bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endosidin2 targets conserved exocyst complex subunit EXO70 to inhibit exocytosis
Authors: Zhang Chunhua , Brown Michelle Q. , van de Ven Wilhelmina , Zhang Zhi-Min , Wu Bin , Young Michael C. , Synek Lukáš , Borchardt Dan , Harrison Reed , Pan Songqin , Luo Nan , Huang Yu-ming M. , Ghang Yoo-Jin , Ung Nolan , Li Ruixi , Isley Jonathan , Morikis Dimitrios , Song Jikui , Guo Wei , Hooley Richard J. , Chang Chia-en A. , Yang Zhenbiao , Zarsky Viktor , Muday Gloria K. , Hicks Glenn R. , Raikhel Natasha V. 
Published: November 2015

SignificanceThe exocyst complex is a conserved protein complex that tethers the secretory vesicles to the site of membrane fusion during exocytosis, an essential cellular process that transports molecules, such as protein, to the cell surface or extracellular space. We identified a small molecule that targets the EXO70 (exocyst component of 70 kDa) subunit of the exocyst complex to inhibit exocytosis. This compound made it possible to control the dynamics of the exocytosis process in a dosage-dependent manner in different organisms and overcame the mutant lethality and genetic redundancy issues in studying mechanisms of exocyst complex regulation. Further design of molecules with higher affinity and more potent activity may make it possible to use drugs to control human diseases related to exocytosis, such as cancer and diabetes.
Genefu: an R/Bioconductor package for computation of gene expression-based signatures in breast cancer
Authors: Gendoo Deena M. A. , Ratanasirigulchai Natchar , Schröder Markus S. , Paré Laia , Parker Joel S. , Prat Aleix , Haibe-Kains Benjamin 
Published: November 2015

Abstract
Summary: Breast cancer is one of the most frequent cancers among women. Extensive studies into the molecular heterogeneity of breast cancer have produced a plethora of molecular subtype classification and prognosis prediction algorithms, as well as numerous gene expression signatures. However, reimplementation of these algorithms is a tedious but important task to enable comparison of existing signatures and classification models between each other and with new models. Here, we present the genefu R/Bioconductor package, a multi-tiered compendium of bioinformatics algorithms and gene signatures for molecular subtyping and prognostication in breast cancer.
Availability and implementation: The genefu package is available from Bioconductor. http://www.bioconductor.org/packages/devel/bioc/html/genefu.html. Source code is also available on Github https://github.com/bhklab/genefu.
Contact: bhaibeka@uhnresearch.ca
Supplementary information: Supplementary data are available at Bioinformatics online.
Minocycline as A Substitute for Doxycycline in Targeted Scenarios: A Systematic Review
Authors: Carris Nicholas W. , Pardo Joe , Montero Jose , Shaeer Kristy M. 
Published: November 2015

AbstractDoxycycline, a commonly prescribed tetracycline, remains on intermittent shortage. We systematically reviewed the literature to assess minocycline as an alternative to doxycycline in select conditions, given doxycycline's continued shortage. We identified 19 studies, 10 of which were published before 2000. Thirteen of the studies were prospective, but only 1 of these studies was randomized. Based on the available data, we found minocycline to be a reasonable substitute for doxycycline in the following scenarios: skin and soft-tissue infections and outpatient treatment of community-acquired pneumonia in young, otherwise healthy patients or in patients with macrolide-resistant Mycoplasma pneumoniae, as well as Lyme disease prophylaxis and select rickettsial disease should doxycycline be unavailable.
Effects of Smoking on Central Corneal Thickness and the Corneal Endothelial Cell Layer in Otherwise Healthy Subjects
Authors: Ilhan Nilufer , Ilhan Ozgur , Coskun Mesut , Daglioglu Mutlu C. , Ayhan Tuzcu Esra , Kahraman Hilal , Keskin Ugurcan 
Published: November 2015

