bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic limitations to RNA sequencing expression profiling
Authors: Hirsch Cory D. , Springer Nathan M. , Hirsch Candice N. 
Published: September 2015

SummaryThe field of genomics has grown rapidly with the advent of massively parallel sequencing technologies, allowing for novel biological insights with regards to genomic, transcriptomic, and epigenomic variation. One widely utilized application of high‐throughput sequencing is transcriptional profiling using RNA sequencing (RNAseq). Understanding the limitations of a technology is critical for accurate biological interpretations, and clear interpretation of RNAseq data can be difficult in species with complex genomes. To understand the limitations of accurate profiling of expression levels we simulated RNAseq reads from annotated gene models in several plant species including Arabidopsis, brachypodium, maize, potato, rice, soybean, and tomato. The simulated reads were aligned using various parameters such as unique versus multiple read alignments. This allowed the identification of genes recalcitrant to RNAseq analyses by having over‐ and/or under‐estimated expression levels. In maize, over 25% of genes deviated by more than 20% from the expected count values, suggesting the need for cautious interpretation of RNAseq data for certain genes. The reasons identified for deviation from expected expression varied between species due to differences in genome structure including, but not limited to, genes encoding short transcripts, overlapping gene models, and gene family size. Utilizing existing empirical datasets we demonstrate the potential for biological misinterpretation resulting from inclusion of ‘flagged genes’ in analyses. While RNAseq is a powerful tool for understanding biology, there are limitations to this technology that need to be understood in order to improve our biological interpretations.
An inventory of concerns behind blood safety policies in five Western countries
Authors: Kramer Koen , Verweij Marcel F. , Zaaijer Hans L. 
Published: September 2015

BACKGROUNDThe availability of costly safety measures against transfusion‐transmissible infections forces Western countries to confront difficult ethical questions. How to decide about implementing such measures? When are such decisions justified? As a preliminary to addressing these questions, we assessed which concerns shape actual donor blood safety policymaking in five Western countries.STUDY DESIGN AND METHODSOur qualitative study involved determining which issues had been discussed in advisory committee meetings and capturing these issues in general categories. Appropriate documents were identified in collaboration with local decision‐making experts in Canada, Germany, the Netherlands, the United States, and the United Kingdom. The introduction of hepatitis B virus nucleic acid testing and selected measures against variant Creutzfeldt‐Jakob disease, West Nile virus, and Q‐fever were chosen as cases representing decision‐making on safety measures with high costs and low or uncertain added safety.RESULTSA broad inventory of concerns was established, including: 1) nine categories of advantages and disadvantages of candidate safety policies; 2) six kinds of difficulties in assessing risks and forecasting the effects of safety policies; 3) 13 decision‐making principles; and 4) six kinds of practical barriers hampering the translation of candidate policies into decisions.CONCLUSIONBlood safety policymaking involves a wide variety of competing concerns, and approaches to reconcile these considerations are themselves contested. Developing a systematic decision‐making approach requires ethical reflection on, among others, reasonable costs of safety and the value of transparency in public policy.
Fat removal during cell salvage: an optimized program for a discontinuous autotransfusion device
Authors: Seyfried Timo F. , Gruber Michael , Breu Anita , Aumeier Christoph , Zech Nina , Hansen Ernil 
Published: September 2015

BACKGROUNDFat in wound blood observed in orthopedic or cardiac surgery might pose a risk for fat embolism during blood salvage. Fat removal was optimized in the washing process.STUDY DESIGN AND METHODSIn an experimental study blood from fresh donations was adjusted to a hematocrit (Hct) of 25% and an admixture of 1.25% human tissue fat. This blood was processed with the cell salvage device XTRA in a modified program mode. Volumetric quantification of fat was performed after centrifugation of blood samples in Pasteur pipettes. From the volumes, the Hct levels and the concentrations of fat and other variables elimination rates and RBC recovery were calculated.RESULTSPretests showed wash volume, wash flow, and process interruptions affecting fat elimination. With the new optimized fat elimination program Pfat removal rate of fat increased to 98.5 ± 0.9% for the 225‐mL bowl. The product had a mean Hct of 48.7 ± 1.2% and a RBC recovery rate of 93.5 ± 2.3%. The program conserved the high elimination rates for albumin, heparin, potassium, and free plasma hemoglobin (98.8, 99.3, 95.3, and 94.9%, respectively). Similar high fat removal was also observed with bowls of smaller size, namely, 98.1% for the 175‐mL bowl and 98.2% for the 125‐ and the 55‐mL bowls. With test blood of Hct 10% a mean fat elimination of 99.6 ± 01% was observed.CONCLUSIONSA special program modification Pfat involving extra washing and RBC concentration steps significantly improves fat removal by the Latham bowl–based autotransfusion device XTRA, thus yielding results equivalent to the continuous cell salvage system.
Determinants of International Student Migration
Authors: Abbott Andrew , Silles Mary 
Published: September 2015

