bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combining images and anatomical knowledge to improve automated vein segmentation in MRI
Authors: Ward Phillip G. D. , Ferris Nicholas J. , Raniga Parnesh , Dowe David L. , Ng Amanda C. L. , Barnes David G. , Egan Gary F. 
Published: June 2017

AbstractPurposeTo improve the accuracy of automated vein segmentation by combining susceptibility-weighted images (SWI), quantitative susceptibility maps (QSM), and a vein atlas to produce a resultant image called a composite vein image (CV image).MethodAn atlas was constructed in common space from 1072 manually traced 2D-slices. The composite vein image was derived for each subject as a weighted sum of three inputs; a SWI image, a QSM image and the vein atlas. The weights for each input and each anatomical location, called template priors, were derived by assessing the accuracy of each input over an independent data set. The accuracy of venograms derived automatically from each of the CV image, SWI, and QSM image sets was assessed by comparison with manual tracings. Three different automated vein segmentation techniques were used, and ten performance metrics evaluated.ResultsVein segmentations using the CV image were comprehensively better than those derived from SWI or QSM images (mean Cohen’s d = 1.1). Sixty permutations of performance metric and automated segmentation technique were evaluated. Vein identification improvements that were both large and significant (Cohen’s d>0.80, p<0.05) were found in 77% of the permutations, compared to no improvement in 5%.ConclusionThe accuracy of automated venograms derived from the composite vein image was overwhelmingly superior to venograms derived from SWI or QSM alone.
Impact of fluorescent protein fusions on the bacterial flagellar motor
Authors: Heo M , Nord AL , Chamousset D , Rijn E van , Beaumont HJE , Pedaci F 
Published: June 2017

AbstractFluorescent fusion proteins open a direct and unique window onto protein function. However, they also introduce the risk of perturbation of the function of the native protein. Successful applications of fluorescent fusions therefore rely on a careful assessment and minimization of the side effects. Such insight, however, is still lacking for many applications of fluorescent fusions. This is particularly relevant in the study of the internal dynamics of motor protein complexes, where both the chemical and mechanical reaction coordinates can be affected. Fluorescent proteins fused to thestatorof the bacterial flagellar motor (BFM) complex have previously been used to successfully unveil the internal subunit dynamics of the motor. Here we report the effects of three different fluorescent proteins fused to the stator, all of which altered BFM behavior. The torque generated by individual stators was reduced while their stoichiometry in the complex remained unaffected. MotB fusions decreased the rotation-direction switching frequency of single motors and induced a novel BFM behavior: a bias-dependent asymmetry in the speed attained in the two rotation directions. All these effects could be mitigated by the insertion of a linker at the fusion point. These findings provide a quantitative account of the effects of fluorescent fusions on BFM dynamics and their alleviation—new insights that advance the use of fluorescent fusions to probe the dynamics of protein complexes.Author summaryMuch of what is known about the biology of proteins was discovered by fusing them to fluorescent proteins that allow detection of their location. But the label comes at a cost: the presence of the tag can alter the behavior of the protein of interest in unforeseen, yet biologically relevant ways. These side effects limit the depth to which fluorescent proteins can be used to probe protein function. One of the systems that has been successfully studied with fluorescent fusions for which these effects have not been addressed are dynamic protein complexes that carry out mechanical work. We examined how fluorescent proteins fused to a component of the bacterial flagellar motor complex impacts its function. Our findings show that the fusion proteins altered biologically relevant dynamical properties of the motor, including induction of a novel mechanical behavior, and demonstrate an approach to alleviate this. These results advance our ability to dissect the bacterial flagellar motor, and the internal dynamics of protein complexes in general, with fluorescent fusion proteins while causing minimal perturbation.
ORIGAMI: A Software Suite for Activated Ion Mobility Mass Spectrometry (aIM-MS) Applied To Multimeric Protein Assemblies
Authors: Migas Lukasz G. , France Aidan P. , Bellina Bruno , Barran Perdita E. 
Published: June 2017