Objectives:The effects of smoking on central corneal thickness (CCT), corneal endothelial cell density (ECD), and morphology were evaluated in otherwise healthy subjects.Methods:The study included 103 current smokers and 106 healthy nonsmoking subjects without any eye disease apart from refractive errors. Endothelial cell density, percentage of hexagonality, and coefficient of variation (CV) in cell size were measured using noncontact specular microscopy. Central corneal thickness was measured by ultrasound pachymetry.Results:The mean age of participants in the nonsmoker group was 31.4 ± 5.1 years (18–60) and 33.0±9.1 years (18–58) in the current smoker group. The mean CCT value was 523.7±34 μm in the nonsmoker group and 518.5±37 μm in the smoker group. The mean ECD, CV, and percentage of hexagonality values were 2,881±293.7 cells per square millimeter, 32.5±6%, and 56.6±11% in the nonsmoker group, and 2,681±323.9 cells per square millimeter, 33.4±5%, and 55.5±10% in the smoker group, respectively. Although there was no difference between the groups in terms of CCT, CV, and percentage of hexagonality values, a significant difference was determined in the case of ECD values​​ (P<0.001). The smoker group comprised 67 light smokers (65.0%) and 36 (35.0%) heavy smokers. Between these groups, there was no statistically significant difference in the mean values of CCT, ECD, CV, and the percentage of hexagonality.Conclusions:Although cigarette smoking has no effect on cell polymorphism and polymegethism, the results suggest that smoking reduces endothelial cell count.
Helicobacter pylori Infection and Children's Growth
Authors: Dror Gal , Muhsen Khitam 
Published: November 2015

ABSTRACTObjectives:Helicobacter pylori infection is acquired in early childhood, yet its role in children's health is still not fully clear. In this narrative review, we focused on the association between H pylori infection and children's growth.Methods:A literature search of the Ovid MEDLINE (till June 2015) and EMBASE (till August 2015) databases was performed using the terms “Helicobacter pylori, growth, body height, growth disorders and child development.” Original studies that addressed the association between H pylori infection or eradication and children's growth were reviewed and the risk of bias of each study was assessed.Results:The existing evidence is based on observational studies (N = 48) and suggests that H pylori infection may adversely influence children's growth; findings were more consistent across studies with low risk of bias. Regarding linear growth, observational studies have repeatedly linked between H pylori infection and slower or diminished linear growth; yet, it is not known whether this association is causal. The association between H pylori infection and ponderal growth has been less consistent. Scarce evidence exists on the effect of H pylori eradication on children's skeletal growth and weight gain, but there is an indication that H pylori eradication may benefit nutritional status.Conclusions:H pylori infection may impair children's growth. Additional studies, especially clinical trials, are needed to elucidate the role of H pylori eradication in children's growth, and the mechanisms that may be involved in such.
Early farmers from across Europe directly descended from Neolithic Aegeans
Authors: Hofmanová Zuzana , Kreutzer Susanne , Hellenthal Garrett , Sell Christian , Diekmann Yoan , Díez-del-Molino David , van Dorp Lucy , López Saioa , Kousathanas Athanasios , Link Vivian , Kirsanow Karola , M. Cassidy Lara , Martiniano Rui , Strobel Melanie , Scheu Amelie , Kotsakis Kostas , Halstead Paul , Triantaphyllou Sevi , Kyparissi-Apostolika Nina , Urem-Kotsou Dushanka-Christina , Ziota Christina , Adaktylou Fotini , Gopalan Shyamalika , M. Bobo Dean , Winkelbach Laura , Blöcher Jens , Unterländer Martina , Leuenberger Christoph , Çilingiroğlu Çiler , Horejs Barbara , Gerritsen Fokke , Shennan Stephen , Bradley Daniel G. , Currat Mathias , R. Veeramah Krishna , Wegmann Daniel , Thomas Mark G. , Papageorgopoulou Christina , Burger Joachim 
Published: November 2015

