bluuebunny/crossref_metadata_2025 huggingface dataset:
Volar Vascularized Strut Graft for Avascular Scaphoid Nonunion Using the 1,2 Intercompartmental Supraretinacular Artery
Authors: Ingari John V. , Nayar Suresh K. , Taylor Kenneth F.
Published: November 2018

In this retrospective study, we report the preliminary results of a novel technique for volar vascularized strut grafting to treat avascular scaphoid nonunion by using the 1,2 intercompartmental supraretinacular artery through a single incision. Forty-three of 45 patients with avascular scaphoid nonunion healed at a mean of 13 weeks (range, 3 to 10 mo). Complications consisted of 1 pin tract infection that resolved with oral antibiotics and 4 cases of transient dysesthesia of the radial sensory nerve. In 4 patients with equivocal radiographs, computed tomography scans confirmed bony union. The 2 patients who remained unhealed subsequently underwent proximal row carpectomy. Two other patients had persistent pain with the progression of radiocarpal arthritis. Our technique provides good results for the treatment of avascular scaphoid fracture nonunion. Notable advantages include performance through a single incision, use of an already established vascularized bone graft, volar graft placement, and no requirement for microvascular free graft reconstruction. It also provides the surgeon with the ability to adjust the procedure intraoperatively in the event of unexpected avascularity, without requiring substantially longer operative time or additional equipment.
A Changing Spectrum of Colorectal Cancer Biology With Age: Implications for the Young Patient
Authors: Chouhan Hanumant , Ferrandon Sylvain , DeVecchio Jennifer , Kalady Matthew F. , Church James M.
Published: November 2018

BACKGROUND:

The methylator pathway of colorectal carcinogenesis, characterized by CpG island hypermethylation and BRAF mutations, accounts for ≈25% of colorectal cancers. Because these cancers tend to be right sided and because DNA methylation in the right colon increases with age, we expect an increasing proportion of right-sided cancer over time. Conversely, we expect young patients (age <50 y) to have less methylated and fewer right-sided cancers

OBJECTIVE:

The purpose of this study was to analyze the distribution and genetic traits of colorectal cancer from different age groups.

DESIGN:

This was a retrospective cohort study.

SETTING:

The study was conducted at a high-volume tertiary referral center.

PATIENTS:

Patient samples included those from our colorectal cancer biobank of resected colorectal cancer specimens.

MAIN OUTCOME MEASURES:

Tumor CpG island hypermethylation, microsatellite instability, and mutations in KRAS and BRAF oncogenes were analyzed in resected specimens and stratified by age and tumor location. Comparisons included age >50 or <50 years and decade of diagnosis (≤50, 51–60, 61–70, 71–80, and >81 y). Patients with IBD or hereditary syndromes were excluded.

RESULTS:

A total of 497 colorectal cancers were analyzed (266 men and 231 women); 57 patients (11.5%) were ≤50 years of age. No young cancers (0/57) were hypermethylated compared with 97 (22%) of 440 cancers of patients aged >50 years (p < 0.001). An increasing percentage of tumors were CpG island phenotype high with each decade of age at diagnosis. No cancers in patients <50 years of age were microsatellite unstable compared with 91 (23.6%) of 346 for those >50 years of age. No young cancers contained a BRAF mutation compared with 46 (10.6%) of 434 in older cancers (p < 0.001). KRAS mutations were less common in young cancers compared with older cancers (13/57 (22.8%) vs 126/410 (30.7%); p < 0.01). Eleven (19.3%) of 57 young cancers were proximal compared with 228 (51.8%) of 440 (p < 0.001) older cancers.

LIMITATIONS:

This study was limited by its retrospective design.

CONCLUSIONS:

The lack of CpG island methylator phenotype tumors in young patients is consistent with the dominant left-sided cancer distribution seen in the young and focuses efforts to understand and prevent cancer in this age group on causes of chromosomal instability. See Video Abstract at http://links.lww.com/DCR/A709.
Consequences of Increasing Complexity in Anorectal Surgery Performed at an Academic Center
Authors: Hiller David J. , Chadi Sami A. , Rosen Lester , Wexner Steven D.
Published: November 2018

BACKGROUND:

Anorectal surgery encompasses a wide range of procedures with varying complexity. The Accreditation Council for Graduate Medical Education Review Committee for Colon and Rectal Surgery recommends minimum case numbers (60) for 1-year specialty trainees in 6 categories of anorectal surgery, with definitions for procedural complexity.

OBJECTIVE:

The purpose of this study was to assess the scope of anorectal procedures and propose a stratification of procedures based on a consensus of levels of difficulty, as well as to identify a predictive charge cutoff suggestive of procedural complexity.

DESIGN:

This was a retrospective review.

SETTINGS:

The study was conducted at a tertiary academic center.

PATIENTS:

Patients undergoing anorectal procedures between January 2011 and December 2014 identified by Current Procedural Terminology coding were entered into 6 categories. Codes were stratified as routine or complex based on an assessment of perioperative care and technical expertise required. Patients with an abdominal portion to any procedure were excluded.

MAIN OUTCOMES MEASURES:

The study measured distribution of complexity in anorectal surgical procedures and procedural charge associated with differentiating routine from complex procedures.