AbstractWe present here a software suite (ORIGAMI) that facilitates the rapid acquisition and analysis of ion mobility data following collisional activation.ORIGAMIwas developed for use on Waters Synapt instruments where data acquisition is achieved by interfacing WREnS (Waters Research Enabled Software) and MassLynx. Two components are presented, the first isORIGAMIMSwhich enables activation of ions by sequential increase of collision voltages prior to ion mobility analysis. We demonstrate the use ofORIGAMIon the tetrameric assemblies formed by the proteins concanavalin A (103 kDa) and alcohol dehydrogenase (143 kDa). Activation is performed in the trap collision cell of the Synapt TriWave assembly, where the collision voltage can be ramped from 0-200 V. All of the acquired data is recorded in a single file which simplifies data acquisition. This substantially decreases the time needed to perform a typical activated IM-MS experiment on a single protein charge state from approx. 2 hours to ~25 minutes. Following data acquisition the data is analysed in the second component,ORIGAMIANALYSE, which allows the user to visualise the effect of activation on the mobility of the parent ion, as well as on any produced fragment ion. The user can export the data in the form of heat maps, waterfall or wire plots. In addition, tools implemented inORIGAMIenable easy data extraction from single or multiple MassLynx .raw files, in-depth interrogation of large datasets, statistical analysis and figure creation capabilities. We demonstrate the use ofORIGAMIon concanavalin A and alcohol dehydrogenase acquired using the traditional protocols and theORIGAMIMSmethod.Highlights-New methodology for faster acquisition and data analysis following activation of ions separated by ion mobility mass spectrometry-Software package capable of simultaneous analysis of multiple MassLynx .raw files-Visualization of the change in mobility of parent and fragment ions following activation-Easy extraction, data processing and extensive plotting tools
The Diagnostic Potential & Interactive Dynamics of the Colorectal Cancer Virome
Authors: Hannigan Geoffrey D , Duhaime Melissa B , Ruffin Mack T , Koumpouras Charlie C , Schloss Patrick D 
Published: June 2017

AbstractHuman viruses (those that infect human cells) have been associated with many cancers, largely due to their mutagenic and functionally manipulative abilities. Despite this, cancer microbiome studies have almost exclusively focused on bacteria instead of viruses. We began evaluating the cancer virome by focusing on colorectal cancer, a primary cause of morbidity and mortality throughout the world, and a cancer linked to altered colonic bacterial community compositions but with an unknown association with the gut virome. We used 16S rRNA gene, whole shotgun metagenomic, and purified virus metagenomic sequencing of stool to evaluate the differences in human colorectal cancer virus and bacterial community composition. Through random forest modeling we identified differences in the healthy and colorectal cancer virome. The cancer-associated virome consisted primarily of temperate bacteriophages that were also predicted to be bacteria-virus community network hubs. These results provide foundational evidence that bacteriophage communities are associated with colorectal cancer and potentially impact cancer progression by altering the bacterial host communities.
Is internal and external mechanism of governance enriching the performance of the banking sector of Pakistan?
Authors: Sohail Sundas , Rasul Farhat , Fatima Ummara 
Published: June 2017