AbstractThis paper considers what factors determine the migration of overseas students, when students cross borders for higher education. We utilise a gravity model for international student mobility and derive estimates for a sample of 18 countries of destination and 38 countries of origin over the period 2005–11. Our results confirm that geographical distance and the presence of a common language are powerful in explaining bilateral student flows. Our most interesting finding is that time zone differences have a statistically significant and economically large effect in determining international student flows.
Development of a Pefloxacin Disk Diffusion Method for Detection of Fluoroquinolone-Resistant Salmonella enterica
Authors: Skov Robert , Matuschek Erika , Sjölund-Karlsson Maria , Åhman Jenny , Petersen Andreas , Stegger Marc , Torpdahl Mia , Kahlmeter Gunnar 
Published: September 2015

ABSTRACT

Fluoroquinolones (FQs) are among the drugs of choice for treatment of
Salmonella
infections. However, fluoroquinolone resistance is increasing in
Salmonella
due to chromosomal mutations in the quinolone resistance-determining regions (QRDRs) of the topoisomerase genes
gyrA
,
gyrB
,
parC
, and
parE
and/or plasmid-mediated quinolone resistance (PMQR) mechanisms including
qnr
variants,
aac
(
6
′)-
Ib-cr
,
qepA
, and
oqxAB
. Some of these mutations cause only subtle increases in the MIC, i.e., MICs ranging from 0.12 to 0.25 mg/liter for ciprofloxacin (just above the wild-type MIC of ≤0.06 mg/liter). These isolates are difficult to detect with standard ciprofloxacin disk diffusion, and plasmid-mediated resistance, such as
qnr
, is often not detected by the nalidixic acid screen test. We evaluated 16 quinolone/fluoroquinolone disks for their ability to detect low-level-resistant
Salmonella enterica
isolates that are not serotype Typhi. A total of 153
Salmonella
isolates characterized for the presence (
n
= 104) or absence (
n
= 49) of
gyrA
and/or
parC
topoisomerase mutations,
qnrA
,
qnrB
,
qnrD
,
qnrS
,
aac
(
6
′)-
Ib-cr
, or
qepA
genes were investigated. All isolates were MIC tested by broth microdilution against ciprofloxacin, levofloxacin, and ofloxacin and by disk diffusion using EUCAST or CLSI methodology. MIC determination correctly categorized all isolates as either wild-type isolates (MIC of ≤0.06 mg/liter and absence of resistance genes) or non-wild-type isolates (MIC of >0.06 mg/liter and presence of a resistance gene). Disk diffusion using these antibiotics and nalidixic acid failed to detect some low-level-resistant isolates, whereas the 5-μg pefloxacin disk correctly identified all resistant isolates. However, pefloxacin will not detect isolates having
aac
(
6
′)-
Ib-cr
as the only resistance determinant. The pefloxacin disk assay was approved and implemented by EUCAST (in 2014) and CLSI (in 2015).
Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii
Authors: Farrer Rhys A. , Desjardins Christopher A. , Sakthikumar Sharadha , Gujja Sharvari , Saif Sakina , Zeng Qiandong , Chen Yuan , Voelz Kerstin , Heitman Joseph , May Robin C. , Fisher Matthew C. , Cuomo Christina A. 
Published: September 2015

