia, and hemolysis among the invasive therapies evaluated.

Conclusion:
Following this analysis, ECMO+IABP might be a more suitable intervention measure in improving short-term mortality for patients with CS and who underwent HS-PCI. However, the result was limited by the lack of sufficient direct comparisons and evidence from randomized controlled trials. Moreover, bleeding and other device-related complications should be considered in clinical applications.
A Novel Staging System for De Novo Metastatic Breast Cancer Refines Prognostic Estimates
Authors: Plichta Jennifer K. , Thomas Samantha M. , Sergesketter Amanda R. , Greenup Rachel A. , Rosenberger Laura H. , Fayanju Oluwadamilola M. , Kimmick Gretchen , Force Jeremy , Hyslop Terry , Hwang E. Shelley 
Published: July 2020

Objective:
We aim to identify prognostic groups within a de novo metastatic cohort, incorporating both anatomic and biologic factors.

Background:
Staging for breast cancer now includes anatomic and biologic factors, although the guidelines for stage IV disease do not account for how these factors may influence outcomes.

Methods:
Adults with de novo metastatic breast cancer were selected from the National Cancer DataBase (2010–2013). Recursive partitioning analysis was used to group patients with similar overall survival (OS) based on clinical T/N stage, tumor grade, ER, PR, HER2, number of metastatic sites, and presence of bone-only metastases. Categories were created by amalgamating homogeneous groups based on 3-year OS rates (stage IVA: >50%, stage IVB: 30%–50%, stage IVC: <30%).

Results:
16,187 patients were identified; median follow-up was 32 months. 65.2% had 1 site of distant metastasis, and 42.9% had bone-only metastases. Recursive partitioning analysis identified the number of metastatic sites (1 vs >1) as the first stratification point, and ER status as the second stratification point for both resulting groups. Additional divisions were made based on HER2 status, PR status, cT stage, tumor grade, and presence of bone-only metastases. After bootstrapping, significant differences in 3-year OS were noted between the 3 groups [stage IVB vs IVA: HR 1.58 (95% confidence interval 1.50–1.67), stage IVC vs IVA: HR 3.54 (95% confidence interval 3.33–3.77)].

Conclusions:
Both anatomic and biologic factors yielded reliable and reproducible prognostic estimates among patients with metastatic disease. These findings support formal stratification of de novo stage IV breast cancer into 3 distinct prognosis groups.
Predictors of retained hemothorax in trauma: Results of an Eastern Association for the Surgery of Trauma multi-institutional trial
Authors: Prakash Priya S. , Moore Sarah A. , Rezende-Neto Joao B. , Trpcic Sandy , Dunn Julie A. , Smoot Brittany , Jenkins Donald H. , Cardenas Tatiana , Mukherjee Kaushik , Farnsworth Joshua , Wild Jeffrey , Young Katelyn , Schroeppel Thomas J. , Coimbra Raul , Lee Jeanne , Skarupa David J. , Sabra Michel J. , Carrick Matthew M. , Moore Forrest O. , Ward Jeanette , Geng Thomas , Lapham David , Piccinini Alice , Inaba Kenji , Dodgion Christopher , Gooley Brian , Schwartz Tim , Shraga Sarrina , Haan James M. , Lightwine Kelly , Burris Jennifer , Agrawal Vaidehi , Seamon Mark J. , Cannon Jeremy W. 
Published: July 2020

BACKGROUND
The natural history of traumatic hemothorax (HTX) remains unclear. We aimed to describe outcomes of HTX following tube thoracostomy drainage and to delineate factors that predict progression to a retained hemothorax (RH). We hypothesized that initial large-volume HTX predicts the development of an RH.

METHODS
We conducted a prospective, observational, multi-institutional study of adult trauma patients diagnosed with an HTX identified on computed tomography (CT) scan with volumes calculated at time of diagnosis. All patients were managed with tube thoracostomy drainage within 24 hours of presentation. Retained hemothorax was defined as blood-density fluid identified on follow-up CT scan or need for additional intervention after initial tube thoracostomy placement for HTX.

