bluuebunny/crossref_metadata_2025 huggingface dataset:
Pulmonary Pressure Assessment with the Total Artificial Heart
Authors: Joyce David L. , Redfield Margaret M. , Kushwaha Sudhir S. , Behfar Atta , Borlaug Barry A. , Daly Richard C. , Sandhu Gurpreet S. , Joyce Lyle D.
Published: July 2017

Reversal of pulmonary hypertension has been observed in patients during a bridge to transplant with a left ventricular assist device. Total artificial heart (TAH) implant prevents subsequent right heart catheterization. Consequently, controversy exists over whether the prosthetic right ventricle improves or exacerbates pulmonary hypertension. A pulmonary artery (PA) pressure monitor was placed in two patients undergoing TAH implant, as a bridge to transplant. One patient had pulmonary hypertension at implant; the other had normal pulmonary pressures. Daily measurements were taken of systolic, diastolic, and mean PA pressures throughout support. Patient 1 received successful transplant after TAH support of 91 days. Systolic/diastolic (mean) PA pressures steadily decreased from 55/39 (28) mm Hg at implant to 29/18 (7) mm Hg currently. Patient 2 received support for 101 days before death due to abdominal ischemic complications. Pulmonary arterial pressures stayed consistent throughout this period, from 26/17 (20) mm Hg at implant to 23/13 (17) mm Hg at the time of death. These findings suggest that an implantable PA pressure monitor may be useful in optimizing hemodynamics and planning appropriate timing of transplant with TAH support.
The Marginal Costs of Adverse Drug Events Associated With Exposures to Anticoagulants and Hypoglycemic Agents During Hospitalization
Authors: Spector William D. , Limcangco Rhona , Furukawa Michael F. , Encinosa William E.
Published: July 2017

Background:

Anticoagulants and hypoglycemic agents are 2 of the most challenging drug classes for medical management in the hospital resulting in many adverse drug events (ADEs).

Objective:

Estimating the marginal cost (MC) of ADEs associated with anticoagulants and hypoglycemic agents for adults in 5 patient groups during their hospital stay and the total annual ADE costs for all patients exposed to these drugs during their stay.

Research Design and Subject:

Data are from 2010 to 2013 Healthcare Cost and Utilization Project (HCUP) State Inpatient Databases and Medicare Patient Safety Monitoring System (MPSMS). Deidentified patients were linked using probabilistic matching in the same hospital and year for 5 patient groups. ADE information was obtained from the MPSMS using retrospective structured record review. Costs were derived using HCUP cost-to-charge ratios. MC estimates were made using Extended Estimating Equations controlling for patient characteristics, comorbidities, hospital procedures, and hospital characteristics. MC estimates were applied to the 2013 HCUP National Inpatient Sample to estimate annual ADE costs.

Results:

Adjusted MC estimates were smaller than unadjusted measures with most groups showing estimates that were at least 50% less. Adjusted anticoagulant ADE costs added >45% and Hypoglycemic ADE costs added >20% to inpatient costs. The 2013 hospital cost estimates for ADEs associated with anticoagulants and hypoglycemic agents were >$2.5 billion for each drug class.

Conclusions:

This study demonstrates the importance of accounting for confounders in the estimation of ADEs, and the importance of separate estimates of ADE costs by drug class.
Prediction of Orthokeratology Lens Decentration with Corneal Elevation
Authors: Chen Zhi , Xue Feng , Zhou Jiaqi , Qu Xiaomei , Zhou Xingtao
Published: July 2017

SIGNIFICANCE

Lens decentration is common and unavoidable to some extent during ortho-k treatment. By using a simplified method, we are able to predict the magnitude and direction of ortho-k lens decentration, which provides useful insights in screening for ideal ortho-k candidates and to make a quick decision when decentration happens.

PURPOSE

The aim of this study was to investigate the influence of corneal elevation asymmetry on ortho-k lens decentration.

METHODS

Thirty-six eyes of 36 subjects were fitted with four-curve reverse geometry ortho-k contact lenses. Corneal topography was collected before and 1 month after ortho-k lens wear. The difference in corneal elevation at the 8-mm chord of the respective two principal meridians of corneal astigmatism was calculated. Vector analyses were performed on these differences to calculate the magnitude and direction of a vector (corneal asymmetry vector). The relationship between the angle and magnitude of corneal asymmetry vector and lens decentration was analyzed.

RESULTS

Baseline refractive sphere and cylinder for the 36 tested eyes were −2.84 ± 1.04 diopters (D) (range, −4.75 to −1.00 D) and −0.21 ± 0.28 D (range, −1.00 to 0 D), respectively. The mean magnitude of lens decentration was 0.72 ± 0.26 mm (0 to 1.34 mm). For overall displacement, inferotemporal decentration was the most common as observed in 24 eyes (67%). The mean angle of the corneal asymmetry vector (202 ± 39 degrees) was significantly correlated to the mean angle of lens decentration (200 ± 39 degrees) (r = 0.76, P < .001). The magnitude of corneal asymmetry vector significantly contributed to the magnitude of lens decentration (standardized β = 0.448, P = .002) whereas the other tested variables did not affect lens decentration (all P > .05).