RESULTS:

Seven colorectal surgeons performed 2483 anorectal procedures (mean = 620 per year). Mean age was 48 ± 16 years. Forty six (64%) of 71 procedures were classified as routine and 25 (36%) of 71 as complex. Most disease processes had subsets with routine or complex procedures, whereas all of the procedures performed for fecal incontinence or advanced anorectal techniques were considered complex. Fistula procedures and transanal excisions were most heterogeneous, with a high procedural complexity rate (37% and 50%). After a procedural complexity rating, intraclass correlation by 6 surgeons was 0.70, demonstrating good correlation. Receiver operating curve assessments of consensus categorization according to billing codes revealed $553 as the optimal cutoff between routine and complex procedures.

LIMITATIONS:

This was a single-institution retrospective review.

CONCLUSIONS:

Colorectal residents may benefit from anorectal case stratification, because it serves as a dialogue for those interested in complex anorectal surgery during training. Surgeon categorization of procedures correlates well with a charge-based model of complexity. See Video Abstract at http://links.lww.com/DCR/A806.
Effects of Dual Sofosbuvir/Daclatasvir Therapy on Weight and Linear Growth in Adolescent Patients with Chronic Hepatitis C Virus Infection
Authors: Yakoot Mostafa , El-Shabrawi Mortada H. , AbdElgawad Manal M. , Mahfouz Aml A. , Khalil Ahmed F. , Kamal Naglaa M. , Helmy Sherine , Abdo Alaa M. , Kamal Enas M. , El-Khayat Hisham R.
Published: November 2018

Negative effects on growth indices had been reported in children treated with interferon for chronic viral hepatitis. Forty chronic hepatitis C virus-infected adolescents, 12–17 years of age, were treated with sofosbuvir/daclatasvir therapy for 12 weeks. The intent-to-treat sustained virologic response rate at 12 weeks after end of treatment was 39/40 (97.5%). Unlike interferon-based therapy, we did not detect significant negative effects on linear growth or weight. Contrarily, a trend to increased appetite and insignificant weight gain was observed, but further larger studies are needed to confirm. See Video-Abstract, http://links.lww.com/ASAIO/A381.
Hemodynamic Impact of Oxygen Desaturation During Tracheal Intubation Among Critically Ill Children With Cyanotic and Noncyanotic Heart Disease*
Authors: Mokhateb-Rafii Tanya , Bakar Adnan , Gangadharan Sandeep , Gradidge Eleanor A. , Tellez David , Ruppe Michael , Tallent Sarah , Bird Geoffrey , Lavin Natasha , Lee Anthony , Napolitano Natalie , Nadkarni Vinay , Shults Justine , Nishisaki Akira
Published: November 2018

Objectives:

To determine a level of oxygen desaturation from baseline that is associated with increased risk of tracheal intubation associated events in children with cyanotic and noncyanotic heart disease.

Design:

Retrospective analysis of prospectively collected data from the National Emergency Airway Registry for Children, an international multicenter quality improvement collaborative for airway management in critically ill children.

Setting:

Thirty-eight PICUs from July 2012 to December 2016.

Patients:

Children with cyanotic and noncyanotic heart disease who underwent tracheal intubation in a pediatric or cardiac ICU.

Interventions:

None.

Measurements and Main Results:

Our exposure of interest was oxygen desaturation measured by a fall in pulse oximetry from baseline after preoxygenation. Primary outcome was the occurrence of hemodynamic tracheal intubation associated events defined as cardiac arrest, hypotension or dysrhythmia. One-thousand nine-hundred ten children (cyanotic, 999; noncyanotic, 911) were included. Patients with cyanotic heart disease who underwent tracheal intubations were younger (p < 0.001) with higher Pediatric Index of Mortality 2 scores (p < 0.001), more likely to have a cardiac surgical diagnosis (p < 0.001), and less likely to have hemodynamic instability (p = 0.009) or neurologic failure as an indication (p = 0.008). Oxygen desaturation was observed more often in children with cyanotic versus noncyanotic heart disease (desaturation of 15% to < 30%: 23% vs 16%, desaturation ≥ 30%: 23% vs 17%; p < 0.001), with no significant difference in occurrence of hemodynamic tracheal intubation associated events (7.5% vs 6.9%; p = 0.618). After adjusting for confounders, oxygen desaturation by 30% or more is associated with increased odds for adverse hemodynamic events (odds ratio, 4.03; 95% CI, 2.12–7.67) for children with cyanotic heart disease and (odds ratio, 3.80; 95% CI, 1.96–7.37) for children with noncyanotic heart disease.

Conclusions:

Oxygen desaturation was more commonly observed during tracheal intubation in children with cyanotic versus noncyanotic heart disease. However, hemodynamic tracheal intubation associated event rates were similar. In both groups, oxygen desaturation greater than or equal to 30% was significantly associated with increased occurrence of hemodynamic tracheal intubation associated events.
A Pilot Study of the Association of Amino-Terminal Pro-B-Type Natriuretic Peptide and Severity of Illness in Pediatric Septic Shock*
Authors: Melendez Elliot , Whitney Jane E. , Norton Jackson S. , Silverman Melanie , Monuteaux Michael C. , Bachur Richard G.
Published: November 2018

Objectives:

Biomarkers that can measure illness severity and predict the risk of delayed recovery may be useful in guiding pediatric septic shock. Amino-terminal pro-B-type natriuretic peptide has not been assessed in pediatric septic patients at the time of presentation to the emergency department prior to any interventions. The primary aim was to assess if emergency department amino-terminal pro-B-type natriuretic peptide is associated with worse outcomes and severity of illness.