AbstractFarming and sedentism first appear in southwest Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion and admixture with local foragers in the early Neolithisation of Europe. Here we present paleogenomic data for five Neolithic individuals from northwestern Turkey and northern Greece – spanning the time and region of the earliest spread of farming into Europe. We observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.
Quantitative proteome-based guidelines for intrinsic disorder characterization
Authors: Vincent Michael , Whidden Mark , Schnell Santiago 
Published: November 2015

AbstractIntrinsically disordered proteins fail to adopt a stable three-dimensional structure under physiological conditions. It is now understood that many disordered proteins are not dysfunctional, but instead engage in numerous cellular processes, including signaling and regulation. Disorder characterization from amino acid sequence relies on computational disorder prediction algorithms. While numerous large-scale investigations of disorder have been performed using these algorithms, and have offered valuable insight regarding the prevalence of protein disorder in many organisms, critical proteome-based descriptive statistical guidelines that would enable the objective assessment of intrinsic disorder in a protein of interest remain to be established. Here we present a quantitative characterization of numerous disorder features using a rigorous non-parametric statistical approach, providing expected values and percentile cutoffs for each feature in ten eukaryotic proteomes. Our estimates utilize multipleab initiodisorder prediction algorithms grounded on physicochemical principles. Furthermore, we present novel threshold values, specific to both the prediction algorithms and the proteomes, defining the longest primary sequence length in which the significance of a continuous disordered region can be evaluated on the basis of length alone. The guidelines presented here are intended to improve the interpretation of disorder content and continuous disorder predictions from the proteomic point of view.
FecalSeq: methylation-based enrichment for noninvasive population genomics from feces
Authors: Chiou Kenneth L. , Bergey Christina M. 
Published: November 2015

AbstractObtaining high-quality samples from wild animals is a major obstacle for genomic studies of many taxa, particular at the population level, as collection methods for such samples are typically invasive. DNA from feces is easy to obtain noninvasively, but is dominated by a preponderance of bacterial and other non-host DNA. Because next-generation sequencing technology sequences DNA largely indiscriminately, the high proportion of exogenous DNA drastically reduces the efficiency of high-throughput sequencing for host animal genomics. In order to address this issue, we developed an inexpensive methylation-based capture method for enriching host DNA from noninvasively obtained fecal DNA samples. Our method exploits natural differences in CpG-methylation density between vertebrate and bacterial genomes to preferentially bind and isolate host DNA from majority-bacterial fecal DNA samples. We demonstrate that the enrichment is robust, efficient, and compatible with downstream library preparation methods useful for population studies (e.g., RADseq). Compared to other enrichment strategies, our method is quick and inexpensive, adding only a negligible cost to sample preparation for research that is often severely constrained by budgetary limitations. In combination with downstream methods such as RADseq, our approach allows for cost-effective and customizable genomic-scale genotyping that was previously feasible in practice only with invasive samples. Because feces are widely available and convenient to collect, our method empowers researchers to explore genomic-scale population-level questions in organisms for which invasive sampling is challenging or undesirable.
Expression, purification, crystallization and X-ray diffraction analysis of ChiL, a chitinase fromChitiniphilus shinanonensis
Authors: Ueda Miruku , Shimosaka Makoto , Arai Ryoichi 
Published: November 2015