CONCLUSIONS

Lens decentration is a common phenomenon in ortho-k that mostly happens toward the inferotemporal quadrant of the cornea. The magnitude and direction of lens decentration are predetermined by paracentral corneal asymmetry.
The Influence of Chloride for the Interpretation of Plasma Bicarbonate During the Treatment of Diabetic Ketoacidosis
Authors: Ferreira Juan Pablo , Hamui Magali , Torrents Milagros , Carrano Romina , Ferraro Mabel , Toledo Ismael
Published: July 2017

Introduction

Hyperchloremic metabolic acidosis can occur in diabetic ketoacidosis (DKA) and may affect the acid-base interpretation during treatment.

Objectives

This study aims to describe the prevalence of hyperchloremia during the treatment of DKA and its effect on the interpretation of bicarbonate value.

Methods

A cross-sectional study, including all cases of DKA in patients aged 1 to 18 years old admitted from 2010 to 2015, was performed. Laboratory tests were performed on admission (baseline), 2 and 6 hours after admission, and when resolution of DKA was achieved. Adjusted bicarbonate value was calculated using regression equations.

Results

Seventy-nine DKA episodes were included. The average age was 13.3 ± 3.8 years. Baseline levels were as follows: plasma glucose, 479 ± 133 mg/dL; pH 7.1 ± 0.083; bicarbonate, 9.65 ± 2.9; and anion gap, 23.9 ± 7.5. The time to achieve resolution of DKA was 12.2 ± 4.4 hours, and the decrease in capillary glucose was 25.5 (19.7–38.2) mg/dL per hour. After 6 hours of treatment, the proportion of patients presenting hyperchloremia increased from 23% to 77%. By using adjusted bicarbonate, the percentage of patients achieving resolution of DKA after 6 hours of treatment would have been 35.4% (confidence interval 95%, 28–49), in comparison with 24.1% (confidence interval 95%, 18–37) using observed bicarbonate (P = 0.004).

Conclusions

The hyperchloremia developed during the treatment of DKA could modify the value of measured plasma bicarbonate concentration and unnecessarily prolong the initial phase of treatment.
Evaluation of Gadolinium Retention After Serial Administrations of a Macrocyclic Gadolinium-Based Contrast Agent (Gadobutrol)
Authors: Yoo Roh-Eul , Sohn Chul-Ho , Kang Koung Mi , Yun Tae Jin , Choi Seung Hong , Kim Ji-hoon , Park Sun-Won
Published: July 2017

Objective

There has been controversy as to whether gadobutrol, one of the widely used macrocyclic gadolinium-based contrast agents, can lead to gadolinium retention after serial injections. Our aim was to validate whether serial administrations of gadobutrol can cause signal increase in the dentate nucleus (DN) and globus pallidus (GP) on unenhanced T1-weighted magnetic resonance (MR) images due to gadolinium retention.

Materials and Methods

A total of 189 patients who had undergone at least 2 contrast-enhanced MR scans using only gadobutrol between August 2009 and August 2016 were retrospectively included. The DN–to–pons and GP-to-thalamus signal intensity (SI) ratio differences on unenhanced T1-weighted MR images were calculated by subtracting the SI ratios at the first MR images from those at the last MR images. One-sample t tests were used to evaluate whether the SI ratio differences differed from 0. Linear regression and Pearson correlations were performed to assess correlations between SI ratio differences and various confounding variables, including the number of MR scans, mean time interval between MR scans, age, sex, history of radiation therapy or chemotherapy, and renal and liver functions.

Results

Patients underwent a mean of 5.9 ± 6.3 contrast-enhanced MR scans with a mean interval of 42.8 ± 49.5 weeks between the scans. Sixty-three patients underwent 6 or more MR scans, whereas 126 patients underwent fewer than 6 MR scans. Neither the DN-to-pons SI nor the GP-to-thalamus SI ratio differences differed significantly from 0, with mean values of −0.012 ± 0.115 (P = 0.148) and 0.012 ± 0.111 (P = 0.126), respectively.

Conclusions

Serial administrations of gadobutrol did not result in signal increases in the DN or GP on unenhanced T1-weighted MR images due to gadolinium retention.
Specialist Physicians’ Attitudes and Practice Patterns Regarding Disclosure of Pre-referral Medical Errors
Authors: Dossett Lesly A. , Kauffmann Rondi M. , Lee Jay S. , Singh Harkamal , Lee M. Catherine , Morris Arden M. , Jagsi Reshma , Quinn Gwendolyn P. , Dimick Justin B.
Published: July 2017

Objective:

Our objective was to determine specialist physicians’ attitudes and practices regarding disclosure of pre-referral errors.

Summary Background Data:

Physicians are encouraged to disclose their own errors to patients. However, no clear professional norms exist regarding disclosure when physicians discover errors in diagnosis or treatment that occurred at other institutions before referral.

Methods:

We conducted semistructured interviews of cancer specialists from 2 National Cancer Institute-designated Cancer Centers. We purposively sampled specialists by discipline, sex, and experience-level who self-described a >50% reliance on external referrals (n = 30). Thematic analysis of verbatim interview transcripts was performed to determine physician attitudes regarding disclosure of pre-referral medical errors; whether and how physicians disclose these errors; and barriers to providing full disclosure.