Design:

Prospective observational pilot study.

Settings:

Tertiary free-standing children’s hospital.

Patients:

Children 0–17 years old with a diagnosis of septic shock were enrolled. Patients with preexisting cardiac and renal dysfunction were excluded.

Interventions:

None.

Measurements and Main Results:

Amino-terminal pro-B-type natriuretic peptide analysis was performed on samples obtained in the emergency department prior to any intervention. The association between biomarkers and clinical outcomes and illness severity using Pediatric RISk of Mortality 3 were assessed. Eighty-two patients with septic shock underwent analysis. The median (interquartile range) amino-terminal pro-B-type natriuretic peptide levels was 394 pg/mL (102–1,392 pg/mL). Each decile change increase in amino-terminal pro-B-type natriuretic peptide was associated with a change in ICU length of stay by 8.7%, (95% CI, 2.4–15.5), hospital length of stay by 5.7% (95% CI, 0.4–11.2), organ dysfunction by 5.1% (95% CI, 1.8–8.5), a higher inotropic score at 12, 24, and 36 hours, and longer time requiring vasoactive agents. There was a significant correlation between baseline amino-terminal pro-B-type natriuretic peptide and the Pediatric RISk of Mortality 3 score (Spearman rho = 0.247; p = 0.029).

Conclusions:

This pilot study shows an association between emergency department amino-terminal pro-B-type natriuretic peptide on presentation and worse septic shock outcomes and amino-terminal pro-B-type natriuretic peptide levels correlates with an ICU severity score.
Efficacy and Safety of Pediatric Critical Care Physician Telemedicine Involvement in Rapid Response Team and Code Response in a Satellite Facility*
Authors: Berrens Zachary J. , Gosdin Craig H. , Brady Patrick W. , Tegtmeyer Ken
Published: November 2018

Objectives:

Satellite inpatient facilities of larger children’s hospitals often do not have on-site intensivist support. In-house rapid response teams and code teams may be difficult to operationalize in such facilities. We developed a system using telemedicine to provide pediatric intensivist involvement in rapid response team and code teams at the satellite facility of our children’s hospital. Herein, we compare this model with our in-person model at our main campus.

Design:

Cross-sectional.

Setting:

A tertiary pediatric center and its satellite facility.

Patients:

Patients admitted to the satellite facility.

Interventions:

Implementation of a rapid response team and code team model at a satellite facility using telemedicine to provide intensivist support.

Measurements and Main Results:

We evaluated the success of the telemedicine model through three a priori outcomes: 1) reliability: involvement of intensivist on telemedicine rapid response teams and codes, 2) efficiency: time from rapid response team and code call until intensivist response, and 3) outcomes: disposition of telemedicine rapid response team or code calls. We compared each metric from our telemedicine model with our established main campus model.

Main Results:

Critical care was involved in satellite campus rapid response team activations reliably (94.6% of the time). The process was efficient (median response time 7 min; mean 8.44 min) and effective (54.5 % patients transferred to PICU, similar to the 45–55% monthly rate at main campus). For code activations, the critical care telemedicine response rate was 100% (6/6), with a fast response time (median 1.5 min). We found no additional risk to patients, with no patients transferred from the satellite campus requiring a rapid escalation of care defined as initiation of vasoactive support, greater than 60 mL/kg in fluid resuscitation, or endotracheal intubation.

Conclusions:

Telemedicine can provide reliable, timely, and effective critical care involvement in rapid response team and Code Teams at satellite facilities.
Median Arcuate Ligament Syndrome Related to Bodybuilding
Authors: Ulualp Kenan , Masnyj Stephen V. , Lee Cheong J. , Gould Jon C.
Published: November 2018

Background:

Median arcuate ligament syndrome (MALS), also known as celiac artery compression syndrome, is characterized by postprandial abdominal pain and weight loss thought to be secondary to compression of the celiac artery ganglia by the median arcuate ligament (MAL).

Methods:

A young female powerlifter presented with a 3-month history of postprandial epigastric pain and involuntary weight loss following the start of a vigorous weightlifting program. The diagnosis of MALS was established after excluding other possibilities and by detailed evaluation including magnetic resonance imaging and celiac plexus block. She was treated by laparoscopic MAL release.

Results:

The patient experienced immediate and complete cessation of her pain. She has continued to be asymptomatic at 6 months after surgery.

