bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive quantification of the modified proteome reveals oxidative heart damage in mitochondrial heteroplasmy
Authors: Bagwan Navratan , Bonzon-Kulichenko Elena , Calvo Enrique , Lechuga-Vieco Ana Victoria , Michalakopoulos Spiros , Trevisan-Herraz Marco , Ezkurdia Iakes , Rodríguez José Manuel , Magni Ricardo , Latorre-Pellicer Ana , Enríquez José Antonio , Vázquez Jesús 
Published: April 2018

SUMMARYPost-translational modifications hugely increase the functional diversity of proteomes. Recent algorithms based on ultratolerant database searching are forging a path to unbiased analysis of peptide modifications by shotgun mass spectrometry. However, these approaches identify only half of the modified forms potentially detectable and do not map the modified residue. Moreover, tools for the quantitative analysis of peptide modifications are currently lacking. Here, we present a suite of algorithms that allow comprehensive identification of detectable modifications, pinpoint the modified residues, and enable their quantitative analysis through an integrated statistical model. These developments were used to characterize the impact of mitochondrial heteroplasmy on the proteome and on the modified peptidome in several tissues from 12-week old mice. Our results reveal that heteroplasmy mainly affects cardiac tissue, inducing oxidative damage to proteins of the oxidative phosphorylation system, and provide a molecular mechanism that explains the structural and functional alterations produced in heart mitochondria.HighlightsIdentifies all protein modifications detectable by mass spectrometryLocates the modified site with 85% accuracyIntegrates quantitative analysis of the proteome and the modified peptidomeReveals that mtDNA heteroplasmy causes oxidative damage in heart OXPHOS proteins
The structural basis for cancer drug interactions with the catalytic and allosteric sites of SAMHD1
Authors: Knecht Kirsten M. , Buzovetsky Olga , Schneider Constanze , Thomas Dominique , Srikanth Vishok , Tofoleanu Florentina , Reiss Krystle , Ferreirós Nerea , Geisslinger Gerd , Batista Victor S. , Ji Xiaoyun , Cinatl Jindrich , Keppler Oliver T. , Xiong Yong 
Published: April 2018

AbstractSAMHD1 is a deoxynucleoside triphosphate triphosphohydrolase (dNTPase) that depletes cellular dNTPs in non-cycling cells to promote genome stability and to inhibit retroviral and herpes viral replication. In addition to being substrates, cellular nucleotides also allosterically regulate SAMHD1 activity. Recently, it was shown that high expression levels of SAMHD1 are also correlated with significantly worse patient responses to nucleotide analogue drugs important for treating a variety of cancers, including Acute Myeloid Leukemia (AML). In this study, we used biochemical, structural, and cellular methods to examine the interactions of various cancer drugs with SAMHD1. We found that both the catalytic and the allosteric sites of SAMHD1 are sensitive to sugar modifications of the nucleotide analogs, with the allosteric site being significantly more restrictive. We crystallized cladribine-TP, clofarabine-TP, fludarabine-TP, vidarabine-TP, cytarabine-TP, and gemcitabine-TP in the catalytic pocket of SAMHD1. We find that all of these drugs are substrates of SAMHD1 and that the efficacy of most of these drugs is affected by SAMHD1 activity. Of the nucleotide analogues tested, only cladribine-TP with a deoxyribose sugar efficiently induced the catalytically active SAMHD1 tetramer. Together, these results establish a detailed framework for understanding the substrate specificity and allosteric activation of SAMHD1 with regards to nucleotide analogues, which can be used to improve current cancer and antiviral therapies.SignificanceNucleoside analogue drugs are widely used to treat a variety of cancers and viral infections. With an essential role in regulating the nucleotide pool in the cell by degrading cellular nucleotides, SAMHD1 has the potential to decrease the cellular concentration of frequently prescribed nucleotide analogues and thereby decrease their clinical efficacy in cancer therapy. To improve future nucleotide analogue treatments, it is important to understand SAMHD1 interactions with these drugs. Our work thoroughly examines the extent to which nucleotide analogues interact with the catalytic and allosteric sites of SAMHD1. This work contributes to the assessment of SAMHD1 as a potential therapeutic target for cancer therapy and the future design of SAMHD1 modulators that might improve the efficacy of existing therapies.
Transcranial direct current stimulation alters functional network structure in humans
Authors: Ruttorf M. , Kristensen S. , Schad L.R. , Almeida J. 
Published: April 2018

