bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three Simultaneous Free Flaps to Reconstruct a Complex Frozen Neck and a Large Hypopharyngeal Fistula
Authors: Fodor Lucian , Chirila Magdalena , Sobec Raluca , Sita Laura , Fodor Marius 
Published: January 2019

Abstract
Frozen neck and hypopharyngeal fistula are sometimes present after tumor ablation of the larynx, multiple local surgeries with scar tissue, and radiotherapy and chemotherapy. This multiorgan involvement requires 1 or even 2 flaps. We present a 63-year-old heavy smoker with frozen neck tissue and simultaneous large hypopharyngeal fistula and neck defect. After careful preoperative planning, he was successfully treated with 3 simultaneous free flaps: 2 anterolateral thigh flap (ALT) and 1 lateral arm flap (LAF). One ALT was used as a patch to restore the hypopharynx continuity. A second ALT was used to cover the anterior neck defect and the LAF flap was used to reconstruct the submandibular area. The flaps survived and the patient had a 5 mm proximal fistula which was sutured, and he was able to eat per mouth. By combining multiple free flaps, we were able to restore the function of the hypopharynx and to cover the esthetic units of the neck by avoiding the “turkey neck” appearance.
Secondary Reconstruction of Calvarial Defects by Using Free Flap: Report of Consecutive Cases and Analysis of Strategy
Authors: Heron Antoine , Michot Audrey , Menez Tiphaine , Jecko Vincent , Penchet Guillaume , Casoli Vincent 
Published: January 2019

Introduction:
Multiplication of incisions and/or radiotherapy on the scalp, lead to skin necrosis and chronic osteitis. In this situation, reconstructive surgery can be useful to cover complex lack of tissue.

Materials and Methods:
The 5 patients were treated with the neurosurgery department of our hospital. The procedure included debridement of the infected calvarian bone and tissues and coverage by free antebrachial flap. A 2 stages skin graft, using a dermal regeneration template, or direct closure was used for the donor site. Evaluation of flap quality and donor site morbidity was done during hospitalization and 3 months after the procedure.

Results:
The procedure was achieved on 5 patients. All the patients were healed 3 months after surgery. For 1 patient, a second procedure was done in emergency for anastomosis revision. There was non-complication concerning the donor site. All the patients healed with a good coverage.

Conclusion:
Treatment of calvarian bone necrosis needs a very good and reliable coverage, such as free flap can provide. In our opinion, the antebrachial free flap is an interesting option, despite the fact that it is still underused for scalp coverage.
Preferred Experience of Modifications to Emergency Surgical Treatment for Total Scalp Avulsion With Halo-Vest Head Ring and Quick Hair Removing
Authors: Lin Jian , Zhou Feng , Wu Li-Zhi , Li Yu-fei , Li Qing-feng , Zhang Ying-fan , Liu Cai-yue 
Published: January 2019

Background:
Total scalp avulsion is a fairly rear but severe soft tissue injury. Even with microsurgical replantation, the survival rate is still low. In this study, the authors incorporated 2 main modifications (Halo-Vest head ring and quick hair removing) and assessed the surgical outcomes versus those of traditional replantation.

Methods: :
Eighteen patients were included in the study who suffered from total scalp avulsion. After consideration of the outcomes from the first 7 patients, the authors modified our surgical procedures and introduced the use of Halo-Vest head ring and quick hair removing in the treatments for the rest 11 patients. The surgical outcomes with both approaches were observed and compared, including the operation time and incidence of scalp necrosis.

Results: :
The mean debridement time was 3.5 hours in traditional treatment versus 1.68 hours in modified treatment. The mean operative time was 11.14 hours in traditional treatment versus 8.05 hours in modified treatment. After the replantation, in those 7 patients without modifications, there was 1 total scalp necrosis and 6 partial scalp necrosis. In those 11 patients with modifications, there was 1 total scalp necrosis and 1 suffered a partial scalp necrosis, while the scalp survived well in other 9 patients. Classical cases with modified or traditional methods were reported respectively.