Conclusions:

Heavy weightlifting may potentially lead to MALS. The laparoscopic approach to MAL release can be utilized to treat this condition with favorable results.
Show the model – A Harrell plot combines a forest plot of effects and uncertainty with a dot plot of the data
Authors: Walker Jeffrey A.
Published: November 2018

Several high profile editorials and articles have advocated replacing the ubiquitous, but not especially informative, bar plot with dot plots or box plots which show the data or some summary of the data distribution. I argue that the biggest deficiency of bar plots (and other mean-and-error plots) is that they fail to directly communicate modeled effects and uncertainty, and dot and box plots do not address this deficiency. A Harrell plot combines a forest plot of modeled treatment effects and uncertainty, a dot plot of raw data, and a box plot of the distribution of the raw data into a single, two-part graph. A Harrell plot encourages best practices such as communication of the distribution of the data and a focus on effect size and uncertainty, while discouraging poor practices such as hiding distributions and focusing onp-values.
A New Family of Similarity Measures for Scoring Confidence of Protein Interactions using Gene Ontology
Authors: Paul Madhusudan , Anand Ashish
Published: November 2018

The large-scale protein-protein interaction (PPI) data has the potential to play a significant role in the endeavor of understanding cellular processes. However, the presence of a considerable fraction of false positives is a bottleneck in realizing this potential. There have been continuous efforts to utilize complementary resources for scoring confidence of PPIs in a manner that false positive interactions get a low confidence score. Gene Ontology (GO), a taxonomy of biological terms to represent the properties of gene products and their relations, has been widely used for this purpose. We utilize GO to introduce a new set of specificity measures: Relative Depth Specificity (RDS), Relative Node-based Specificity (RNS), and Relative Edge-based Specificity (RES), leading to a new family of similarity measures. We use these similarity measures to obtain a confidence score for each PPI. We evaluate the new measures using four different benchmarks. We show that all the three measures are quite effective. Notably, RNS and RES more effectively distinguish true PPIs from false positives than the existing alternatives. RES also shows a robust set-discriminating power and can be useful for protein functional clustering as well.
To CRUNCH or not to CRUNCH: Task Difficulty Affects Functional Brain Reorganisation during Visuospatial Working Memory Performance in Premanifest Huntington’s Disease
Authors: Soloveva Maria V. , Jamadar Sharna D. , Velakoulis Dennis , Poudel Govinda , Georgiou Karistianis Nellie
Published: November 2018

Presymptomatic Huntington’s disease (pre-HD) individuals tend to increase functional brain activity to compensate for HD-related brain anomalies. We used a quantitative model of compensation, known as the CRUNCH (Compensation-Related Utilization of Neural Circuits Hypothesis) to explicitly characterise compensation in pre-HD. We acquired functionalmagnetic resonance imaging (fMRI) data (n = 15 pre-HD; n = 15 controls) during performance of an 18-minute fMRI visuospatial working memory task with low, intermediate-1, intermediate-2, and high memory loads. Consistent with the CRUNCH prediction, pre-HD individuals showed decreased fMRI activity in left intraparietal sulcus at high memory load, compared to healthy controls who showed increased fMRI activity in left intraparietal sulcus at high memory load. Contrary to the other CRUNCH prediction, the pre-HD group did not show compensatory increase in fMRI activity at lower levels of memory loads in left intraparietal sulcus. Our findings provide partial support for the validity of CRUNCH in pre-HD.

Highlights

Visuospatial working memory deficits in pre-HD occur 25 years prior to predicted disease onset

Task demands differentially affect fMRI activity in left intraparietal sulcus

CRUNCH can partially apply in Huntington’s disease
Detection of enterovirus protein and RNA in multiple tissues from nPOD organ donors with type 1 diabetes
Authors: Oikarinen Maarit , Laiho Jutta E , Oikarinen Sami , Richardson Sarah J , Kusmartseva Irina , Campbell-Thompson Martha , Morgan Noel G , Pugliese Alberto , Tauriainen Sisko , Toniolo Antonio , Hyöty Heikki ,   the nPOD-V study group
Published: November 2018

Epidemiological studies have shown an association between enterovirus (EV) infections and type 1 diabetes (T1D), and EV protein has been detected in the pancreatic islets of T1D patients. Here we correlated the detection of EVs in lymphoid tissues (spleen and pancreatic lymph nodes) and small intestinal mucosa to the virus detection in the pancreas of T1D, autoantibody-positive (aab+) and non-diabetic control organ donors of the Network for Pancreatic Organ Donors with Diabetes (nPOD) study. Formalin-fixed paraffin-embedded tissue samples were screened for insulin and EV protein using immunohistochemistry, and frozen tissue for EV genome using RT-PCR. The presence of EV protein in the pancreatic islets correlated with the presence of insulin-positive cells. Altogether 62 % of T1D and aab+ donors were positive for EV protein in pancreatic islets (only insulin-positive donors included), 40 % in duodenum and 32 % in spleen, compared to 33 %, 14 %, and 27 % of non-diabetic controls. Pancreatic lymph nodes were positive for EV protein in 60 % of T1D and aab+ cases. T1D and aab+ donors were more frequently VP1-positive in multiple organs than control donors (39 % vs. 11 %; including only insulin-positive donors). EV RNA was found in selected donors and from multiple tissue types except for duodenum, and individual T1D and aab+ donors were EV RNA-positive in multiple organs. The role of extra-pancreatic organs and their interplay with EV in T1D pathogenesis remains to be solved, but we hypothesize that these organs may serve as a reservoir for the virus which may reside in these tissues in a slow-replicating persistent form.
Near-infrared light increases functional connectivity with a non-thermal mechanism
Authors: Dmochowski Grzegorz M. , Shereen Ahmed (Duke) , Berisha Destiny , Dmochowski Jacek P.
Published: November 2018