Chitin, a linear polysaccharide consisting of β-1,4-linkedN-acetyl-D-glucosamine (GlcNAc), is widely used because of its biochemical properties. GlcNAc oligomers prepared from chitin have useful biological activities, such as immunostimulation and the induction of plant defence responses. Microbial chitinolytic enzymes have been investigated extensively for their potential use in the eco-friendly enzymatic production of GlcNAc and its oligomers.Chitiniphilus shinanonensisSAY3Tis a recently found bacterium with a strong chitinolytic activity. The chitinolytic enzymes from this strain are potentially useful for the efficient production of GlcNAc and its oligomers from chitin. ChiL fromC. shinanonensisis an endo-type chitinase belonging to the family 18 glycoside hydrolases (GH18). To understand the enzymatic reaction mechanism of ChiL and utilize it for further enzyme engineering, the catalytic domain (41–406) of ChiL, the construct for which was carefully designed, was expressed, purified and crystallized by the vapour-diffusion method. The crystal belonged to the orthorhombic space groupP212121, with unit-cell parametersa= 69.19,b = 81.55,c= 130.01 Å, and diffracted to 1.25 Å resolution. The Matthews coefficient (VM= 2.2 Å3 Da−1) suggested the presence of two monomers per asymmetric unit with a solvent content of 45%.
Medknow Publications: a success model in the digital era
Authors: Joseph Rojers Puthur 
Published: November 2015

Subject area
Innovation Strategy/Entrepreneurship.

Study level/applicability
The case can be used in an MBA/postgraduate management program for a course on Innovations Strategy with a focus on disruptive innovation, specifically in relation to disruption in the value chain with the adoption of new technologies or for a course on Entrepreneurship focusing on the opportunities created by the Internet-based technologies for start-up businesses. Alternatively, it can be used in a course on e-commerce strategies, particularly to demonstrate the efficiency of online distribution vis-à-vis physical channels.

Case overview
The case illustrates how Medknow Publications created a profitable e-commerce model out of a struggling conventional business, namely, the learned society journal publishing. It also provides a useful ground to discuss the challenges faced by the conventional scholarly journal publishing models, the current crisis in scholarly journal publishing and how Medknow, a disruptive business model innovation, would address these issues. Besides, the case illustrates how Medknow created a sustainable “for-profit” alternative to the prevailing not-for-profit models of open access publishing.

Expected learning outcomes
After the analysis and discussion of this case, students will be able to: appreciate how technological innovation can disrupt existing business models; understand how digitization helps improve the efficiency of value chain in the content industry, particularly the scholarly journal publishing industry; and appreciate that the flexibility of digitized content and the global reach of the Internet have the potential to transform the scholarly journal publishing industry for good.

Supplementary materials
Teaching notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.
M-Pesa: an evolution in organisational strategy
Authors: Cassim Mariam , Ronnie Linda 
Published: November 2015

Subject area
Change Management.

Study level/applicability
Postgraduate business courses, including MBA courses in change management and human resource management.

Case overview
This case study emphasises how important it is for organisations operating in today's turbulent and rapidly changing business environment to have an emergent approach to change. It focuses on the dilemmas faced by Hemmanth Singh, the newly appointed Managing Executive responsible for Mobile Commerce at Vodacom South Africa. Singh is responsible for the execution of the new strategy into financial services, the relaunch of M-Pesa into the South African market being the immediate task. The case sets the context for the relaunch of M-Pesa, and the reader is introduced to some of the limitations and challenges experienced by the company when trying to replicate a successful business model from one market to another, especially after an unsuccessful initial launch.

Expected learning outcomes
After reading and analysing the information contained in the case study and appendices, students should be able to evaluate the critical role that leadership needs to play when introducing and implementing a change initiative at an organisation that is stimulated by evolving external market conditions; understand the importance of adopting an emergent approach to change in current operating conditions; identify the factors that contribute to or hinder the creation and sustainability of an adaptive culture within an organisation; and appreciate the challenges of attempting to replicate a successful business model from one market into another.

Supplementary materials
Teaching Notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.
Cognizant India: reinventing the value proposition
Authors: Sharma Tripti , Ghosh Tapabrata 
Published: November 2015

Subject area
Strategic management, IT strategy, Business & IT Consulting, International Business.

Study level/applicability
PGDM and Executive programmes.