Conclusion:
The application of Halo-Vest head ring and quick hair removing provides a reliable method to treat total scalp avulsion. It is safe, technically easy and worth being widely used in the clinical application.
A Different Stabilization Technique of Autogenous Cartilage Grafts in Saddle Nose Deformity: Prevention Warping and Resorption
Authors: Gundeslioglu A. Ozlem , Yildirim Mehmet Emin Cem , Yarar Serhat , Uyar Ilker , Ismayilzade Majid 
Published: January 2019

Background:
Saddle nose deformity (SND) is a collapse of the cartilage and bone structures forming the dorsal projection of the nose. After the use of autologous cartilage in the treatment of SND, resorption and warping continue to be a problem.

Methods:
This study presents results from 11 patients with SND types III and IV from 2005 to 2017 treated with autologous cartilage fixed with microplates and microscrews. The patients were monitored for at least 1 year. Resorption and warping were measured using postoperative photographs of the patients in the 3rd and 12th months after treatment.

Results:
No signs of resorption or warping were noted in the patients.

Conclusions:
Our findings indicate autologous cartilage use with microplates and microscrews is a viable, long-term treatment option for patients with SND types III and IV.
Outcomes of the Learning Curve in Our First 100 Consecutive Laparoscopic Gastrectomies
Authors: Priego Pablo , Cuadrado Marta , Ballestero Araceli , Galindo Julio , Carda Pedro , Lobo Eduardo 
Published: January 2019

Introduction:
Laparoscopic surgery has been increasingly used for treatment of gastric cancer. However, standardization of this minimally invasive approach has not been reached yet because of its technical difficulties and the concern about oncological safety. The aim of the study was to analyze the outcomes of our learning curve in this complex surgical technique.

Material and Methods:
The first consecutive 100 cases of laparoscopic gastrectomy performed at our Hospital from November 2008 to February 2018 were enrolled. Patients were divided into 2 groups on the basis of the period during which they were operated upon. The training phase was considered between 2008 and 2014 (46 cases) and the more developed phase (MDP) between 2015 and 2018 (54 cases). Conversion, lymphadenectomy and retrieved lymph nodes, hospital length of stay, mean operative time, complications, reintervention, and mortality rates were compared between the 2 phases of learning curve.

Results:
The number of retrieved lymph nodes was higher in the MDP (17±8.6 vs. 23.3±10.4; P=0.004). Furthermore, we have also found less complications (47.8% vs. 27.8%; P=0.038), a decreased reintervention rate (15.2% vs. 1.85%; P=0.023), and overall mortality (8.7% vs. 0%; P=0.003) in the MDP. There were no significant differences in conversion rate, mean operative time, and hospital length of stay between phases.

Conclusions:
Although we consider that our learning curve is not yet completed, as the average of monitored parameters have not reached a steady state, the improvement on surgical parameters and postoperative course in the last 2 years have showed that our results are close to the best results published in the literature.
Single Biaxillary Tunneling for Working Space Creation in Bilateral Axillo-Breast Approach (BABA) Thyroidectomy
Authors: Tsai Chung-Yu , Liu Shiuh-Inn , Chen I-Shu , Liang Tsung-Jung 
Published: January 2019

Background:
Endoscopic thyroidectomy using the bilateral axillo-breast approach (BABA) achieves excellent cosmetic results. However, concerns have been raised about the extensive dissection and violation of the breast during working space preparation.

Materials and Methods:
We developed a “single biaxillary tunneling” technique for working space creation in BABA thyroidectomy; this technique was applied in 30 cases.

Results:
Skin bruise was hardly visible, and only minor and small bruises were observed. The whole process of working space creation typically finished within 20 to 30 minutes.