AbstractTranscranial direct current stimulation (tDCS) is routinely used in basic and clinical research, but its efficacy has been challenged on a methodological and statistical basis recently. The arguments against tDCS derive from insufficient understanding of how this technique interacts with brain processes physiologically. Because of its potential as a central tool in neuroscience, it is important to clarify whether and how tDCS affects neuronal activity. Here, we investigate influences of offline tDCS on network architecture measured by functional magnetic resonance imaging. Our results reveal a tDCS-induced reorganisation of a functionally-defined network that is dependent on whether we are exciting or inhibiting a node within this network, confirming in a functioning brain, and in a bias free and independent fashion that tDCS influences neuronal activity. Moreover, our results suggest that network-specific connectivity has an important role in defining the effects of tDCS and the relationship between brain states and behaviour.
Translocation of structured biomolecule through a vibrating nanopore
Authors: Shahzad M. A. 
Published: April 2018

ABSTRACTWe study the effect of fluctuating environment in protein transport dynamics. In particular, we investigate the translocation of a structured biomolecule (protein) across a temporally modulated nano-pore. We allow the radius of the cylindrical pore to oscillate harmonically with certain frequency and amplitude about an average radius. The protein is imported inside the pore whose dynamics is influences by the fluctuating nature of the pore. We investigate the dynamic and thermodynamical properties of the translocation process by revealing the statistics of translocation time as a function of the pulling inward force acting along the axis of the pore, and the frequency of the time dependent radius of the channel. We also examine the distribution of translocation time in the intermediate frequency regime. We observe that the shaking mechanism of pore leads to accelerate the translocation process as compared to the static channel that has a radius equal to the mean radius of oscillating pore. Moreover, the translocation time shows a global maximum as a function of frequency of the oscillating radius, hence revealing a resonant activation phenomenon in the dynamics of protein translocation.
Improving Accuracy of Nuclei Segmentation by Reducing Histological Image Variability BMI 260 - Spring 2017
Authors: Roohani Yusuf , Kiss Eric 
Published: April 2018

AbstractCancer is the second leading cause of death in United States. Early diagnosis of this disease is essential for many types of treatment. Cancer is most accurately observed by pathologists using tissue biopsy. In the past, evaluation of tissue samples was done manually, but to improve efficiency and ensure consistent quality, there has been a push to evaluate these algorithmically. One important task in histological analysis is the segmentation and evaluation of nuclei. Nuclear morphology is important to understand the grade and progression of cancer. Convolutional neural networks (CNN) were used to segment train models for nuclei segmentation. Stains are used to highlight cellular features. However, there is significant variability in imaging of stained slides due to differences in stain, slide preparation and slide storage. This make automated methods challenging to implement across different datasets. This paper evaluates four stain normalization methods to reduce the variability between slides. Nuclear segmentation accuracy was evaluated for each normalized method. Baseline segmentation accuracy was improved by more than 50% of its base value as measured by the AUC and Recall. We believe this is the first study to look at the impact of four stain normalization approaches (histogram equalization, Reinhart, Macenko, Khan) on segmentation accuracy.
Firms in Transition: A Review of the Venture Capital, IPO, and M&A Literature
Authors: Cormier Denis , Coulombe Daniel , Gomez Gutierrez Luania , Mcconomy Bruce J. 
Published: April 2018

AbstractA key area of research focuses on firms in transition, particularly those going public via initial public offerings, those growing via venture capital infusions, and acquirers and targets in merger and acquisition deals. In this article, we provide a review of research regarding firms in transition, with a primary focus on accounting‐related research. As part of our review we include key contributions both in the Canadian context and internationally, and discuss areas to be considered for future research.
Successive short‐selling ban lifts and gradual price efficiency: evidence from China
Authors: Xiong Xiong , Gao Ya , Feng Xu 
Published: April 2018