Although techniques for non-invasive brain stimulation are under intense investigation, an approach that has received limited attention is transcranial photobiomodulation (tPBM), the delivery of near-infrared light to the brain with a laser directed at the scalp. Here we employed functional magnetic resonance imaging (fMRI) to measure the Blood-Oxygenation-Level Dependent (BOLD) signal in n = 20 healthy humans while concurrently stimulating their right frontal pole with a near-infrared laser. We failed to detect an evoked BOLD response at illumination. However, functional connectivity with the illuminated region increased by an average of 10% during stimulation, with some connections strengthening by as much as 40%. 23% of connections with the illuminated region experienced a significant acute increase, with the time course of connectivity exhibiting a sharp rise at illumination onset. Brain-wide connectivity increases were also observed, with connections in the stimulated hemisphere showing a significantly larger increase than those in the non-stimulated hemisphere. We subsequently employed MR Thermometry to measure brain temperature during tPBM (separate cohort, n = 20), and found no significant temperature differences between active and sham stimulation. Our findings suggest that near-infrared light synchronizes brain activity with a non-thermal mechanism, underscoring the promise of tPBM as a new technique for stimulating brain function.
Integrative inference of brain cell similarities and differences from single-cell genomics
Authors: Welch Joshua , Kozareva Velina , Ferreira Ashley , Vanderburg Charles , Martin Carly , Macosko Evan
Published: November 2018

Defining cell types requires integrating diverse measurements from multiple experiments and biological contexts. Recent technological developments in single-cell analysis have enabled high-throughput profiling of gene expression, epigenetic regulation, and spatial relationships amongst cells in complex tissues, but computational approaches that deliver a sensitive and specific joint analysis of these datasets are lacking. We developed LIGER, an algorithm that delineates shared and dataset-specific features of cell identity, allowing flexible modeling of highly heterogeneous single-cell datasets. We demonstrated its broad utility by applying it to four diverse and challenging analyses of human and mouse brain cells. First, we defined both cell-type-specific and sexually dimorphic gene expression in the mouse bed nucleus of the stria terminalis, an anatomically complex brain region that plays important roles in sex-specific behaviors. Second, we analyzed gene expression in the substantia nigra of seven postmortem human subjects, comparing cell states in specific donors, and relating cell types to those in the mouse. Third, we jointly leveraged in situ gene expression and scRNA-seq data to spatially locate fine subtypes of cells present in the mouse frontal cortex. Finally, we integrated mouse cortical scRNA-seq profiles with single-cell DNA methylation signatures, revealing mechanisms of cell-type-specific gene regulation. Integrative analyses using the LIGER algorithm promise to accelerate single-cell investigations of cell-type definition, gene regulation, and disease states.
Imaging of sub-cellular fluctuations provides a rapid way to observe bacterial viability and response to antibiotics
Authors: Bermingham Charlotte R , Murillo Isabel , Payot Alexandre D J , Balram Krishna C , Kloucek Maximilian B , Hanna Simon , Redmond Niamh M , Baxter Helen , Oulton Ruth , Avison Matthew B , Antognozzi Massimo
Published: November 2018

Determining the viability of bacteria in a sample is an essential microbiological technique used in healthcare, industrial bioprocesses and research. Increasingly, attention has been focussing on antimicrobial susceptibility tests (AST), allowing rapid and appropriate prescribing of antibiotics. Current AST are limited in speed as they rely on detecting growth of microorganisms. Faster AST could be enabled by the recent discovery that living bacteria manifest nano-scale fluctuations, which reduce when the bacteria die. Here, we demonstrate a direct method of visualising fluctuations within bacterial cells using Sub-Cellular Fluctuation Imaging (SCFI), which is based on Total Internal Reflection Microscopy (TIRM). We show that SCFI can measure the viability of bacterial samples within minutes, distinguishing not only between live and dead bacteria but also live bacteria in different metabolic states. Importantly, we subsequently show that SCFI can rapidly distinguish antibiotic-treated resistant and susceptible bacteria, and therefore has particular application as a rapid AST.
Respiratory heterogeneity shapes biofilm formation and host colonization in uropathogenic Escherichia coli
Authors: Beebout Connor J. , Eberly Allison R. , Werby Sabrina H. , Reasoner Seth A. , Brannon John R. , De Shuvro , Fitzgerald Madison J. , Huggins Marissa M. , Clayton Douglass B. , Cegelski Lynette , Hadjifrangiskou Maria
Published: November 2018