Conclusions:
Limited blunt dissection by a single stroke of biaxillary tunneling is a simple method, which significantly reduces ecchymosis formation and is time-efficient. This method can be used in routine practice and is feasible for beginner surgeons.
The roles of histidine kinases in sensing host plant and cell–cell communication signal in a phytopathogenic bacterium
Authors: Wang Fang-Fang , Qian Wei 
Published: January 2019

It has long been known that phytopathogenic bacteria react to plant-specific stimuli or environmental factors. However, how bacterial cells sense these environmental cues remains incompletely studied. Recently, three kinds of histidine kinases (HKs) were identified as receptors to perceive plant-associated or quorum-sensing signals. Among these kinases, HK VgrS detects iron depletion by binding to ferric iron via an ExxE motif, RpfC binds diffusible signal factor (DSF) by its N-terminal peptide and activates its autokinase activity through relaxation of autoinhibition, and PcrK specifically senses plant hormone–cytokinin and elicits bacterial responses to oxidative stress. These HKs are critical sensors that regulate the virulence of a Gram-negative bacterium,Xanthomonas campestrispv.campestris. Research progress on the signal perception of phytopathogenic bacterial HKs suggests that inter-kingdom signalling between host plants and pathogens controls pathogenesis and can be used as a potential molecular target to protect plants from bacterial diseases.This article is part of the theme issue ‘Biotic signalling sheds light on smart pest management’.
The generation of a comprehensive spectral library for the analysis of the guinea pig proteome by SWATH-MS
Authors: Palmowski Pawel , Watson Rachael , Nicholas Europe-Finner G. , Karolczak-Bayatti Magdalena , Porter Andrew , Treumann Achim , Taggart Michael J 
Published: January 2019

AbstractAdvances in liquid chromatography-mass spectrometry have facilitated the incorporation of proteomic studies to many biology experimental workflows. In particular, the introduction of Data-Independent Acquisition platforms, such as SWATH, offers several advantages for label-free quantitative assessment of complex proteomes over Data-Dependent Acquisition (DDA) approaches. However, SWATH data interpretation requires spectral libraries as a reference resource. This is often not available for many species of experimental models. The guinea pig (cavia porcellus) is an excellent experimental model for translation to many aspects of human physiology and disease yet there is limited experimental information regarding its proteome. In an effort to overcome this knowledge gap, we generated a comprehensive spectral library of the guinea pig proteome. Homogenates and tryptic peptide digests were prepared from 16 tissues and subjected to >200 DDA runs. Analysis of >250,000 peptide-spectrum matches resulted in the construction of a library of 73594 peptides corresponding to 7667 proteins. This spectral library furnishes the research community with the first comprehensive guinea pig proteomic resource that will facilitate future molecular-phenotypic studies using (re-engaging) the guinea pig as an experimental model of relevance to human biology. The guinea pig spectral library and MS data are freely accessible in the MassIVE repository (MSV000083199).
ScaR - A tool for sensitive detection of known fusion transcripts: Establishing prevalence of fusions in testicular germ cell tumors
Authors: Zhao Sen , Hoff Andreas M. , Skotheim Rolf I. 
Published: January 2019

AbstractBioinformatics tools for fusion transcript detection from RNA-sequencing data are in general developed for identification of novel fusions, which demands a high number of supporting reads and strict filters to avoid false discoveries. As our knowledge of bona-fide fusion genes becomes more saturated, there is a need to establish their prevalence with high sensitivity. We present ScaR, a tool that uses a scaffold realignment approach for sensitive fusion detection in RNA-seq data. ScaR detects a set of 50 synthetic fusion transcripts from simulated data at a higher sensitivity compared to established fusion finders. Applied to fusion transcripts potentially involved in testicular germ cell tumors (TGCTs), ScaR detects the fusions RCC1-ABHD12B and CLEC6A-CLEC4D in 9% and 28% of 150 TGCTs, respectively. The fusions were not detected in any of 198 normal testis tissues. Thus, we demonstrate high prevalence of RCC1-ABHD12B and CLEC6A-CLEC4D in TGCTs, and their cancer specific features. Further, we find that RCC1-ABHD12B and CLEC6A-CLEC4D are predominantly expressed in the seminoma and embryonal carcinoma histological subtypes of TGCTs, respectively. In conclusion, ScaR is useful for establishing the frequency of known fusion transcripts in larger data sets and detecting clinically relevant fusion transcripts with high sensitivity.Availabilityhttps://github.com/senzhaocode/ScaR
Longitudinal Intravital Imaging of Biosensor-labeled In Situ Islet Beta Cells
Authors: Reissaus Christopher A. , Twigg Ashley N. , Orr Kara S. , Conteh Abass M. , Martinez Michelle M. , Kamocka Malgorzata M. , Day Richard N. , Tersey Sarah A. , Dunn Kenneth W. , Mirmira Raghavendra G. , Linnemann Amelia K. 
Published: January 2019