Results:

Participants described their experiences identifying different types of pre-referral errors including errors of diagnosis, staging and treatment resulting in adverse events ranging from decreased quality of life to premature death. The majority of specialists expressed the belief that disclosure provided no benefit to patients, and might unnecessarily add to their anxiety about their diagnoses or prognoses. Specialists had varying practices of disclosure including none, non-verbal, partial, event-dependent, and full disclosure. They identified a number of barriers to disclosure, including medicolegal implications and damage to referral relationships, the profession's reputation, and to patient–physician relationships.

Conclusions:

Specialist physicians identify pre-referral errors but struggle with whether and how to provide disclosure, even when clinical circumstances force disclosure. Education- or communication-based interventions that overcome barriers to disclosing pre-referral errors warrant development.
Idiopathic Intracranial Hypertension Progressing to Venous Sinus Thrombosis, Subarachnoid Hemorrhage, and Stroke
Authors: Hardin Joshua S. , Ramakrishnaiah Raghu H. , Pemberton John D. , Phillips Paul H. , Chacko Joseph G.
Published: July 2017

Idiopathic intracranial hypertension (IIH) is a syndrome characterized by increased intracranial pressure (ICP), the absence of structural lesions on neuroimaging, and normal cerebrospinal fluid composition. Cerebral venous sinus thrombosis (CVST) is a common cause of increased ICP and can be differentiated from IIH with magnetic resonance venography. We describe a young woman with typical IIH who underwent lumbar puncture and was treated with a short course of high-dose corticosteroids followed by acetazolamide. She subsequently developed CVST, subarachnoid hemorrhage, and stroke. Risk factors that may have resulted in CVST are discussed.
Frustration across the periodic table: heterolytic cleavage of dihydrogen by metal complexes
Authors: Bullock R. Morris , Chambers Geoffrey M.
Published: July 2017

This perspective examines frustrated Lewis pairs (FLPs) in the context of heterolytic cleavage of H
2
by transition metal complexes, with an emphasis on molecular complexes bearing an intramolecular Lewis base. FLPs have traditionally been associated with main group compounds, yet many reactions of transition metal complexes support a broader classification of FLPs that includes certain types of transition metal complexes with reactivity resembling main group-based FLPs. This article surveys transition metal complexes that heterolytically cleave H
2
, which vary in the degree that the Lewis pairs within these systems interact. Many of the examples include complexes bearing a pendant amine functioning as the base with the metal functioning as the hydride acceptor. Consideration of transition metal compounds in the context of FLPs can inspire new innovations and improvements in transition metal catalysis.

This article is part of the themed issue ‘Frustrated Lewis pair chemistry’.
Attempted synthesis of
ortho
-phenylene phosphino-tritylium cations
Authors: Chansaenpak Kantapat , Yang Mengxi , Gabbaï François P.
Published: July 2017

With the synthesis of
ortho
-phenylene phosphino-tritylium cations as an objective, we generated (2-lithiophenyl)diphenylphosphine and (2-lithiophenyl)di-isopropylphosphine and allowed these organolithium reagents to react with benzophenone. The resulting phosphino-triarylcarbinols were allowed to react with HBF
4
in the presence of trifluoroacetic anhydride in order to generate the corresponding cations. Instead of the targeted
ortho
-phenylene phosphino-tritylium, the cations formed in these reactions were identified as the four-membered phosphonium species 7,7-bis(phenyl)-8,8-bis(phenyl)-7-phosphoniabicyclo[4.2.0]octa-1,3,5-triene (
3
+
) and 7,7-bis(phenyl)-8,8-bis(isopropyl)-7-phosphoniabicyclo[4.2.0]octa-1,3,5-triene (
4
+
), which were both isolated as tetrafluoroborate salts. The structure of these compounds has been confirmed by X-ray analysis. These new cations are thermally unstable and isomerize into the corresponding 5,10-dihydro-5,5-diphenyl-10-phenyl-acridophosphinium (
5
+
) and 5,10-dihydro-5,5-di(isopropyl)-10-phenyl-acridophosphinium (
6
+
) as tetrafluoroborate salts. These reactions suggest the involvement of
ortho
-phenylene phosphino-tritylium cations, which would be obtained by dissociation of the R
3
P
+
–CAr
3
bonds in
4
+
and
5
+
.

This article is part of the themed issue ‘Frustrated Lewis pair chemistry’.
Halogenated triphenylgallium and -indium in frustrated Lewis pair activations and hydrogenation catalysis
Authors: Xu Maotong , Possart Josephine , Waked Alexander E. , Roy Julie , Uhl Werner , Stephan Douglas W.
Published: July 2017

The Lewis acids Ga(C
6
F
5
)
3
, In(C
6
F
5
)
3
and Ga(C
6
Cl
5
)
3
are prepared and their Lewis acidity has been probed experimentally and computationally. The species Ga(C
6
F
5
)
3
and In(C
6
F
5
)
3
in conjunction with phosphine donors are shown to heterolytically split H
2
and catalyse the hydrogenation of an imine. In addition, frustrated Lewis pairs (FLPs) derived from Ga(C
6
F
5
)
3
and In(C
6
F
5
)
3
and phosphines react with diphenyldisulfide to phosphoniumgallates or indates of the form [
t
Bu
3
PSPh][PhSE(C
6
F
5
)
3
] and [
t
Bu
3
PSPh][(μ-SPh)(E(C
6
F
5
)
3
)
2
] (E = Ga, In). The potential of the FLPs based on Ga(C
6
F
5
)
3
, In(C
6
F
5
)
3
and Ga(C
6
Cl
5
)
3
and phosphines is also shown in reactions with phenylacetylene to give pure or mixtures of the products [
t
Bu
3
PH][PhCCE(C
6
X
5
)
3
] and R
3
P(Ph)C=C(H)E(C
6
X
5
)
3
. A number of these species are crystallographically characterized. The implications for the use of these species in FLP chemistry are considered.