ABSTRACTCryptococcus gattiiis a fungal pathogen of humans, causing pulmonary infections in otherwise healthy hosts. To characterize genomic variation among the four major lineages ofC. gattii(VGI, -II, -III, and -IV), we generated, annotated, and compared 16de novogenome assemblies, including the first for the rarely isolated lineages VGIII and VGIV. By identifying syntenic regions across assemblies, we found 15 structural rearrangements, which were almost exclusive to the VGI-III-IV lineages. Using synteny to inform orthology prediction, we identified a core set of 87% ofC. gattiigenes present as single copies in all four lineages. Remarkably, 737 genes are variably inherited across lineages and are overrepresented for response to oxidative stress, mitochondrial import, and metal binding and transport. Specifically, VGI has an expanded set of iron-binding genes thought to be important to the virulence ofCryptococcus, while VGII has expansions in the stress-related heat shock proteins relative to the other lineages. We also characterized genes uniquely absent in each lineage, including a copper transporter absent from VGIV, which influencesCryptococcussurvival during pulmonary infection and the onset of meningoencephalitis. Through inclusion of population-level data for an additional 37 isolates, we identified a new transcontinental clonal group that we name VGIIx, mitochondrial recombination between VGII and VGIII, and positive selection of multidrug transporters and the iron-sulfur protein aconitase along multiple branches of the phylogenetic tree. Our results suggest that gene expansion or contraction and positive selection have introduced substantial variation with links to mechanisms of pathogenicity across this species complex.IMPORTANCEThe genetic differences between phenotypically different pathogens provide clues to the underlying mechanisms of those traits and can lead to new drug targets and improved treatments for those diseases. In this paper, we compare 16 genomes belonging to four highly differentiated lineages ofCryptococcus gattii, which cause pulmonary infections in otherwise healthy humans and other animals. Half of these lineages have not had their genomes previously assembled and annotated. We identified 15 ancestral rearrangements in the genome and over 700 genes that are unique to one or more lineages, many of which are associated with virulence. In addition, we found evidence for recent transcontinental spread, mitochondrial genetic exchange, and positive selection in multidrug transporters. Our results suggest that gene expansion/contraction and positive selection are diversifying the mechanisms of pathogenicity across this species complex.
P1: Competing in the Broadband Service Industry
Authors: Said Mohd Fuaad , Adham Khairul Akmaliah 
Published: September 2015

In 2008, Packet One Networks (Malaysia) Sdn. Bhd., or P1, launched its Worldwide Interoperability for Microwave Access (WiMAX) service, P1W1MAX, in Kuala Lumpur. This event kicked off the company's pioneering effort to provide Malaysians with WiMAX wireless broadband access, which it promised to be a better alternative to the current wired and 3G broadband offerings. Within a year, it had built a customer base of about 80,000 subscribers, and achieved an average revenue per user of about RM89 (approximately US$30). One year later, the company rolled out its Sudah Potong (Cut Already) marketing campaign and by the end of 2010, it had gathered about 280,000 customers and its ARPU of RM72 was among the highest in the industry. P1's five-year, three-phase plan (2007–2012) involving an investment of RM1 billion (about US$330 million) for the development of its WiMAX services, aimed to reach 65% area coverage throughout Malaysia by 2012. In December 2010, it announced its goal to increase its customer base to 450,000 by the end of 2011 to achieve its planned break-even. These efforts, however, attracted increased attention from the public, and even more so from its industry rivals, which reacted aggressively to P1's expansion. P1's top management knew that the company needed to act quickly, especially since the company's breakeven target date had reportedly been deferred several times. This case provides a scenario that can stimulate discussion on business strategies to be pursued by the top management of a growing firm operating in a very competitive industry.
Caffé Bene Disrupts the Stagnating Korean Coffee Shop Market
Authors: Park Kiwan , Jun Sunghee , Han Jerry Jisang , Lee Jiyoung , Kim Hwain , Kim Joonkyung 
Published: September 2015