RESULTS
A total of 369 patients who presented with an HTX initially managed with tube thoracostomy drainage were enrolled from 17 trauma centers. Retained hemothorax was identified in 106 patients (28.7%). Patients with RH had a larger median (interquartile range) HTX volume on initial CT compared with no RH (191 [48–431] mL vs. 88 [35–245] mL, p = 0.013) and were more likely to be older with a higher burden of thoracic injury. After controlling for significant differences between groups, RH was independently associated with a larger HTX on presentation, with a 15% increase in risk of RH for each additional 100 mL of HTX on initial CT imaging (odds ratio, 1.15; 95% confidence interval, 1.08–1.21; p < 0.001). Patients with an RH also had higher rates of pneumonia and longer hospital length of stay than those with successful initial management. Retained hemothorax was also associated with worse functional outcomes at discharge and first outpatient follow-up.

CONCLUSION
Larger initial HTX volumes are independently associated with RH, and unsuccessful initial management with tube thoracostomy is associated with worse patient outcomes. Future studies should use this experience to assess a range of options for reducing the risk of unsuccessful initial management.

LEVEL OF EVIDENCE
Therapeutic/care management study, level III.
Performance characteristics of a high throughput automated transcription mediated amplification test for SARS-CoV-2 detection
Authors: Pham Jimmykim , Meyer Sarah , Nguyen Catherine , Williams Analee , Hunsicker Melissa , McHardy Ian , Gendlina Inessa , Goldstein D. Yitzchak , Fox Amy S. , Hudson Angela , Darby Paul , Hovey Paul , Morales Jose , Mitchell James , Harrington Karen , Majlessi Mehrdad , Moberly Joshua , Shah Ankur , Worlock Andrew , Walcher Marion , Eaton Barbara , Getman Damon , Clark Craig 
Published: July 2020

ABSTRACTThe COVID-19 pandemic caused by the new SARS-CoV-2 coronavirus has imposed severe challenges on laboratories in their effort to achieve sufficient diagnostic testing capability for identifying infected individuals. In this study we report the analytical and clinical performance characteristics of a new, high-throughput, fully automated nucleic acid amplification test system for the detection of SARS-CoV-2. The assay utilizes target capture, transcription mediated amplification, and acridinium ester-labeled probe chemistry on the automated Panther System to directly amplify and detect two separate target sequences in the ORF1ab region of the SARS-CoV-2 RNA genome. The probit 95% limit of detection of the assay was determined to be 0.004 TCID50/ml using inactivated virus, and 25 c/ml using synthetic in vitro transcript RNA targets. Analytical sensitivity (100% detection) was confirmed to be 83 – 194 c/ml using three commercially available SARS-CoV-2 nucleic acid controls. No cross reactivity or interference was observed with testing six related human coronaviruses, as well as 24 other viral, fungal, and bacterial pathogens, at high titer. Clinical nasopharyngeal swab specimen testing (N=140) showed 100%, 98.7%, and 99.3% positive, negative, and overall agreement, respectively, with a validated reverse transcription PCR NAAT for SARS-CoV-2 RNA. These results provide validation evidence for a sensitive and specific method for pandemic-scale automated molecular diagnostic testing for SARS-CoV-2.
Synthetic promoter based azide biosensor toolkit to advance chemical-biology
Authors: Bandi Chandra Kanth , Skalenko Kyle S. , Agrawal Ayushi , Sivaneri Neelan , Thiry Margaux , Chundawat Shishir P.S. 
Published: July 2020