This article is part of the themed issue ‘Frustrated Lewis pair chemistry’.
The CURE for Cultivating Fastidious Microbes
Authors: Bakshi Arundhati , Webber Austen T. , Patrick Lorelei E. , William Wischusen E. , Cameron Thrash J.
Published: July 2017

Course-based Undergraduate Research Experiences (CUREs) expand the scientific educational benefits of research to large groups of students in a course setting. As part of an ongoing effort to integrate CUREs into first-year biology labs, we developed a microbiology CURE (mCURE) that uses a modified dilution-to-extinction high throughput culturing protocol for isolating abundant yet fastidious aquatic bacterioplankton during one semester. Students learn common molecular biology techniques like nucleic acid extraction, PCR, and molecular characterization; read and evaluate scientific literature; and receive training in scientific communication through written and oral exercises that incorporate social media elements. In the first three semesters, the mCUREs achieved similar cultivability success as implementation of the protocol in a standard laboratory setting. Our modular framework facilitates customization of the curriculum for use in multiple settings and we provide classroom exercises, assignments, assessment tools, and examples of student output to assist with implementation.
beachmat: a Bioconductor C++ API for accessing single-cell genomics data from a variety of R matrix types
Authors: Lun Aaron T. L. , Pagès Hervé , Smith Mike L.
Published: July 2017

Recent advances in single-cell RNA sequencing have dramatically increased the number of cells that can be profiled in a single experiment. This provides unparalleled resolution to study cellular heterogeneity within biological processes such as differentiation. However, the explosion of data that are generated from such experiments poses a challenge to the existing computational infrastructure for statistical data analysis. In particular, large matrices holding expression values for each gene in each cell require sparse or file-backed representations for manipulation with the popular R programming language. Here, we describe a C++ interface namedbeachmat, which enables agnostic data access from various matrix representations. This allows package developers to write efficient C++ code that is interoperable with simple, sparse and HDF5-backed matrices, amongst others. We perform simulations to examine the performance ofbeachmaton each matrix representation, and we demonstrate howbeachmatcan be incorporated into the code of other packages to drive analyses of a very large single-cell data set.
Mosquito Mapper: a phone application to map urban mosquitoes
Authors: Guilbaud Camille S.E. , Guilbaud Théophile G.D.P.V.
Published: July 2017

This paper presents mosquito mapper: an android phone application created with the goal of giving science-driven citizens the means to monitor mosquito populations in an urban environment. Mosquito mapper allows the recording of mosquito encounters as well as conditions surrounding the encounter. It also features a rudimentary identification tool. The goal of the application is to create a database and construct a map of the encounters free to consult for citizens and scientists. Such database constitutes a necessary first step for the development of useful management strategies addressing potential human health threats induced by mosquitoes. The citizen scientist may voluntarily provide other additional information on the circumstances of the encounter that may contain scientifically useful information. We describe the current features of the application, discuss their strength, limits, potential scientific value and suggest possible future extensions. The original city for which the application was developed is Berlin, Germany, but the application is coded in such a way that it is easily applicable to any urban environment.
Conformational dynamics of Cas9 governing DNA cleavage revealed by single molecule FRET
Authors: Yang Mengyi , Peng Sijia , Sun Ruirui , Lin Jingdi , Wang Nan , Chen Chunlai
Published: July 2017

Off-target binding and cleavage by Cas9 pose as major challenges in its applications. How conformational dynamics of Cas9 governs its nuclease activity under on- and off-target conditions remains largely unknown. Here, using intra-molecular single molecule fluorescence resonance energy transfer measurements, we revealed that Cas9 in apo, sgRNA-bound, and dsDNA/sgRNA-bound forms all spontaneously transits between three major conformational states, mainly reflecting significant conformational mobility of the catalytic HNH domain. We furthermore uncovered a surprising long-range allosteric communication between the HNH domain and RNA/DNA heteroduplex at the PAM-distal end to ensure correct positioning of the catalytic site, which demonstrated a unique proofreading mechanism served as the last checkpoint before DNA cleavage. Several Cas9 residues were likely to mediate the allosteric communication and proofreading step. Modulating interactions between Cas9 and heteroduplex at the distal end by introducing mutations on these sites provides an alternative route to improve and optimize the CRISPR/Cas9 toolbox.
Common patterns of gene regulation associated with Cesarean section and the development of islet autoimmunity – indications of immune cell activation
Authors: Laimighofer M. , Lickert R. , Fürst R. , Theis F. J. , Winkler C. , Bonifacio E. , Ziegler A.-G. , Krumsiek J.
Published: July 2017

Background

Birth by Cesarean section increases the risk of developing type 1 diabetes later in life; however, the underlying molecular mechanisms of this effect remain unclear. We aimed to elucidate common regulatory processes observed after Cesarean section and the development of islet autoimmunity, which precedes type 1 diabetes, by investigating the transcriptome of blood cells in the developing immune system.