Case overview
Cognizant Technology Solutions, one of the giants in the Indian information technology (IT) industry, has been continually evolving new strategies and business models to cater to the global IT demand. Starting as an in-house technology unit of Duns & Bradstreet, the case highlights the various pioneering and transformative decisions taken by Cognizant to become one among the Fortune 500 companies of the world. However, despite its supremacy in the global market, they are facing tremendous competition from the other IT giants – TCS, Infosys and Wipro, to name a few. Also, the expansion of global IT players like Accenture and International Business Machines (IBM) in India is making matters worse. This intense competition, when juxtaposed with commoditization and price sensitivity on behalf of the IT demand, makes sustainability a big question mark. The million-dollar question remains “How should Cognizant strategize to ensure inorganic growth in the price-sensitive industry?”

Expected learning – outcomes
The case highlights the market dynamics of the Indian IT industry – from its humble beginning as an attraction for low-cost labour to being one of the strategic outsourcing geographies of the IT sector – and thereby categorically points out the significance of continuous evolution on behalf of the IT firms to stay alive in this client-driven industry. The students are expected to analyze the IT industry of India, keeping in mind its vulnerabilities – price sensitivity, dependence on developed economies and intense competition – and relate the same to different strategies incorporated by Cognizant to remain one of the powerhouses of the Indian IT industry.

Supplementary materials
Teaching notes are available for educators only. Please contact your library to gain login details or email support@emeraldinsight.com to request teaching notes.
Examining the relationship between war and interest based transaction
Authors: Mubasshera Hamida , Kassim Salina H. 
Published: November 2015

Purpose
– The purpose of this paper is to examine the relationship between war and interest-based transaction by analyzing the case of the late Ottoman Empire from a historical economic perspective. It also attempts to provide a deeper understanding of the Quranic verses where Allah has declared war against people who deal with interest.

Design/methodology/approach
– It provides a snapshot of major economic events that occurred in the last phase of the Ottoman rule that contributed in shaping the fate of the empire and, then, systematically explores them.

Findings
– A careful study of the chain of events reveals that there exists a strong relationship between war and interest-based transactions, as indicated in the parable given in the Quran where dealing with interest has been described as equivalent to waging war against Allah and His Messenger. The paper claims that Muslims are sure to be defeated in the hands of disbelievers if they themselves are at war with Allah and His Messenger by being involved in interest-based transactions, as validated by the case of the Ottoman Empire. The paper goes on to argue that this is why no specific punishment in this life is mentioned for this crime; rather extreme psychological pressure is imposed, so that the believers do not even consider getting close to dealing with interest.

Originality/value
– This paper addresses a missing component in the existing literature of Islamic economics where the political economic aspects of interest has seldom received due attention. A careful analysis of these issues is expected to help people better understand the dire consequences of dealing in interest on a micro level. On a macro level, it can always help to formulate prudent foreign policy by learning from the mistakes of our ancestors.
Reviving the Islamic economic system through shariah-based public policy
Authors: Mahyudi Mohd 
Published: November 2015

Purpose– The paper aims to revive the Islamic economic system discourse given the increasing interest in the moral economy agenda.Design/methodology/approach– Proponents of Islamic economics theorise that the Islamic system presents the ideal form of a socio-economic order. However, the reported huge gap between theoretical construct and real activities seems to support the critics’ claim that it is a mere utopian state that directly challenges the viability of the Islamic economy idea.Findings– The fact of the matter is thathomo economicusis overpoweringhomo Islamicusdespite the presupposed position ofhomo Islamicusas the mainstay of Islamic economics.Research limitations/implications– To manifest the Islamic economic system notion further, it is argued that a shariah-based values infusion policy (VIP) needs to be formulated to actualise the predominance ofhomo Islamicus.Practical implications– Owing to the overarching and holistic nature of the proposed public policy, the operations of individuals, firms and state agencies should have the tendency to reflect the expected behaviour ofhomo Islamicusbetter than the present state of affairs.Social implications– The success of the VIP would include the enhancement of social integration and cohesion.Originality/value– The link between moral economy,homo Islamicusand public policy is clearly established. Thus, this research guides policy makers in promoting the Islamic economic system as a universally-aspired moral economy project.