Biofilms are multicellular bacterial communities encased in a self-secreted extracellular matrix comprised of polysaccharides, proteinaceous fibers, and DNA. Organization of these components lends spatial organization to the biofilm community such that biofilm residents can benefit from the production of common goods, while being protected from exogenous insults. Spatial organization is driven by the presence of chemical gradients, such as oxygen. Here we quantified and localized the expression of two Escherichia coli cytochrome oxidases in cells found in the biofilm state and defined their contribution to biofilm architecture. These studies elucidated a role for the high-affinity quinol oxidase cytochrome bd in matrix production and biofilm resident protection. Cytochrome bd was the most abundantly expressed respiratory complex in the biofilm community and was localized in the biofilm interior. Depletion of the cytochrome bd-expressing subpopulation led to decreased extracellular matrix and increased sensitivity of the community to exogenous stresses. Interrogation of the distribution of cytochrome oxidases in the planktonic state revealed that ∼15% of the population expresses cytochrome bd at atmospheric oxygen concentration, and this population dominates during acute urinary tract infection. These data point towards a bet-hedging mechanism in which heterogeneous expression of respiratory complexes ensures respiratory plasticity of E. coli across diverse host niches.
Simulation and reconstruction ofmetabolite-metabolite association networks usinga metabolic dynamic model and correlation based-algorithms
Authors: Jahagirdar Sanjeevan , Suarez-Diez Maria , Saccenti Edoardo
Published: November 2018

Biological networks play a paramount role in our understanding of complex biological phenomena and metabolite-metabolite association networks are now commonly used in metabolomics applications. In this study we evaluate the performance of several network inference algorithms (PCLRC, MRNET, GENIE3, TIGRESS and modifications of the MR-NET algorithm, together with standard Pearson’s and Spearman’s correlation) using as a test case data generated using a dynamic metabolic model describing the metabolism of arachidonic acid (consisting of 83 metabolites and 131 reactions) and simulation individual metabolic profiles of 550 subjects. The quality of the reconstructed metabolite-metabolite association networks was assessed against the original metabolic network taking into account different degrees of association among the metabolites and different sample size and noise levels. We found that inference algorithms based on resampling and bootstrapping to perform better when correlations are used as indexes to measure the strength of metabolite-metabolite associations. We also advocate for the use of data generated using dynamic models to test the performance of algorithms for network inference since they produce correlation patterns which are more similar to those observed in real metabolomics data.
A machine-learning approach for accurate detection of copy-number variants from exome sequencing
Authors: Pounraja Vijay Kumar , Jayakar Gopal , Jensen Matthew , Kelkar Neil , Girirajan Santhosh
Published: November 2018

Copy-number variants (CNVs) are a major cause of several genetic disorders, making their detection an essential component of genetic analysis pipelines. Current methods for detecting CNVs from exome sequencing data are limited by high false positive rates and low concordance due to the inherent biases of individual algorithms. To overcome these issues, calls generated by two or more algorithms are often intersected using Venn-diagram approaches to identify “high-confidence” CNVs. However, this approach is inadequate, as it misses potentially true calls that do not have consensus from multiple callers. Here, we present CN-Learn, a machine-learning framework (https://github.com/girirajanlab/CN_Learn) that integrates calls from multiple CNV detection algorithms and learns to accurately identify true CNVs using caller-specific and genomic features from a small subset of validated CNVs. Using CNVs predicted by four exome-based CNV callers (CANOES, CODEX, XHMM and CLAMMS) from 503 samples, we demonstrate that CN-Learn identifies true CNVs at higher precision (~90%) and recall (~85%) rates while maintaining robust performance even when trained with minimal data (~30 samples). CN-Learn recovers twice as many CNVs compared to individual callers or Venn diagram-based approaches, with features such as exome capture probe count, caller concordance and GC content providing the most discriminatory power. In fact, about 58% of all true CNVs recovered by CN-Learn were either singletons or calls that lacked support from at least one caller. Our study underscores the limitations of current approaches for CNV identification and provides an effective method that yields high-quality CNVs for application in clinical diagnostics.
Corrosion inhibition of N80 steel in 10% HCl + 8% HBF4solution
Authors: Du Juan , He Yuning , Liu Pingli , Liu Yigang , Meng Xianghai , Zhao Liqiang
Published: November 2018

Purpose

This paper aims to analyze the corrosion and corrosion inhibition of N80 in 10 per cent HCl + 8 per cent fluoroboric acid (HBF4) solution for acidizing operation.

Design/methodology/approach

The corrosion rate, kinetic parameters (Ea, A) and thermodynamic parameters (ΔH, ΔS) of N80 steel in fresh acid and spent acid, 10 per cent HCl + 8 per cent HBF4, 10 per cent HCl and 8 per cent HBF4solutions were calculated through immersion tests. The corrosion and inhibition properties were studied through X-ray diffraction and electrochemical measurements. The corrosion morphology of the corrosion product was examined by scanning electron microscopy (SEM).

Findings

The results demonstrated that the spent acid was the main cause of acidification corrosion, and the HBF4would cause serious corrosion to N80 steel. The results showed that the N80 steel was more seriously corroded in the spent acid than in fresh acid, and the hydrolysis of HBF4accelerates the dissolution process of N80 steel anode to control the corrosion reaction. The results showed that the acidification will definitely cause serious corrosion to the oil tube; therefore, necessary anti-corrosion measures must be taken in the acidification process.

Originality/value

The results showed that acidizing the formation with 10 per cent HCl + 8 per cent HBF4will definitely cause serious corrosion to the oil tube, especially when the spent acid flows back. Therefore, necessary anti-corrosion measures must be taken in the acidification process, especially in the spent acid flowback stage.
Factors affecting the development of accounting practices in Jordan: an institutional perspective
Authors: Tahat Yasean , Omran Mohamed A. , AbuGhazaleh Naser M.
Published: November 2018

Purpose

Based on the institutional theory, the purpose of this paper is to examine institutional factors that affect the development of accounting practices in Jordan.