AbstractUsing a database of five successive short‐selling ban lifts in the Chinese stock market, we find that the stock price efficiency gradually changes. Specifically, the price efficiency of stocks that can be shorted later improves more than the price efficiency of stocks that can be shorted earlier. Two hypotheses are tested to explain the gradual changed price efficiency: the private information hypothesis and the analysis capability hypothesis. We further show that short selling is more associated with private information than with public information and that the relationship grows stronger after each ban lift, which supports the private information hypothesis.
Media sentiment, institutional investors and probability of stock price crash: evidence from Chinese stock markets
Authors: Zhu Yanjian , Wu Zhaoying , Zhang Hua , Yu Jing 
Published: April 2018

AbstractUsing a large sample of firm‐level media reports data, we examine whether and how media reports affect the probability of stock price crash in China. We find that positive media reports reduce the probability of stock price crash, while the relationship between negative reports and the probability of price crash is U‐shaped. The probability of stock price crash is more sensitive to the media reports in SOEs and large firms. Furthermore, we find evidence to support the media management behaviour of institutional investors. Such behaviour significantly changes the probability of stock price crash. However, we only observe the media management behaviour of institutional investors in firms held by non‐block institutions, in support of the notion that transient investors behave opportunistically and reap short‐term investment gains through media management.
Versatile facial osteotomies
Authors: Lim L , Heggie AA 
Published: April 2018

AbstractFacial Osteotomy techniques have evolved enormously over the past 20 years providing significant and often life‐changing benefits to our dental patients with skeletal malocclusions. Advancements in technology and refined surgical techniques have resulted in improvements in surgical outcomes, a reduction in post‐operative complications and a quicker recovery for today's patients undergoing orthognathic surgery. This paper aims to an update on the contemporary approach to the correction of skeletal malocclusions with facial osteotomies.
Implant based rehabilitation options for the atrophic edentulous jaw
Authors: Spencer KR 
Published: April 2018

AbstractThe atrophic and edentulous jaw can pose a number of challenges for the implant clinician. In simple terms, the amount of bone that remains is insufficient for the conventional placement of a dental implant. A variety of treatment strategies can be employed to enable implants to be placed despite the paucity of bone stock in either the mandible or the maxilla. Conceptually these strategies follow one of two pathways: either augmentation of the bone, or the novel utilization of the remaining bone. This article will discuss patient assessment, treatment planning, and the range of contemporary options available to enable fixed implant based rehabilitation of each jaw. “The edentulous patient is an amputee, an oral invalid, to whom we should pay total respect and rehabilitation ambitions” (P‐I Branemark, September 2005).
Case series: Salvia divinorum as a potential addictive hallucinogen
Authors: El‐Khoury Joseph , Baroud Evelyne 
Published: April 2018

Background and ObjectiveRecreational use of salvia divinorum (salvia), a potent, naturally occurring hallucinogen, is on the rise internationally. Despite the paucity of information about its long‐term health effects, salvia is readily available and generally portrayed as a safe non‐addictive substance.Methods and ResultsWe report on two patients who presented with an enduring and pervasive pattern of salvia use.Discussion and ConclusionsEvaluating patients for salvia use during clinical assessment is strongly encouraged, especially among young polysubstance users.Scientific SignificanceClinicians should be mindful of the multifaceted psychiatric effects of salvia, including the potential for a use disorder. (Am J Addict 2018;27:163–165)
Corporations and Nations: Power Imbalance in the Extractive Sector
Authors: Oshionebo Evaristus 
Published: April 2018

AbstractThis article examines the nature and significance of the power imbalance between developing countries and transnational corporations (TNCs) in the natural resource sector. It situates this power imbalance within the context of global economic realities, including the high profitability of extractive TNCs; rampant poverty in developing countries; dependence of many developing countries on the extractive sector for economic sustenance; and lack of regulatory expertise on the part of developing countries. The article suggests two potential avenues for addressing this power imbalance. First, it advocates for the recognition of TNCs as “subjects” of international law, thus paving way for the imposition of some international law duties on TNCs. Secondly, the article argues that civil society groups should be empowered to participate actively in the regulatory process and that an empowered civil society could potentially counterbalance the power of TNCs and other corporations.
Controlling Corporate Power in China: Case Studies of Seed Companies and Water Distribution
Authors: Zhang Lanying , Li Guanqi , He Huili 
Published: April 2018