Caffé Bene was founded in 2007, during which the coffee shop market in Korea had been experiencing rapid growth. Caffé Bene had to compete with existing brands, including Starbucks, The Coffee Bean and Tea Leaf, and other coffee shop chains native to Korea. Sun-Kwon Kim, the founder and current CEO of Caffé Bene, tried to differentiate his brand on the basis of a new concept of European ambience mixed with Korean culture, new and localized menus, and celebrity endorsements; all of which were unheard of in the retail coffee industry at that time. This novel approach allowed Caffé Bene to gain great popularity in a short period of time. Despite its extraordinary success, however, Caffé Bene faced numerous challenges, including managerial issues caused by excessive expansion and rapid growth, dilution of differentiation as a result of new entrants that mimicked Caffé Bene's unique strategies, and an overall sluggish growth rate in the coffee shop market. In this case, the challenges that Caffé Bene faced and the strategies it employed to successfully deal with them are discussed.
ΔNp63α Promotes Breast Cancer Cell Motility through the Selective Activation of Components of the Epithelial-to-Mesenchymal Transition Program
Authors: Dang Tuyen T. , Esparza Matthew A. , Maine Erin A. , Westcott Jill M. , Pearson Gray W. 
Published: September 2015

Abstract
Cell identity signals influence the invasive capability of tumor cells, as demonstrated by the selection for programs of epithelial-to-mesenchymal transition (EMT) during malignant progression. Breast cancer cells retain canonical epithelial traits and invade collectively as cohesive groups of cells, but the signaling pathways critical to their invasive capabilities are still incompletely understood. Here we report that the transcription factor ΔNp63α drives the migration of basal-like breast cancer (BLBC) cells by inducing a hybrid mesenchymal/epithelial state. Through a combination of expression analysis and functional testing across multiple BLBC cell populations, we determined that ΔNp63α induces migration by elevating the expression of the EMT program components Slug and Axl. Interestingly, ΔNp63α also increased the expression of miR-205, which can silence ZEB1/2 to prevent the loss of epithelial character caused by EMT induction. In clinical specimens, co-expression of various elements of the ΔNp63α pathway confirmed its implication in motility signaling in BLBC. We observed that activation of the ΔNp63α pathway occurred during the transition from noninvasive ductal carcinoma in situ to invasive breast cancer. Notably, in an orthotopic tumor model, Slug expression was sufficient to induce collective invasion of E-cadherin–expressing BLBC cells. Together, our results illustrate how ΔNp63α can drive breast cancer cell invasion by selectively engaging promigratory components of the EMT program while, in parallel, still promoting the retention of epithelial character. Cancer Res; 75(18); 3925–35. ©2015 AACR.
Comparison of the Abilities of Summary Measures of International Normalized Ratio Control to Predict Clinically Relevant Bleeding
Authors: Rose Adam J. , Delate Thomas , Ozonoff Al , Witt Daniel M. 
Published: September 2015

Background—
Limited research has compared the measures of summarizing international normalized ratio (INR) control over time. Measures that are more predictive of patient outcomes would be preferred as would those that are easier to calculate and understand.

Methods and Results—
We examined 676 patients who received long-term warfarin therapy to treat atrial fibrillation: 125 patients who experienced major hemorrhage and 551 matched controls who did not. Patient INR control was characterized using various measures, from simple (proportion of INR values in range) to complex (eg, area under the curve above target range, squared) measures. Conditional logistic regression was used to examine the ability of each measure to predict the outcome of clinically relevant bleeding across quintiles of control. All measures were associated with clinically relevant bleeding to some extent: patients with the poorest control had significantly more bleeding events compared with patients with the best control. The measure most strongly associated with bleeding was a combination of percent time in therapeutic range and INR variability (odds ratio of 4.34, comparing the lowest to the highest quintiles of control). The strongest single predictor was INR variability, followed closely by time in therapeutic range. More computationally complex measures, which had been expected to perform better, were not so strongly associated with bleeding.