Design/methodology/approach

The current study surveys the perceptions of 306 participants and 20 interviewees.

Findings

First, the early formation of accounting practices in Jordan has been affected by the legacy of Ottoman Empire’s and the British Colony’s accounting systems. Second, the results indicate that government of Jordan (regulatory frameworks), pressures from international donors and large economic organizations (politico-economic factors), education and training/development (cultural inputs), and the efforts to attract foreign investments and getting access into the international fund and trade (economic factors) have been influential influences in the development of accounting practices and the adoption of International Accounting Standards/International Financial Reporting Standards (IAS/IFRS) in Jordan. Finally, the findings reveal that “Secrecy” construct (a culture input) has been a problematic in the implementation of IAS/IFRS.

Practical implications

The current study provides policy implications for the Jordanian policy makers and for other developing countries that are working hard to improve the quality of financial reporting of their business entities. Finally, the authors suggest some great opportunities for future research.

Originality/value

First, this paper contributes to Jordan’s policy developments including fundamental strategies in terms of attracting foreign investments to expand the economy and the international and regional trade. Second, it fills a gap in the international accounting research by empirically assessing how institutional factors affect the development of accounting practices in emerging country such as Jordan.
Hygiene behavior assessment of a hazelnut processing plant
Authors: Botondi Rinaldo
Published: November 2018

Purpose

The purpose of this paper is to evaluate the possible microbiological contamination in terms of total counts and representative microbial groups found in the hazelnuts as well as in work areas and on the working surfaces of a hazelnut processing plant.

Design/methodology/approach

Some microbiological parameters related to the manufacturing process (e.g. aerobic colony count yeast and fungi) were evaluated. Indoor air samples were tested in order to evaluate the possible contamination of fungal strains (i.e. mycotoxin producing fungi).

Findings

The results showed that the highest values (>of 500 CFU/m3) for bacteria and fungi were only observed in the shelling and sorting areas. Some species such as Aspergillus and Penicillium (potential mycotoxin-producers) as well as some noxious colonies ofAspergillus fumigatuswere detected along the processing line. No occurrence of aflatoxins was observed in the finished product. Microbial loads obtained through surface analyses were in accordance to the reference data.

Originality/value

The aim of this study was to monitor and improve the procedures currently used in a hazelnut processing plant.
Benchmarking of TQM practices in the Jordanian pharmaceutical industry (a comparative study)
Authors: Yaseen Maysoon Mohammed , Sweis Rateb J. , Abdallah Ayman Bahjat , Obeidat Bader Yousef , Sweis Nadia J.
Published: November 2018

Purpose

The purpose of this paper is to establish practical guidelines for benchmarking eight total quality management (TQM) practices vital to pharmaceutical companies’ performance. The paper also proposes the use of an analytic total quality index (TQI) as a benchmarking tool and illustrates the importance and effectiveness of this benchmarking methodology by applying it in two comparative studies of three Jordanian pharmaceutical companies.

Design/methodology/approach

In order to achieve the above-mentioned purpose, the data were gathered through a questionnaire that was used to evaluate the gap between the ideal and current status of the quality management system and distributed to the quality units from three companies: pharmaceutical manufacturing company, a pharmaceutical manufacturing company working in the same field and a pharmaceutical service providing research services to a pharmaceutical manufacturing companies. And the mean differences between the current and ideal states for the eight critical TQM practices were compared for these two comparative studies using thet-test.

Findings

Each of the two comparisons reveals statistically significant differences regarding the perceptions of actual and ideal scores for manufacturing and service companies on five out of eight critical factors and, on two out of eight critical factors for manufacturing and manufacturing companies.

Practical implications

The pharmaceutical companies, regardless of whether they are manufacturing or service company, can adopt benchmarking techniques which were applied in this case study to improve their performance and their product/service quality.

Originality/value

The consequences of this research can support organization managers and policy makers in effectively benchmarking the identified TQM practices in their organizations using the proposed TQI benchmarking tool.
The influence of social media marketing activities on customer loyalty
Authors: Yadav Mayank , Rahman Zillur
Published: November 2018

Purpose

The purpose of this paper is to examine the impact of perceived social media marketing activities (SMMAs) on customer loyalty via customer equity drivers (CEDs) in an e-commerce context.

Design/methodology/approach

The study surveyed 371 students from a large university in India. The data were analyzed via confirmatory factor analysis and the research hypotheses were examined using SEM.

Findings

The study revealed three key findings. First, perceived SMMAs of e-commerce comprise five dimensions, namely, interactivity, informativeness, word-of-mouth, personalization and trendiness. Second, perceived SMMAs of e-commerce have significantly and positively influenced all the drivers of customer equity (CEDs). Third, the CEDs of e-commerce exhibit a significant and positive influence on customer loyalty toward the e-commerce sites.

Practical implications

This study will help e-commerce managers to boost customer loyalty toward the e-commerce sites through perceived SMMA.