Methods

We analyzed gene expression of peripheral blood mononuclear cells taken at several time points from children with increased familial and genetic risk for type 1 diabetes (n = 109). We investigated effects of Cesarean section on gene expression profiles of children in the first year of life using a generalized additive mixed model to account for the longitudinal data structure. To investigate the effect of islet autoimmunity, we compared gene expression differences between children after initiation of islet autoimmunity and age-matched children who did not develop islet autoantibodies. Finally, we compared both results to identify common regulatory patterns of Cesarean section and islet autoimmunity at the gene expression level.

Results

We identified two differentially expressed pathways in children born by Cesarean section: the pentose phosphate pathway and pyrimidine metabolism, both involved in nucleotide synthesis and cell proliferation. Islet autoantibody analysis revealed multiple differentially expressed pathways generally involved in immune processes, including both of the above-mentioned nucleotide synthesis pathways. Comparison of global gene expression signatures showed that transcriptomic changes were systematically and significantly correlated between Cesarean section and islet autoimmunity. In addition, signatures of both Cesarean section and islet autoimmunity correlated with transcriptional changes observed during activation of isolated CD4+ T lymphocytes.

Conclusions

We identified coherent gene expression signatures for Cesarean section, an early risk factor for type 1 diabetes, and islet autoantibodies positivity, an obligatory stage of autoimmune response prior to the development of type 1 diabetes. Both transcriptional signatures were correlated with changes in gene expression during the activation of CD4+ T lymphocytes, reflecting common molecular changes in immune cell activation.
Characterizing and Managing Missing Structured Data in Electronic Health Records
Authors: Beaulieu-Jones Brett K. , Lavage Daniel R. , Snyder John W. , Moore Jason H. , Pendergrass Sarah A , Bauer Christopher R.
Published: July 2017

Missing data is a challenge for all studies; however, this is especially true for electronic health record (EHR) based analyses. Failure to appropriately consider missing data can lead to biased results. Here, we provide detailed procedures for when and how to conduct imputation of EHR data. We demonstrate how the mechanism of missingness can be assessed, evaluate the performance of a variety of imputation methods, and describe some of the most frequent problems that can be encountered. We analyzed clinical lab measures from 602,366 patients in the Geisinger Health System EHR. Using these data, we constructed a representative set of complete cases and assessed the performance of 12 different imputation methods for missing data that was simulated based on 4 mechanisms of missingness. Our results show that several methods including variations of Multivariate Imputation by Chained Equations (MICE) and softImpute consistently imputed missing values with low error; however, only a subset of the MICE methods were suitable for multiple imputation. The analyses described provide an outline of considerations for dealing with missing EHR data, steps that researchers can perform to characterize missingness within their own data, and an evaluation of methods that can be applied to impute clinical data. While the performance of methods may vary between datasets, the process we describe can be generalized to the majority of structured data types that exist in EHRs and all of our methods and code are publicly available.
Profiling of accessible chromatin regions across multiple plant species and cell types reveals common gene regulatory principles and new control modules
Authors: Maher Kelsey A. , Bajic Marko , Kajala Kaisa , Reynoso Mauricio , Pauluzzi Germain , West Donnelly A. , Zumstein Kristina , Woodhouse Margaret , Bubb Kerry , Dorrity Michael W. , Queitsch Christine , Bailey-Serres Julia , Sinha Neelima , Brady Siobhan M. , Deal Roger B.
Published: July 2017

The transcriptional regulatory structure of plant genomes remains poorly defined relative to animals. It is unclear how manycis-regulatory elements exist, where these elements lie relative to promoters, and how these features are conserved across plant species. We employed the Assay for Transposase-Accessible Chromatin (ATAC-seq) in four plant species (Arabidopsis thaliana,Medicago truncatula,Solanum lycopersicum, andOryza sativa) to delineate open chromatin regions and transcription factor (TF) binding sites across each genome. Despite 10-fold variation in intergenic space among species, the majority of open chromatin regions lie within 3 kb upstream of a transcription start site in all species. We find a common set of four TFs that appear to regulate conserved gene sets in the root tips of all four species, suggesting that TF-gene networks are generally conserved. Comparative ATAC-seq profiling ofArabidopsisroot hair and non-hair cell types revealed extensive similarity as well as many cell type-specific differences. Analyzing TF binding sites in differentially accessible regions identified a MYB-driven regulatory module unique to the hair cell, which appears to control both cell fate regulators and abiotic stress responses. Our analyses revealed common regulatory principles among species and shed light on the mechanisms producing cell type-specific transcriptomes during development.
Diagnostic and Prognostic Implications of Ribosomal Protein Transcript Coordination in Human Cancers
Authors: Dolezal James M. , Dash Arie P. , Prochownik Edward V.
Published: July 2017