PurposeThe purpose of this study is to explore how governance mechanisms (internal and external) enhance the performance of the return on asset (ROA), return on equity (ROE), earning per share (EPS) and dividend payout ratios (DP) of the banks of Pakistan. The study incorporates not only the internal factors of governance (board size, out-ratio, annual general meeting, managerial ownership, institutional ownership, block holder stock ownership and financial transparency) but also the external factors (legal infrastructure and protection of minority shareholders, and the market for corporate control).Design/methodology/approachThe sample size of the study consists of 30 banks (public, private and specialized) listed at the Pakistan Stock Exchange (PSE) for the period 2008-2014. The panel data techniques (fixed or random effect model) have been used for the empirical analysis after verification by Hausman (1978) test.FindingsThe results revealed that not only do the internal mechanisms of governance enhance the performance of the banking sector of Pakistan but external governance also plays a substantial role in enriching the performance. The findings conclude that for a good governance structure, both internal and external mechanisms are equally important, to accelerate the performance of the banking sector.Research limitations/implicationsInternal and external mechanisms of corporate governance can also be checked by adding some more variables (ownership i.e. foreign, female and family as internal and auditor as external), but they are not added in this work due to data unavailability.Practical implicationsThe study contributes to the literature and could be useful for the policy makers who need to force banks to mandate codes of governance through which they can create an efficient board structure and augment the performance. The investments from different forms of ownership can be accelerated if they follow the codes properly.Social implicationsThe study facilitates the bankers in incorporating sound codes of corporate governance to enhance the performance of the banks.Originality/valueThis work is unique as no one has explored the impact of external mechanism of governance on the performance of the banking sector of Pakistan.
A spherical element subdivision method for the numerical evaluation of nearly singular integrals in 3D BEM
Authors: Zhang Jianming , Wang Pan , Lu Chenjun , Dong Yunqiao 
Published: June 2017

Purpose
The purpose of this paper is to preset a spherical element subdivision method for the numerical evaluation of nearly singular integrals in three-dimensional (3D) boundary element method (BEM).

Design/methodology/approach
In this method, the source point is first projected to the tangent plane of the element. Then two cases are considered: the projection point is either inside or outside the element. In both cases, the element is subdivided into a number of patches using a sequence of spheres with decreasing radius.

Findings
With the proposed method, the patches obtained are automatically refined as they approach the projection point and each patch of the integration element is “good” in shape and size for standard Gaussian quadrature. Therefore, all kinds of nearly singular boundary integrals on elements of any shape and size with arbitrary source point location related to the element can be evaluated accurately and efficiently.

Originality/value
Numerical examples for planar and slender elements with various relative location of the source point are presented. The results demonstrate that our method has much better accuracy, efficiency and stability than conventional methods.
Due diligence: Plantation Shutters®, South Africa
Authors: Sutherland Margie , Pearson Hayley , Fisher Greg 
Published: June 2017

Subject area
Company turnaround, General Management.

Study level/applicability
Executive education, MBA.

Case overview
This is a four-part case study in which the case of a company turnaround emerges as the students work through a series of decision-making processes. In teaching the case, the students would only be given Part A to begin with, about which they need to make decisions as to what they would do, as preparation for the first part of the lecture. After that has been discussed, they are provided with the second part which tells them what in fact happened in the situation and leads them to the next decision point, and so on. The case deals with an entrepreneur hearing about a business that has gone insolvent; it then tracks the process from investigating the small manufacturing and sales company through the various stages of its subsequent remarkable turnaround to the point where the protagonist was voted Entrepreneur of the Year in South Africa. It covers the period 2007 to 2012 and includes the annual financial statements.

Expected learning outcomes
Following are the expected learning outcomes: an understanding of the broad range of management competencies; an understanding of how to turnaround a small organisation; and to experience group-based decision-making.

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.

Subject code
CSS 11: Strategy.
Using experimentation to understand the 10‐year snowshoe hare cycle in the boreal forest of North America
Authors: Krebs Charles J. , Boonstra Rudy , Boutin Stan 
Published: June 2017