Originality/value

The study is the first to identify five dimensions of e-commerce perceived SMMA. The current study also introduces the stimulus–organism–response model as a theoretical support to connect perceived SMMAs of e-commerce to customers’ loyalty via CEDs. This is supposed to be the first study to examine the impact of perceived SMMA on customer loyalty toward the e-commerce sites via CEDs in the e-commerce industry.
Determinants of customer loyalty: a study with customers of a Brazilian bank
Authors: Milan Gabriel Sperandio , Slongo Luiz Antonio , Eberle Luciene , De Toni Deonir , Bebber Suélen
Published: November 2018

Purpose

The purpose of this paper is to analyze customer loyalty in the context of existing relationships between Brazilian banking service provider and its customers in the context of B2C (Business-to-Consumer) relationships. Hence, a theoretical model was proposed and tested with banking services private individual customers taking into account perceived value, service provider reputation, financial bonding tactics, structural bonding tactics, social bonding tactics and switching costs as customer loyalty determinants.

Design/methodology/approach

A multivariate statistical approach with structural equations modeling was used in a 505 customer sample of the one prominent bank in Brazil.

Findings

Results indicate that the proposed theoretical model confirming a satisfactory fit, presenting a good explanatory power (R2=0.738) and supporting that perceived value influences the service provider reputation; financial bonding tactics, structural bonding tactics and social bonding tactics influence perceived value; service provider reputation influences switching costs; switching costs influence customer loyalty and the social bonding tactics influence customer loyalty.

Practical implications

The results evidenced in the present research could serve as benchmarking for other researchers or managers connected to the financial service sector (or bank service) when looking for a better understanding about the antecedents of customer loyalty, adapting strategies and actions to stimulate and generate better market and economic–financial results for the institutions of this sector.

Originality/value

Finding out which constructs better explain customer loyalty, and its possible relations, is something relevant for the banking sector, once it can generate more effective managerial insights, positively making an impact in a customer portfolio performance, or the financial institution itself, from the construction, maintenance and strengthening of the relationships with customers.
Benchmarking the interactions among performance indicators in dairy supply chain
Authors: Mor Rahul S. , Bhardwaj Arvind , Singh Sarbjit
Published: November 2018

Purpose

The purpose of this paper is to explore the key performance indicators (PIs) that serve as a decision support tool in case of dairy supply chain practices and to analyze their interactions in the context of Indian dairy industry sector. A total of 11 PIs have been identified through the literature review and the opinions of an expert team consisting of managerial and technical experts from dairy industry and academics.

Design/methodology/approach

A solution methodology based on the interpretive structure modeling (ISM) technique is used to analyze the interactions among PIs and to propose a structural model. The developed model not only helps in understanding the contextual relationship among the PIs, but also in determining their interdependence to assess the supply chain performance in dairy industry. Further, the importance of PIs has been determined based on their driving and dependence power by using MICMAC analysis.

Findings

The ISM-based model suggests four PIs at first level, three PIs at second level, one PI at third level as well as one PI at fourth level and two PIs at fifth level. Model allocates to the effective information technology, brand management, responsiveness in shipment and accuracy and a control over wastages as the key PIs in the dairy industry sector. The effective traceability systems, cold chain infrastructure, quality management and the support for technological innovations are the next major PIs. There exists no autonomous PI in MICMAC analysis which proves the importance of identified PIs in the case study.

Research limitations/implications

The proposed model is an attempt to capture the dynamics of milk processing sector and to incorporate all relevant constraints related to internal and external environments that would significantly improve the supply chain performance in the dairy industry.

Practical implications

The model developed in this study has been tested in the cooperative milk processing units based in India and also discussed with the experts from academics. This work may help practitioners, regulators and dairy industry professionals to focus their efforts toward achieving high performance by the effective implementation of the identified PIs.

Originality/value

In this study, 11 PIs are considered. Interactions among PIs are evaluated with the help of the ISM matrix. Out of the 11 PIs, six demonstrate both strong driving and dependence power as explained in the MICMAC analysis.
Factors that influence the quality of services provided by the bus rapid transit system
Authors: Tomaz de Aquino Joás , Valença de Souza Juliana , Lima da Silva Vanessa de Cássia , Jerônimo Taciana de Barros , Melo Fagner José Coutinho De
Published: November 2018

Purpose

This study analyses the factors that can influence the quality of service provided by the bus rapid transit (BRT) system in the state of Pernambuco. It is incipient, considering that the system was implemented in this state in 2014 to the World cup. In this context, the purpose of this paper is to identify the factors considered important for the services provided by this system and their impact on perceived quality.

Design/methodology/approach

The authors analyzed the data using exploratory factorial analysis, and linear and quantile regression techniques. Regarding the classification, this research is applied, exploratory, descriptive and in the form of a case study describing the situation experienced by the users of BRT in Pernambuco.

Findings

The results showed that it was possible to identify five factors that impact the level of satisfaction of the offered services: fluency in the provision of the service; staff training; physical conditions in the provision of the service; convenience/accessibility; and integration between transport lines.

Originality/value

With initial identification, factors 1, 3, 4 and 5 have been found to have an impact on overall service quality in a positive and statistically significant way. Factors 3 and 4 have a different impact with high- and low-quality standard perceived by users, and these should be the guiding elements by companies in establishing actions to improve the services offered.