Conclusions—
INR variability was the most strongly associated predictor of clinically relevant bleeding followed closely by time in therapeutic range. Using both measures together had an even stronger association. These findings support continued use of INR variability, time in therapeutic range, or both for research and quality assurance efforts.
Differential Vascular Pathophysiologic Types of Intracranial Atherosclerotic Stroke
Authors: Ryoo Sookyung , Lee Mi Ji , Cha Jihoon , Jeon Pyoung , Bang Oh Young 
Published: September 2015

Background and Purpose—
Intracranial atherosclerotic stroke (ICAS) has various stroke mechanisms, including branch occlusive disease (BOD), subcortical infarcts caused by parent arterial disease occluding the perforator’s orifice, and non-BOD, infarcts beyond the subcortical area caused by artery-to-artery embolism. To test whether these 2 types of ICAS had different vascular pathophysiologies, we compared the high-resolution magnetic resonance imaging characteristics between BOD and non-BOD ICAS.

Methods—
Eighty patients with acute infarcts caused by ICAS of proximal middle cerebral artery or basilar artery without carotid/cardiac embolic sources or nonatherosclerotic causes were enrolled (36 BOD and 44 non-BOD patients). The steno-occlusive intracranial artery at the maximal stenosis was analyzed for vascular remodeling and wall enhancement.

Results—

BOD had distinct radiological features in terms of vascular morphology and enhancement. BOD showed a milder stenosis than non-BOD (
P
<0.001). Positive remodeling was more frequently observed in non-BOD than in BOD (
P
=0.005). Wall area index was also lower in BOD. Plaque enhancement was observed in all but one non-BOD patient and in one fourth of BOD patients (
P
=0.003). Although both types showed an eccentric enhancement, this enhancement was more frequently distributed in the BOD group on the side where the perforators arose. As the number of asymptomatic intracranial stenosis increased, the degree of stenosis (rho=0.513,
P
=0.003) increased in the BOD group, whereas enhanced plaque area (rho=0.343,
P
=0.030) increased in the non-BOD group.

Conclusions—
Our data indicate that BOD is a common and unique form of ICAS, distinct from non-BOD. These 2 types of ICAS have different vascular pathophysiologies in terms of vascular remodeling and plaque characteristics.
Synopsis of the genus Pharaonus (Coleoptera: Scarabaeidae: Rutelinae), <br />with descriptions of new taxa
Authors: KEITH DENIS , SABATINELLI GUIDO , ULIANA MARCO 
Published: September 2015

An overview of the genus Pharaonus Blanchard, 1851 is presented. Pharaonus farsensis new species and P. adelphus new species are described from Iran, P. lederi turcmenius Ohaus, 1941 is recognized as new synonym of P. lederi (Reitter, 1888), and the subgenus Tamerlanius new subgenus is proposed for the two central-Asian species. New distribution records and systematic notes are presented: P. caucasicus (Reitter, 1888) is removed from the fauna of Iran and P. varicoloreus (Burmeister, 1844) from that of Israel; P. fasciculatus (Burmeister, 1844) is reported for the first time from Israel, P. semenowi (Reitter, 1888) from Tajikistan. All known species are illustrated and a key to species is presented.
A Multiresolution Approach to Estimating the Value Added by Regional Climate Models
Authors: Parker Ryan J. , Reich Brian J. , Sain Stephan R. 
Published: September 2015

Abstract
Climate models have emerged as an essential tool for studying the earth’s climate. Global models are computationally expensive, and so a relatively coarse spatial resolution must be used within the model. This hinders direct application for many impacts studies that require regional and local climate information. A regional model with boundary conditions taken from the global model achieves a finer spatial scale for local analysis. In this paper the authors propose a new method for assessing the value added by these higher-resolution models, and they demonstrate the method within the context of regional climate models (RCMs) from the North American Regional Climate Change Assessment Program (NARCCAP) project. This spectral approach using the discrete cosine transformation (DCT) is based on characterizing the joint relationship between observations, coarser-scale models, and higher-resolution models to identify how the finer scales add value over the coarser output. The joint relationship is computed by estimating the covariance of the data sources at different spatial scales with a Bayesian hierarchical model. Using this model the authors can then estimate the value added by each data source over the others. For the NARCCAP data, they find that the higher-resolution models add value starting with low wavenumbers corresponding to features 550 km apart (or 11 total 50-km grid boxes per cycle) all the way down to higher wavenumbers at 150 km apart (3 grid boxes per cycle).