AbstractPopulation cycles have long fascinated ecologists from the time of Charles Elton in the 1920s. The discovery of large population fluctuations in undisturbed ecosystems challenged the idea that pristine nature was in a state of balance. The 10‐year cycle of snowshoe hares (Lepus americanusErxleben) across the boreal forests of Canada and Alaska is a classic cycle, recognized by fur traders for more than 300 years.Since the 1930s, ecologists have investigated the mechanisms that might cause these cycles. Proposed causal mechanisms have varied from sunspots to food supplies, parasites, diseases, predation and social behaviour. Both the birth rate and the death rate change dramatically over the cycle. Social behaviour was eliminated as a possible cause because snowshoe hares are not territorial and do not commit infanticide.Since the 1960s, large‐scale manipulative experiments have been used to discover the major limiting factors. Food supply and predation quickly became recognized as potential key factors causing the cycle. Experiments adding food and restricting predator access to field populations have been decisive in pinpointing predation as the key mechanism causing these fluctuations.The immediate cause of death of most snowshoe hares is predation by a variety of predators, including the Canada lynx (Lynx canadensisKerr). The collapse in the reproductive rate is not due to food shortage as was originally thought, but is a result of chronic stress from predator chases.Five major issues remain unresolved. First, what is the nature of the predator‐induced memory that results in the prolonged low phase of the cycle? Second, why do hare cycles form a travelling wave, starting in the centre of the boreal forest in Saskatchewan and travelling across western Canada and Alaska? Third, why does the amplitude of the cycle vary greatly from one cycle to the next in the same area? Fourth, do the same mechanisms of population limitation apply to snowshoe hares in eastern North American or in similar ecosystems across Siberia? Finally, what effect will climatic warming have on all the above issues? The answers to these questions remain for future generations of biologists to determine.
A co‐drug conjugate of naringenin and lipoic acid mediates neuroprotection in a rat model of oxidative stress
Authors: Saleh Tarek M , Saleh Monique C , Connell Barry J , Song Yang‐Heon 
Published: June 2017

SummaryUsing our in vitro and in vivo models of oxidative stress, the current study was designed to determine the neuroprotective potential of naringenin, alone or in combination with lipoic acid. In our mixed neuronal culture exposed to hypoxia and subsequent reoxygenation, naringenin was shown to provide significant neuroprotection against cell death at a concentration of 2.5 μmol/L. Lipoic acid (LA) did not produce neuroprotection at any concentration tested (0.25‐100 μmol/L). In contrast, when naringenin was covalently combined with LA, producing a novel compound named “VANL‐100”, significant neuroprotection was observed at a concentration as low as 2×10−2 μmol/L (100‐fold more potent). An ELISA for antioxidant capacity demonstrated that naringenin and VANL‐100 likely resulted in neuroprotection by increasing the free radical scavenging capacity of the neuronal cells. Pretreatment of rats with the above compounds prior to middle cerebral artery occlusion (MCAO) followed by reperfusion, showed similar results. Naringenin significantly reduced infarct volume at a dose of 10 mg/kg while VANL‐100 produced significant neuroprotection at a dose as low as 1×10−4 mg/kg (10 000‐fold more potent). This VANL‐100‐induced neuroprotection persisted even when administered 1 and 3 hours into the reperfusion time course. Taken together, these results suggest that our novel compound, VANL‐100 is neuroprotective, likely via a mechanism that involves increasing the antioxidant capacity of neuronal cells. Our results also show that VANL‐100 is 100‐10 000‐fold more potent than the parent compounds, which adds to the growing evidence in support of combination therapy targeting oxidative stress in neurodegenerative diseases.
Targeting protein for Xenopus kinesin‐like protein 2 knockdown enhances radiation sensitivity of human lung squamous carcinoma cell
Authors: Yang Jie , Gao Feng , Xu Xinjian , Wang Yuxiang , Zhu Shuchai 
Published: June 2017