Ribosomes, the organelles responsible for the translation of mRNA, are comprised of rRNA and ~80 ribosomal proteins (RPs). Although canonically assumed to be maintained in equivalent proportions, some RPs have been shown to possess differential expression across tissue types. Dysregulation of RP expression occurs in a variety of human diseases, notably in many cancers, and altered expression of some RPs correlates with different tumor phenotypes and patient survival. To investigate the impact of global RP transcript (RPT) expression patterns on tumor phenotypes, we analyzed RPT expression of ~10,000 human tumors and 700 normal tissues witht-distributed stochastic neighbor embedding (t-SNE). We show here that normal tissues and cancers possess readily discernible RPT expression patterns. In tumors, this patterning is distinct from normal tissues, distinguishes tumor subtypes from one another, and in many cases correlates with molecular, pathological, and clinical features, including survival. Collectively, RPT expression can be used as a powerful and novel method of tumor classification, offering a potential clinical tool for prognosis and therapeutic stratification.
The IFN response in bat cells consists of canonical and non-canonical ISGs with unique temporal expression kinetics
Authors: De La Cruz-Rivera Pamela C. , Kanchwala Mohammed , Liang Hanquan , Kumar Ashwani , Wang Lin-Fa , Xing Chao , Schoggins John W.
Published: July 2017

Bats are reservoirs for a number of highly pathogenic zoonotic viruses, yet they remain relatively asymptomatic during infection. Whether this viral resistance is due to a unique innate immune system is unknown. An evolutionarily conserved feature of vertebrate antiviral immunity is the interferon (IFN) response, which triggers cellular defenses through interferon-stimulated gene (ISG) expression. While bats encode an intact IFN system, global ISG expression patterns in bat cells are not well characterized. Here, we used RNA-Seq to assess the transcriptional response to IFNα in cells derived from the batPteropus alecto(black flying fox). We show induction of more than 100 transcripts, most of which are canonical ISGs observed in other species. Kinetic gene profiling revealed thatP. alectoISGs fall into two unique temporal subclusters with similar early induction kinetics but distinct late-phase declines. In contrast to bat ISGs, human ISGs generally remained elevated for longer periods following IFN treatment, suggesting host-based differences in gene regulatory mechanisms. Notably, we also identified a small group of non-canonical bat ISGs, including an enzymatically active RNASEL that plays a role in controlling viral infection. These studies provide insight into the innate immune response of an important viral reservoir and lay a foundation for studies into the immunological features that may underlie unique virus-host relationship in bats.

Significance Statement

Bats are considered unique in their ability to resist disease caused by viruses that are often pathogenic in humans. While the nature of this viral resistance is unknown, genomic data suggest bat innate immune systems may be specialized in controlling these disease-causing viruses. A critical cell intrinsic antiviral defense system in vertebrates is the interferon response, which suppresses viral infection through induction of hundreds of interferon-stimulated genes (ISGs). In this study, we report the repertoire of ISGs and several unique features of ISG induction kinetics in bat cells. We also characterize induction and antiviral activity of bat RNASEL, which is induced by IFN in bat, but not human cells. These studies lay the foundation for discovery of potentially new antiviral mechanisms in bats, which may spur research into development of therapies to combat viral infection.
Prop-2-ynyl 2-oxo-1-(prop-2-ynyl)-1,2-dihydroquinoline-4-carboxylate
Authors: Filali Baba Yassir , Kandri Rodi Youssef , Jasinski Jerry P. , Kaur Manpreet , Ouzidan Younes , Essassi El Mokhtar
Published: July 2017

In the title compound, C16H11NO3, the dihedral angles between the mean planes of the quinolone ring system and the prop-2-ynyl and carboxyprop-2-ynyl groups are 87.9 (8) and 41.6 (8)°, respectively. In the crystal, a weak C—H...O interaction links the molecules into chains along the c-axis direction and weak π–π stacking interactions further stabilize the crystal packing.
Effective use of human physiological metrics to evaluate website usability
Authors: Qu Qing-Xing , Guo Fu , Duffy Vincent G.
Published: July 2017

Purpose

The evaluation of website usability is the precondition and a critical step for website design and optimization. The purpose of this paper is to investigate and provide empirical evidence of the interrelationships between human physiological metrics and website usability. This study examines how eye-movement metrics and heart rate variability (HRV) evaluate website usability, and then affect users’ online surfing behavior.

Design/methodology/approach

A physiological measurement experiment is designed to collect participants’ physiological metrics. This paper proposes an objective measurement model for website usability, and partial least squares is used to analyze the measurement and structural models, based on data collected from 200 participants who had experienced online surfing at least four times.

Findings

The analysis supports partially or fully 28 of the 31 hypotheses formulated. The study reveals that human physiological metrics (i.e. fixation duration, fixation count, blink count, HRV) have a strong explanatory ability for website usability.

Research limitations/implications

Data for this study were collected only from mainland China. Therefore, participants may have been influenced by Chinese cultures. The generalizability of this study may be enhanced by collecting data from more diverse samples and validating the model on different cultures.

Originality/value

This study contributes significantly to the industry by providing empirical evidence of the interrelationship between human physiological metrics and website usability. The findings also provide managers with valuable insight into better understanding of the nature of these interrelationships.
An exploratory study of health scientists’ data reuse behaviors
Authors: Joo Soohyung , Kim Sujin , Kim Youngseek
Published: July 2017

Purpose

The purpose of this paper is to examine how health scientists’ attitudinal, social, and resource factors affect their data reuse behaviors.