AbstractImpaired function and apoptosis of insulin-secreting islet β-cells is central to disease progression in both type 1 and type 2 diabetes. Oxidative damage resulting from excess reactive oxygen species (ROS) is a central factor in β-cell dysfunction and death, but the dynamic nature of ROS accumulation and its depletion pose a problem for mechanistic studies in vivo. Biosensors, including the redox-sensitive GFP (roGFPs), coupled with intravital microscopy provide a sensitive and dynamic solution to this problem. Here, we utilize a virally-delivered roGFP2-containing human glutaredoxin-1 (Grx1-roGFP2) to selectively monitor β-cell ROS dynamics in vivo in response to toxic glucose analogs. We paired viral biosensor delivery with implanted abdominal imaging windows over the pancreas, thus allowing longitudinal measurements of β-cell ROS and islet area during and after streptozotocin (STZ) exposure. The studies presented here represent a robust experimental platform that could be readily adapted to various transgenic or physiological mouse models in conjunction with any number of available biosensors, and thus opens a vast realm of potential for discovery in islet biology in vivo.
Genetic dysregulation of gene expression and splicing during a ten-year period of human aging
Authors: Balliu Brunilda , Durrant Matthew , de Goede Olivia , Abell Nathan , Li Xin , Liu Boxiang , Gloudemans Michael J , Cook Naomi L. , Smith Kevin S. , Pala Mauro , Cucca Francesco , Schlessinger David , Jaiswal Siddhartha , Sabatti Chiara , Lind Lars , Ingelsson Erik , Montgomery Stephen B 
Published: January 2019

SummaryMolecular and cellular changes are intrinsic to aging and age-related diseases. Prior cross-sectional studies have investigated the combined effects of age and genetics on gene expression and alternative splicing; however, there has been no long-term, longitudinal characterization of these molecular changes, especially in older age. We performed RNA sequencing in whole-blood from the same individuals from the PIVUS study at ages 70 and 80 to quantify how gene expression, alternative splicing, and their genetic regulation are altered during this 10-year period of advanced aging. We observe that individuals are more similar to their own expression profiles later in life than profiles of other individuals their own age; 93% of samples cluster with their own measurement at another age, and there is a strong correlation of genetic effects on expression between the two ages (median ρG = 0.96). Despite this, we identify 1,291 and 294 genes differentially expressed and alternatively spliced with age, as well as 529 genes with outlying individual trajectories of aging. Further, 7.8% and 9.6% of tested genes show a reduction in genetic associations with expression and alternative splicing in older age, with impacted genes enriched in DNA repair pathways. Together these findings indicate that, although gene expression and alternative splicing and their genetic regulation are mostly stable late in life, a small subset of genes is dynamic and is characterized by changes in expression and splicing and a reduction in genetic regulation.
Orientation-selective adaptation improves perceptual grouping
Authors: Pinchuk-Yacobi Noga , Sagi Dov 
Published: January 2019