AbstractIn the course of China's economic transition, the government set up a policy goal to gradually withdraw from the market, while, at the same time, increasing the intensity of anti‐corruption actions. This article reviews the development of Chinese modern corporations and corresponding policy changes. The development and expansion of modern corporations as a result of reforms that occurred after 1978 reveals the government's decision not to fully withdraw from the market. When private companies are allowed to pursue maximum profits, especially in areas of public resources and services, society and the environment suffer severe negative consequences. Case studies of corporate control of seed companies and water utilities demonstrate in detail the damage caused by privatization. In order to protect the interests of society from corruption, government must concentrate on reducing the rent‐seeking behavior of corporations and collusion between businesses and government officials. The Chinese government's fight against corruption in recent years has been based on its market involvement, as well as on its determination to confine the power of corporations, which is a tough game.
The Pursuit of Power. Europe 1815–1914: To Hell and Back. Europe 1914–1949
Authors: Bonnell Andrew G. 
Published: April 2018

The Pursuit of Power. Europe 1815–1914. By Richard J. Evans (London: Allen Lane, 2016), pp.xxiv + 819, maps and colour plates, £25.00 (hb).To Hell and Back. Europe 1914–1949. By Ian Kershaw (London: Allen Lane, 2015), pp.xx + 593, maps and colour and b/w plates. £30.00 (hb).
Editorial: is proton pump inhibitor use associated with worse outcomes in patients with liver abscesses?
Authors: Tabibian J. H. , Lindor K. D. 
Published: April 2018

Linked contentThis article is linked to Bettinger et al papers. To view these articles visit https://doi.org/10.1111/apt.14512 and https://doi.org/10.1111/apt.14591.
Prediction of Response to Lithotripsy—the Use of Scanning Electron Microscopy and X‐ray Energy Dispersive Spectroscopy
Authors: COHEN N. P. , PARKHOUSE HELEN , SCOTT M. L. , BOWSHER W. G. , CROCKER P. , WHITFIELD H. N. 
Published: April 2018

SummaryA single urine sample was obtained from each of 38 patients before and immediately after treatment with a Wolf Piezolith 2300. Each sample was analysed for crystals using scanning electron microscopy and X‐ray energy dispersive spectroscopy. In all cases it was possible to make a stone diagnosis prior to treatment and there was 100% correlation between the pre‐ and post‐treatment diagnosis. All stones smaller than 90 mm2 on plain X‐ray cleared with piezoelectric lithotripsy alone, regardless of composition. Larger stones composed of calcium oxalate were all successfully fragmented, but 5 of 15 mixed or phosphate stones failed to respond.
Total Nephrectomy in Children: A Clinicopathological Review
Authors: ADAMSON A. S. , NADJMALDIN A. S. , ATWELL J. D. 
Published: April 2018

SummaryThe records of 85 children undergoing total nephrectomy have been reviewed. Diagnoses ranged between pyelonephritis (37 patients), renal tumours (25), renal dysplasia and multicystic kidney (16), obstructive uropathy (6) and renal vein thrombosis (1). In the pyelonephritic group a contributory ipsilateral abnormality was demonstrated in 36 of the 37 children. Vesicoureteric reflux (VUR) was the most common abnormality in this cohort and was usually of a severe grade. Calculus disease was present in 9 patients, only 1 of whom had VUR. Of the remaining 7 patients with pyelonephritis, 6 had evidence of obstruction to the upper tracts. Calculus disease poses a more severe threat to the childhood kidney than the well known risk factors of vesicoureteric reflux and obstructive uropathy.
Prognostic value of nutritional risk screening 2002 scale in nasopharyngeal carcinoma: A large‐scale cohort study
Authors: Peng Hao , Chen Bin‐Bin , Tang Ling‐Long , Chen Lei , Li Wen‐Fei , Zhang Yuan , Mao Yan‐Ping , Sun Ying , Liu Li‐Zhi , Tian Li , Guo Ying , Ma Jun 
Published: April 2018