Design/methodology/approach

A survey method was utilized to investigate to what extent attitudinal, social, and resource factors influence health scientists’ data reuse behaviors. The health scientists’ data reuse research model was validated by using partial least squares (PLS) based structural equation modeling technique with a total of 161 health scientists in the USA.

Findings

The analysis results showed that health scientists’ data reuse intentions are driven by attitude toward data reuse, community norm of data reuse, disciplinary research climate, and organizational support factors. This research also found that both perceived usefulness of data reuse and perceived concern involved in data reuse have significant influences on health scientists’ attitude toward data reuse.

Research limitations/implications

This research evaluated its newly proposed research model based on the theory of planned behavior using a sample from the community of scientists’ scholar database. This research showed an overall picture of how attitudinal, social, and resource factors influence health scientists’ data reuse behaviors. This research is limited due to its sample size and low response rate, so this study is considered as an exploratory study rather than a confirmatory study.

Practical implications

This research suggested for health science research communities, academic institutions, and libraries that diverse strategies need to be utilized to promote health scientists’ data reuse behaviors.

Originality/value

This research is one of initial studies in scientific data reuse which provided a holistic map about health scientists’ data sharing behaviors. The findings of this study provide the groundwork for strategies to facilitate data reuse practice in health science areas.
Simultaneous relationship between performance and executive compensation of Thai non-financial firms
Authors: Buachoom Wonlop
Published: July 2017

Purpose

The purpose of this paper is to determine the two-direction relationship between financial firm performance and executive compensation in Thai listed companies; that is, effect of firm performance on executive compensation and the effect of executive compensation on subsequent firm performance. In investigating the relationship, governance, firm-specific and human capital characteristics, which should influence on the pay-performance system, are also considered. This study helps to shape an understanding of the effectiveness of the incentive system in the Thai context.

Design/methodology/approach

The System GMM, with concern about the endogeneity problem of the simultaneous relationship, is applied to examine the relationship between firm performance and executive compensation. The samples to investigate this relationship composed of 5,139 firm-years observations for 15 years from the years 2000 to 2014 of 432 non-financial firms in the Thai stock market.

Findings

The empirical evidence reveals simultaneous relationship between performance and executive compensation in Thai stock market. It shows that compensation of executives in Thai firms corresponds to firm performance, and compensation of executives leads to an improvement in subsequent performance of Thai listed firms. Moreover, some corporate governance mechanisms and human capital of executives also revealed their particular effects on setting of the pay for performance system in Thailand.

Originality/value

This study confirms that the pay for performance system is applicable in Thailand. Furthermore, the empirical results of this study highlight effects of some governance and human capital characteristics on setting of the pay-performance system. Thus, this study should be a part of the growing body of literature in this area.
Political connections, corporate governance, and tax aggressiveness in Malaysia
Authors: Abdul Wahab Effiezal Aswadi , Ariff Akmalia M. , Madah Marzuki Marziana , Mohd Sanusi Zuraidah
Published: July 2017

Purpose

The purpose of this paper is to examine the relationship between political connections and corporate tax aggressiveness in Malaysia. In addition, this paper investigates the relationship between corporate governance variables and corporate tax aggressiveness. Next, the study investigates the mitigating role of corporate governance in the relationship between political connections and corporate tax aggressiveness.

Design/methodology/approach

The sample of this study is based on 2,538 firm-year observations during the 2000-2009 periods. This study employs a panel least square regression with both period and industry fixed effects. The study retrieved the corporate governance variables from the downloaded annual reports, whilst the remaining data were collected from Compustat Global.

Findings

This study finds that politically connected firms are more tax aggressive than non-connected firms. Furthermore, the study finds that large board size decreases the likelihood of tax aggressiveness and a non-linear relationship exists between institutional ownership and tax aggressiveness suggesting increase in monitoring as the ownership increases. However, the study finds no evidence to suggest that corporate governance mitigates the influence of political connections in promoting tax aggressiveness behavior. The findings suggest that the impact of political connections could outweigh the benefits of changes in corporate governance in Malaysia.

Research limitations/implications

The data are not recent, but it reflects a rather longitudinal research period.

Originality/value

This paper extends the literature of tax research in Malaysia which is in its’ infancy stage. Furthermore, it investigates the role of political connections in tax-planning research.
Does recycling improve information usefulness of income? The case of Japan
Authors: Frendy  , Semba HU Dan
Published: July 2017

Purpose

The Accounting Standards Board of Japan (ASBJ) proposed a new set of endorsed International Financial Reporting Standards in June 2015. ASBJ claims that non-recycling of other comprehensive income (OCI) items decreases the information usefulness of earnings in a proposed comprehensive income standard. There has been no existing empirical evidence which supports the ASBJ’s statement and the purpose of the study is to test whether OCI recycling improves information usefulness of net income from six perspectives: relative and incremental value relevance, persistence, variability, operating cash flow and net income predictive power.

Design/methodology/approach

This paper is an empirical work using a listed Japanese firms sample of 5,385 firm-years from fiscal year 2012-2014.