AbstractReal-time azide or azido-functionalized molecular detection inside living cells using bioorthogonal chemistry-based approaches has been revolutionary to advancing chemical-biology. These methods have enabled diverse applications ranging from understanding the role of cellular glycosylation pathways, identifying diseased cells, and targeting delivery of azido-based therapeutic drugs. However, while classical techniques were applicable only toin-vitrodetection of such functional groups, even recent bioorthogonal based-detection methods require expensive sensing reagents and also cannot selectively identify inorganic azide. Here, we report anin-vivosynthetic promoter based azide biosensor toolkit to selectively detect azide anions. A promiscuous cyanate-specific promoter was engineered to detect azide and rapidly induce expression of green fluorescent protein (GFP) inEscherichia coli. Our synthetic azide operon allows highly-tunable GFP expression, outperforming the classiclac-operon, and also offers an alternative low-cost protein expression system. Finally, we showcase the utility of this toolkit forin-vivobioorthogonal reaction biosensing and glycoengineering based applications.
RefPlantNLR: a comprehensive collection of experimentally validated plant NLRs
Authors: Kourelis Jiorgos , Sakai Toshiyuki , Adachi Hiroaki , Kamoun Sophien 
Published: July 2020

ABSTRACTReference datasets are critical in computational biology. They help define canonical biological features and are essential for benchmarking studies. Here, we describe a comprehensive reference dataset of experimentally validated plant NLR immune receptors. RefPlantNLR consists of 442 NLRs from 31 genera belonging to 11 orders of flowering plants. This reference dataset has several applications. We used RefPlantNLR to determine the canonical features of functionally validated plant NLRs and to benchmark the five most popular NLR annotation tools. This revealed that although NLR annotation tools tend to retrieve the majority of NLRs, they frequently produce domain architectures that are inconsistent with the RefPlantNLR annotation. Guided by this analysis, we developed a new pipeline, NLRtracker, which extracts and annotates NLRs based on the core features found in the RefPlantNLR dataset. The RefPlantNLR dataset should also prove useful for guiding comparative analyses of NLRs across the wide spectrum of plant diversity and identifying under-studied taxa. We hope that the RefPlantNLR resource will contribute to moving the field beyond a uniform view of NLR structure and function.
Several geranylgeranyl diphosphate synthase isoforms supply metabolic substrates for carotenoid biosynthesis in tomato
Authors: Barja M. Victoria , Ezquerro Miguel , Diretto Gianfranco , Florez-Sarasa Igor , Feixes Elisenda , Fiore Alessia , Karlova Rumyana , Fernie Alisdair R. , Beekwilder Jules , Rodriguez-Concepcion Manuel 
Published: July 2020

ABSTRACTGeranylgeranyl diphosphate (GGPP) produced by GGPP synthase (GGPPS) serves as a precursor for many plastidial isoprenoids, including carotenoids. Here we show that five different GGPPS isoforms exist in tomato (Solanum lycopersicum). From these, SlGGPPS1, 2 and 3 (or SlG1-3 in short) produce GGPP in plastids and exhibit similar kinetic parameters. Phytoene synthase (PSY) converts GGPP into phytoene, the first committed intermediate of the carotenoid pathway. Gene expression and co-expression network analyses showed a preferential association of individual GGPPS and PSY isoforms in processes linked to carotenoid biosynthesis such as root mycorrhization, seedling deetiolation and fruit ripening. Co-immunoprecipitation experiments showed that SlG2, but not SlG3, physically interacts with PSY proteins. By contrast, CRISPR-Cas9 mutants defective in SlG3 showed a stronger impact on carotenoid levels and derived metabolic, physiological and developmental phenotypes that those impaired in SlG2. Double mutants with a simultaneous knockout of both genes could not be found. Our work demonstrates that the bulk of GGPP production in tomato chloroplasts and chromoplasts relies on two cooperating GGPPS paralogs, unlike other plant species such asArabidopsis thaliana, rice or pepper, which produce their essential plastidial isoprenoids using a single GGPPS isoform.
Are populations of economically important bonefish and queen conch ‘open’ or ‘closed’ in the northern Caribbean Basin?
Authors: Douglas Marlis R. , Chafin Tyler K. , Claussen Julie E. , Philipp David P. , Douglas Michael E. 
Published: July 2020