AbstractThe role of visual pattern adaptation, and learning, in spatial integration was investigated. Observers performed a perpetual grouping task in which they reported whether a grid of identical tilted bars (45° counterclockwise from the vertical) is perceived as rows or columns. Performance was measured multiple times during a testing session to determine the effects of repeated exposure to the stimuli. To test for possible effects of learning on the within-session dynamics, observers repeated the experiment on five different days. We found that repeated performance produced rapid within-day improvements, which were largely transient, and were not retained when tested on subsequent days. In addition, exposure to stimuli with equal orientation contributed to the within-session improvement, whereas stimuli having an orientation differing by 45° from the orientation used in the grouping task diminished the improvement previously obtained in the same session. Practice with the task, over days, resulted in faster improvements. The transient nature of these exposure-driven improvements and their susceptibility to interference by stimuli designed to reduce adaptation suggests that adaptation was the main cause for the observed improvements. Finally, to investigate the effects of adaptation on internal noise and on spatial integration, we employed an external noise paradigm, showing that internal noise reduction resulted from adaptation. Internal noise was reduced only when spatial integration was effective, suggesting that adaptation improved perception of global stimulus properties. Overall, our results suggest that the grouping task benefits from an adaptation process that rapidly adjusts the visual system to the statistics of the visual stimuli. We suggest that this effect is achieved through spatial decorrelation of neural responses. With practice, the visual system is able to adjust faster to changes in the statistics of the environment.
Pan-cancer genomic amplifications underlie a Wnt hyperactivation phenotype associated with stem cell-like features leading to poor prognosis
Authors: Chang Wai Hoong , Lai Alvina G. 
Published: January 2019

AbstractCancer stem cells pose significant obstacles to curative treatment contributing to tumor relapse and poor prognosis. They share many signaling pathways with normal stem cells that control cell proliferation, self-renewal and cell fate determination. One of these pathways known as Wnt is frequently implicated in carcinogenesis where Wnt hyperactivation is seen in cancer stem cells. Yet, the role of conserved genomic alterations in Wnt genes driving tumor progression across multiple cancer types remains to be elucidated. In an integrated pan-cancer study involving 21 cancers and 18,484 patients, we identified a core Wnt signature of 16 genes that showed high frequency of somatic amplifications linked to increased transcript expression. The signature successfully predicted overall survival rates in six cancer cohorts (n=3,050): bladder (P=0.011), colon (P=0.013), head and neck (P=0.026), pan-kidney (P<0.0001), clear cell renal cell (P<0.0001) and stomach (P=0.032). Receiver operating characteristic analyses revealed that the performance of the 16-Wnt-gene signature was superior to tumor staging benchmarks in all six cohorts and multivariate Cox regression analyses confirmed that the signature was an independent predictor of overall survival. In bladder and renal cancer, high risk patients as predicted by the Wnt signature had more hypoxic tumors and a combined model uniting tumor hypoxia and Wnt hyperactivation resulted in further increased death risks. Patients with hyperactive Wnt signaling had molecular features associated with stemness and epithelial-to-mesenchymal transition. Our study confirmed that genomic amplification underpinning pan-cancer Wnt hyperactivation and transcriptional changes associated with molecular footprints of cancer stem cells lead to increased death risks.List of AbbreviationsTCGAThe Cancer Genome AtlasKEGGKyoto Encyclopedia of Genes and GenomesGOGene OntologyROCReceiver operating characteristicAUCArea under the curveHRHazard ratioTNMTumor, node and metastasisHIFHypoxia inducible factorTFTranscription factorEMTEpithelial-to-mesenchymal transition
Optical determination of absolute membrane potential
Authors: Lazzari-Dean Julia R. , Gest Anneliese M.M. , Miller Evan W. 
Published: January 2019

AbstractAll cells maintain ionic gradients across their plasma membranes, producing transmembrane potentials (Vmem). Mounting evidence suggests a relationship between resting Vmem and the physiology of non-excitable cells with implications in diverse areas, including cancer, cellular differentiation, and body patterning. A lack of non-invasive methods to record absolute Vmem limits our understanding of this fundamental signal. To address this need, we developed a fluorescence lifetime-based approach (VF-FLIM) to visualize and optically quantify Vmem with single-cell resolution. Using VF-FLIM, we report Vmem distributions over thousands of cells, a 100-fold improvement relative to electrophysiological approaches. In human carcinoma cells, we visualize the voltage response to epidermal growth factor stimulation, stably recording a 10-15 mV hyperpolarization over minutes. Using pharmacological inhibitors, we identify the source of the hyperpolarization as the Ca2+-activated K+channel Kca3.1. The ability to optically quantify absolute Vmem with cellular resolution will allow a re-examination of its roles as a cellular signal.