Little is known about the value of the nutritional risk screening 2002 (NRS2002) scale in nasopharyngeal carcinoma (NPC). We conducted a large‐scale study to address this issue. We employed a big‐data intelligence database platform at our center and identified 3232 eligible patients treated between 2009 and 2013. Of the 3232 (12.9% of 24 986) eligible patients, 469 (14.5%), 13 (0.4%), 953 (29.5%), 1762 (54.5%) and 35 (1.1%) had NRS2002 scores of 1, 2, 3, 4 and 5, respectively. Survival outcomes were comparable between patients with NRS2002 <3 and ≥3 (original scale). However, patients with NRS2002 ≤3 vs >3 (regrouping scale) had significantly different 5‐year disease‐free survival (DFS; 82.7% vs 75.0%, P < .001), overall survival (OS; 88.8% vs 84.1%, P = .001), distant metastasis‐free survival (DMFS; 90.2% vs 85.9%, P = .001) and locoregional relapse‐free survival (LRRFS; 91.6% vs 87.2%, P = .001). Therefore, we proposed a revised NRS2002 scale, and found that it provides a better risk stratification than the original or regrouping scales for predicting DFS (area under the curve [AUC] = 0.530 vs 0.554 vs 0.577; P < .05), OS (AUC = 0.534 vs 0.563 vs 0.582; P < .05), DMFS (AUC = 0.531 vs 0.567 vs 0.590; P < .05) and LRRFS (AUC = 0.529 vs 0.542 vs 0.564; P < .05 except scale A vs B). Our proposed NRS2002 scale represents a simple, clinically useful tool for nutritional risk screening in NPC.
Robust Structure‐Based Shape Correspondence
Authors: Kleiman Yanir , Ovsjanikov Maks 
Published: April 2018

AbstractWe present a robust method to find region‐level correspondences between shapes, which are invariant to changes in geometry and applicable across multiple shape representations. We generate simplified shape graphs by jointly decomposing the shapes, and devise an adapted graph‐matching technique, from which we infer correspondences between shape regions. The simplified shape graphs are designed to primarily capture the overall structure of the shapes, without reflecting precise information about the geometry of each region, which enables us to find correspondences between shapes that might have significant geometric differences. Moreover, due to the special care we take to ensure the robustness of each part of our pipeline, our method can find correspondences between shapes with different representations, such as triangular meshes and point clouds. We demonstrate that the region‐wise matching that we obtain can be used to find correspondences between feature points, reveal the intrinsic self‐similarities of each shape and even construct point‐to‐point maps across shapes. Our method is both time and space efficient, leading to a pipeline that is significantly faster than comparable approaches. We demonstrate the performance of our approach through an extensive quantitative and qualitative evaluation on several benchmarks where we achieve comparable or superior performance to existing methods.
Recent alcohol use prolongs hospital length of stay following lung transplant
Authors: Lowery Erin M. , Yong Meagan , Cohen Arala , Joyce Cara , Kovacs Elizabeth J. 
Published: April 2018

AbstractLittle is known about the alcohol habits of people with advanced lung disease. Following lung transplantation, patients are asked to abstain from or minimize alcohol use. The aim of this investigation was to assess alcohol use in a cohort of patients with advanced lung disease undergoing evaluation for lung transplant. This is a prospective observational investigation comparing patient self‐report of alcohol use with their responses on the Alcohol Use Disorders Identification Test (AUDIT), and alcohol biomarkers collected at the time of transplant. There were 86 included in the cohort, 34% currently using alcohol, 13% had AUDIT scores >3, and 10% had positive results for alcohol biomarkers at the time of transplantation. Patients with evidence of recent alcohol use prior to lung transplant surgery had a 1.5‐fold increase in hospital length of stay following lung transplant (P = .028), spent 3 times as long on mechanical ventilation after transplant, and required intensive care unit monitoring nearly 3 times longer than those without recent alcohol use (P = .008). There were no differences in primary graft dysfunction, although several patients with recent alcohol use had post‐transplant atrial arrhythmias, acute kidney injury, and acute cellular rejection. Abstaining from alcohol use may optimize outcomes following lung transplant.