SummaryThe targeting protein for Xenopus kinesin‐like protein 2 (TPX2) has been demonstrated to be associated with the tumourigenesis of many cancers. In the present study, we investigated the role and preliminary mechanism of TPX2 in the resistance of lung squamous carcinoma to radiation therapy. The results showed that SK‐MES‐1R and NCI‐H226R cells were more resistant to X‐ray irradiation than the parental cells (SK‐MES‐1 and NCI‐H226). Moreover, TPX2 was upregulated in the radioresistant cells compared with the parental cells. TPX2 knockdown significantly decreased TPX2 expression in SK‐MES‐1 cells, while TPX2 overexpression increased TPX2 expression in NCI‐H226 cells compared with the corresponding control cells. TPX2 knockdown enhanced the radiosensitivity of SK‐MES‐1 and promoted cell apoptosis following exposure to irradiation, whereas TPX2 overexpression decreased the radiosensitivity of NCI‐H226 and inhibited cell apoptosis. In in vivo studies, the combination of TPX2 knockdown and irradiation significantly inhibited tumour growth, decreased tumour weight, downregulated TPX2 expression in tumour tissue and induced cell apoptosis in nude mice, while TPX2 overexpression exerted an opposite effect. Our results indicated that TPX2 was correlated with cell radioresistance and it might be served as a therapeutic target to enhance cell radiosensitivity in the radiation therapy of lung squamous carcinoma.
High throughput sequencing reveals Drosophila suzukii responses to insecticides
Authors: Mishra Ruchir , Chiu Joanna C. , Hua Gang , Tawari Nilesh R. , Adang Michael J. , Sial Ashfaq A. 
Published: June 2017

AbstractGlobal climate change and acquired resistance to insecticides are threats to world food security. Drosophila suzukii, a devastating invasive pest in many parts of the world, causes substantial economic losses to fruit production industries, forcing farmers to apply broad‐spectrum insecticides frequently. This could lead to the development of insecticide resistance. We determined the Lethal Concentration 50 (median lethal concentration, LC50) values of zeta‐cypermethrin, spinosad, and malathion insecticides against D. suzukii colonies established from Clarke and Pierce county Georgia, United States. The LC50 values were 3 fold higher in the Pierce county population for all insecticide treatments. We then used RNA sequencing to analyze the responses of Pierce and Clarke population flies surviving a LC50 treatment of the 3 insecticides. We identified a high number of differentially expressed genes that are likely involved in detoxification and reduced cuticular penetration, especially in the Pierce population, with extensive overlap in differentially expressed genes between the 3 insecticide treatments. Finally, we predicted fewer nonsynonymous single nucleotide variants having deleterious effects on protein function among detoxification, insecticide target, and cuticular protein encoding genes in Pierce flies. Thus a combination of increased gene expression and fewer deleterious single nucleotide variants highlights molecular mechanisms underlying the higher LC50 values for Pierce population flies.
An empirical test of the role of learning in translocation
Authors: Krochmal A. R. , Roth T. C. , O'Malley H. 
Published: June 2017

AbstractTranslocation centers on the introducing, reintroducing, or augmenting populations by moving individuals from existing wild source populations to different locations with purportedly suitable habitat. Despite much research in and application of translocation, this technique is often marred by low success rates. While many possible factors could contribute to low translocation success, outcomes are often improved when researchers engage in a soft release, which provides the animals with the opportunity for extra time to acclimate to their release site, indicating that aspects of learning may play an important role in translocation success. To test the importance of the time available for learning in translocation success, we performed hard and soft releases into an existing population of Eastern painted turtles Chrysemys picta that has experienced seasonal ephemeral water sources and in which resident turtles navigate to new permanent sources of water with extreme precision (±3.5 m) using specific routes known to be facilitated by learning. Translocated adult turtles in both hard‐ and soft‐release groups failed to successfully negotiate upland habitat, even when given 3 months to prospect and learn (the maximum time possible in our system). Likewise, turtles in both groups moved more slowly, stopped more frequently, and were slower to restart movement than resident adults. Finally, both translocated groups exhibited significant drops in body mass and elevated rates of predation. In contrast, juveniles from the same donor population navigated to alternative water successfully, with movements and mortality rates not different from resident animals. These results indicate that complex aspects of cognition beyond time to learn can influence translocation success and highlight the importance of considering how and when animals learn.