AbstractDemographics of co-occurring species can often be diagnosed through population genomic analyses of single nucleotide polymorphisms (SNPs). These data can define population structure, gene flow, and candidate regions in the genome that potentially reflect local adaptations. They can also gauge if populations are demographically ‘open’ or ‘closed’ (i.e., with global or local recruitment). We derived SNPs from double-digest restriction-site associated DNA (ddRAD) to test the demographics of commercially important bonefishAlbula vulpes(N=117) and queen conchLobatus gigas(N=60) from two northeast Caribbean Basin islands (Grand Bahama to the north and Eleuthera to the south). Specifically, we tested the hypothesis that the strong west-to-east current in the Great Bahama Canyon is a vicariant barrier separating the two islands. We conducted Bayesian assignment tests on putatively neutral (A. vulpes=36,206 SNPs;L. gigas=64,863) and highly-differentiated outlier datasets (A. vulpes=123 and 79 SNPs;L. gigas=88 and 51, respectively). For bonefish, results diagnosed asymmetrical gene flow and north-south differentiation, as potentially driven by adult mobility and easterly currents. However, both analyses indicated genetic structure in conch, substantiating the vicariant hypothesis. These results provide templates for future research endeavors with these impacted species. Outlier loci, for example, can potentially place populations of each within a demographic continuum, rather than within a dichotomous ‘open/closed’ framework, as well as diagnose ‘source’ and ‘sink’ populations, as herein. These methodologies can then be applied to co-distributed species with similar but less well understood ecologies so as to evaluate basin-wide trends in connectivity and local adaptation.
Human B cell clonal expansion and convergent antibody responses to SARS-CoV-2
Authors: Nielsen Sandra C. A. , Yang Fan , Jackson Katherine J. L. , Hoh Ramona A. , Röltgen Katharina , Stevens Bryan , Lee Ji-Yeun , Rustagi Arjun , Rogers Angela J. , Powell Abigail E. , Najeeb Javaria , Otrelo-Cardoso Ana R. , Yost Kathryn E. , Daniel Bence , Chang Howard Y. , Satpathy Ansuman T. , Jardetzky Theodore S. , Kim Peter S. , Wang Taia T. , Pinsky Benjamin A. , Blish Catherine A. , Boyd Scott D. 
Published: July 2020

SUMMARYDuring virus infection B cells are critical for the production of antibodies and protective immunity. Here we show that the human B cell compartment in patients with diagnostically confirmed SARS-CoV-2 and clinical COVID-19 is rapidly altered with the early recruitment of B cells expressing a limited subset of IGHV genes, progressing to a highly polyclonal response of B cells with broader IGHV gene usage and extensive class switching to IgG and IgA subclasses with limited somatic hypermutation in the initial weeks of infection. We identify extensive convergence of antibody sequences across SARS-CoV-2 patients, highlighting stereotyped naïve responses to this virus. Notably, sequence-based detection in COVID-19 patients of convergent B cell clonotypes previously reported in SARS-CoV infection predicts the presence of SARS-CoV/SARS-CoV-2 cross-reactive antibody titers specific for the receptor-binding domain. These findings offer molecular insights into shared features of human B cell responses to SARS-CoV-2 and other zoonotic spillover coronaviruses.
Astrocytic modulation of information processing by layer 5 pyramidal neurons of the mouse visual cortex
Authors: Ryczko Dimitri , Hanini-Daoud Maroua , Condamine Steven , Bréant Benjamin J. B. , Fougère Maxime , Araya Roberto , Kolta Arlette 
Published: July 2020