Findings

The results challenge the ASBJ’s claim that recycling improves the general information usefulness characteristics of net income. The empirical results show that OCI recycling improves net income’s relative value relevance characteristic of financial firms. However, recycling information by itself does not improve the incremental value relevance, and the predictive power of operating cash flow and net income. The authors also find that the inclusion of recycling decreases the persistence and increases the variability of net income.

Research limitations/implications

This paper has two research limitations. First, this study is constrained to analyze a limited OCI recycling data that is recently disclosed by listed Japanese firms. Second, the results of this study have limited external validity to capital markets with OCI reclassification standards that deviate from Japanese GAAP.

Originality/value

This study provides initial empirical evidence that examines information usefulness of OCI recycling in Japan. The findings of this study are relevant for accounting standards setters aiming to increase the information usefulness of earnings for capital market investors.
Students’ experience toward ePortfolios as a reflective assessment tool in a dual mode indigenous business course
Authors: Bodle Kerry Anne , Malin Mirela , Wynhoven Andrew
Published: July 2017

Purpose

The purpose of this paper is to investigate students’ experiences of, and attitudes on, the use of technology – in the form of ePortfolio – as an assessment tool. The authors seek to determine whether ePortfolios aid students in facilitating critical reflection on their learning and academic skill development. The authors also determine whether ePortfolios can provide an alternative assessment tool to the traditional assessment practices in the accounting and business discipline.

Design/methodology/approach

This study surveys students enrolled in an indigenous business course using questions on the usability of ePortfolios, technical support and effectiveness in critical reflection and learning. Formal evaluations were included to capture students’ self-reflections on their ePortfolio experience. The analysis included analysis of variance, t-tests, correlations and hierarchical regression.

Findings

Results indicated that students show positive attitudes toward ePortfolios even after controlling for possible confounding variables such as previous experience, attitudes and accessibility. The authors also found that ePortfolios are a useful vehicle for enhancing students’ learning and understanding of indigenous knowledge in a business context. They were also found to facilitate students’ ability to critically reflect, engage in learning and develop their academic skills.

Research limitations/implications

The findings of this study could benefit those working in higher education, particularly accounting academics in Australian universities, and the adaptation of ePortfolios in a blended learning environment, and contribute to pedagogical knowledge regarding indigenous business issues. Academics could design the curriculum of the accounting courses within the commerce programme that addresses programme learning objectives to align with graduate employability outcomes.

Practical implications

This study provides a foundation for improving the design and assessment of written communication activities in accounting courses to achieve employability skills outcomes commensurate with university accreditation criteria. This could be achieved with the development of a community of practice developed by the professional accounting bodies in collaboration with Australian universities.

Originality/value

The research is not wholly new, although the use of ePortfolios in accounting education is not widely reported and, therefore, may be of interest to those in advancing the accounting education agenda. In light of the recent call by Australian professional accounting bodies, ePortfolios can provide accounting graduates the non-technical or soft skills such as communication, interpersonal and critical thinking.
Enhancing students understanding of introductory accounting by integrating split-attention instructional material
Authors: Sithole Seedwell T.M.
Published: July 2017

Purpose

The purpose of this study is to investigate the effects of two instructional design formats on learning outcomes in introductory accounting.

Design/methodology/approach

This study describes split-source instructional designs and uses an experiment administered to two groups of students enrolled in an undergraduate introductory accounting subject. The performance scores in recall and transfer test items are used to evaluate students’ learning outcomes.

Findings

The study suggests that instructors can enhance students understanding of introductory accounting by integrating text and diagrams in introductory accounting.

Practical implications

University instructors require evidence of teaching and learning activities that enhance student learning during the study of introductory accounting. This study shows that a redesign of accounting instructional material improves students’ performance and learning experience.

Originality/value

This study addresses a gap in the literature by examining the use of integrated instructional materials as an alternative to the separate diagram and text when learning accounting. The study also explores the effect of reorganising learning material on students load by analysing the mental effort reported by students. Finally, the study contributes useful findings on reorganising accounting instructional material aimed at enhancing the understanding of introductory accounting.
Towards superhydrophobic and ultraviolet protective nylon fabrics
Authors: Teli Mangesh , Annaldewar Bhagyashri N.
Published: July 2017

Purpose

The purpose of this paper is to prepare coloured superhydrophobic and ultraviolet (UV) protective nylon fabrics using nanosilica copper oxide coating.

Design/methodology/approach

In this study, brown coloured superhydrophobic nylon fabric exhibiting UV protective properties was prepared by step-wise deposition of silica nanoparticles, copper oxide and sodium stearate. The hydrophobicity of treated fabrics was characterised by water contact angle measurement and UV protection properties of fabric were assessed by Australian/New Zealand Standard. Also, a colouring effect of treatment on nylon fabric was measured using spectrophotometer.

Findings

The modified fabric not only exhibited superhydrophobicity with the water contact angle of 150.6°, but also rendered excellent protection against UV radiation. The fabric showed retention of hydrophobic and UV protection properties up to 20 washing cycles.

Originality/value

A novel method for imparting superhydrophobicity and UV protective properties along with colouration effect on nylon fabrics has been reported. This type of fabric has potential application in the field of protective clothing.