AbstractThe most complex cerebral functions are performed by the cortex which most important output is carried out by its layer 5 pyramidal neurons. Their firing reflects integration of sensory and contextual information that they receive. There is evidence that astrocytes influence cortical neurons firing through the release of gliotransmitters such as ATP, glutamate or GABA. These effects were described at the network and at the synaptic levels, but it is still unclear how astrocytes influence neurons input-output transfer function at the cellular level. Here, we used optogenetic tools coupled with electrophysiological, imaging and anatomical approaches to test whether and how astrocytic activation affected processing and integration of distal inputs to layer 5 pyramidal neurons (L5PN). We show that optogenetic activation of astrocytes near L5PN cell body prolonged firing induced by distal inputs to L5PN and potentiated their ability to trigger spikes. The observed astrocytic effects on L5PN firing involved glutamatergic transmission to some extent but relied on release of S100β, an astrocytic Ca2+-binding protein that decreases extracellular Ca2+once released. This astrocyte-evoked decrease of extracellular Ca2+elicited firing mediated by activation of Nav1.6 channels. Our findings suggest that astrocytes contribute to the cortical fundamental computational operations by controlling the extracellular ionic environment.KeyPointsSummaryIntegration of inputs along the dendritic tree of layer 5 pyramidal neurons is an essential operation as these cells represent the most important output carrier of the cerebral cortex. However, the contribution of astrocytes, a type of glial cell to these operations is poorly documented.Here we found that optogenetic activation of astrocytes in the vicinity of layer 5 in the mouse primary visual cortex induce spiking in local pyramidal neurons through Nav1.6 ion channels and prolongs the responses elicited in these neurons by stimulation of their distal inputs in cortical layer 1.This effect partially involved glutamatergic signalling but relied mostly on the astrocytic calcium-binding protein S100β, which regulates the concentration of calcium in the extracellular space around neurons.These findings show that astrocytes contribute to the fundamental computational operations of the cortex by acting on the ionic environment of neurons.
Sensitive and reproducible determination of clinical HDL proteotypes
Authors: Goetze Sandra , Frey Kathrin , Rohrer Lucia , Radosavljevic Silvija , Krützfeldt Jan , Landmesser Ulf , Bueter Marco , Pedrioli Patrick G. A. , von Eckardstein Arnold , Wollscheid Bernd 
Published: July 2020

AbstractBackgroundHigh-density lipoprotein (HDL) is a heterogenous mixture of blood-circulating multimolecular particles containing many different proteins, lipids, and RNAs. Recent advancements in mass spectrometry-based proteotype analysis strategies enable the sensitive and reproducible quantification of proteins across large patient cohorts.MethodsHDL particles were isolated from plasma of more than 300 healthy individuals or patients with a multiplicity of physiological HDL states. From these, peptides were extracted and HDL proteome spectral libraries were generated. This is a prerequisite for using data-independent acquisition (DIA) strategies to analyze HDL particles from clinical cohorts using mass spectrometry.ResultsThe resulting HDL proteome spectral libraries consist of 296 protein groups and 341 peptidoforms of potential biological significance identified with high confidence. We used the HDL proteome libraries to evaluate HDL proteotype differences in between healthy individuals and patients suffering from diabetes mellitus type 2 (T2DM) and/or coronary heart disease (CHD). Bioinformatic interrogation of the data revealed significant quantitative differences in the HDL proteotypes including a significant depletion of phosphatidylinositol-glycan-specific phospholipase D (PHLD) from disease-derived HDL particles.ConclusionThe DIA-based HDL proteotyping strategy enabled sensitive and reproducible digitization of HDL proteotypes derived from patient cohorts and provides new insights into the composition of HDL particles as a rational basis to decode structure-function-disease relationships of HDL.List of human genes and protein names discussed in the paper- APOA1 (Apolipoprotein A-I)- APOA2 (Apolipoprotein A-II)- APOE (Apolipoprotein E)- APOC3 (Apolipoprotein C3)- CLUS (Clusterin)- PHLD (Phosphatidylinositol-glycan-specific phospholipase D)- PON1 (Serum paraoxonase/arylesterase 1)- PON3 (Serum paraoxonase/lactonase 3)- PSPB (Pulmonary surfactant-associated protein B)- RAB1B (Ras-related protein Rab-1B)- RAB6A (Ras-related protein Rab-6A)- RB11A/B (Ras-related protein Rab-11A/B)- RP1BL (Ras-related protein Rap-1b-like protein)- RAB10 (Ras-related protein Rab-10)- SAA1 (Serum amyloid A-1 protein)- SAA2 (Serum amyloid A-2 protein)- SAA4 (Serum amyloid A-4 protein)- SCRB1 (Scavenger receptor class B member 1)