bluuebunny/crossref_metadata_2025 huggingface dataset:
Gender Discrepancy in Diabetic Patients Hospitalized With Heart Failure
Authors: Mohammed Shaban , El-Menyar Ayman , Rafie Ihsan M. , AlBinAli Hajar A. , Singh Rajvir , Al Suwaidi Jassim
Published: July 2016

Background:

Gender discrepancy in the cardiovascular diseases has been evaluated in several studies. We studied the impact of gender disparity on the presentation and outcome of diabetic heart failure (DHF) patients.

Methods:

A retrospective analysis was conducted including all DHF patients admitted to the Heart Hospital between 1991 and 2013. Patients’ demographics, presentation, management, and hospital outcomes were analyzed and compared based on gender and age.

Results:

Out of 8266 HF patients, 4684 (56.7%) were diabetic, of whom 1817 (39%) were females. Mean age was comparable in both genders. DHF female patients were more likely to be hypertensive (79% vs. 65%, P = 0.001) and obese (13% vs. 4.6%, P = 0.001). DHF females were less likely to receive beta-blockers and angiotensin-converting-enzyme inhibitors/angiotensinogen-receptor blockers (25% vs. 30%, P = 0.001, 54% vs. 57%, P = 0.01, respectively), but were more likely to be on insulin therapy (21% vs. 16%, P = 0.001). In-hospital atrial fibrillation (P =0.90), ventricular tachycardia (P = 0.07), stroke (P = 0.45), and cardiac arrest (P = 0.26) were comparable. Overall in-hospital mortality was comparable in both genders (P = 0.83). In age ≤50 years, male gender was associated with a 3-fold increase in death (13% vs. 4%, P = 0.01), however, this mortality difference disappeared in DHF patients aged >50 years (P = 0.62).

Conclusions:

In DHF, female gender is characterized by having a high prevalence of metabolic syndrome components. Also, females are more likely to have better Left ventricular ejection fraction but less likely to receive cardiovascular evidence based medications. There is no significant difference in the overall hospital mortality between both genders, however, in the younger age; males have a significantly higher mortality.
The Infant Aphakia Treatment Study Contact Lens Experience to Age 5 Years
Authors: Russell Buddy , DuBois Lindreth , Lynn Michael , Ward Michael A. , Lambert Scott R. ,   for The Infant Aphakia Treatment Study Group
Published: July 2016

Purpose:

To describe our experience treating a cohort of unilateral aphakic infants with contact lenses in the Infant Aphakia Treatment Study (IATS).

Materials and methods:

Fifty-seven of the 114 infants in the IATS were randomized to contact lens wear; all were followed until age 5 years, although a few had lapses in care. An examination under anesthesia, including keratometry, was performed at the time of enrollment and at approximately 1 year of age; keratometry was performed again at 5 years of age. A traveling examiner assessed visual acuity at approximately 1 year of age and again at 4.5 years of age.

Results:

Twenty-four treated eyes (46%) wore silicone elastomer (SE) contact lenses, 11 eyes (19%) rigid gas permeable (GP) contact lenses and 17 eyes (29%) wore both lens types at various points of time. Median logMAR visual acuity was +0.70 (interquartile range (IQR), +0.30 to 1.20) in the SE group and 2.03 (IQR, +0.20 to 2.28) in the GP group at age 4.5 years. The mean (±SD) keratometric power of the treated eyes was 46.3±2.8 diopter (D) at baseline, 44.6±2.3 D at 1 year of age, and 44.3±1.7 D at 5 years of age. Keratometric astigmatism of treated eyes was 1.98±1.37 D at baseline, 1.62±0.98 D at 1 year of age, and 2.00±1.00 D at 5 years of age. Thirteen contact lens-related adverse events occurred among 7 patients after age 1 year.

Conclusions:

A cohort of infants with unilateral aphakia successfully wore contact lenses with relatively few adverse events.
Serratia liquefaciens Causing Severe Ocular Damage in Noncontact Lens Wearer
Authors: Ranganatha Akshatha , Rana Mrinal , Murray Aidan
Published: July 2016

Serratia liquefaciens is a rarely encountered gram-negative organism in ophthalmology practice. The only reported ocular infections are from contamination of contact lenses. The authors report the first case of a patient who developed orbital cellulitis secondary to severe S. liquefaciens microbial keratitis.
Prosthetic Replacement of the Ocular Surface Ecosystem (PROSE) Treatment for Complications After LASIK
Authors: Mian Sophia Z. , Agranat Joshua S. , Jacobs Deborah S.
Published: July 2016

Objectives:

To report experience with Prosthetic Replacement of the Ocular Surface Ecosystem (PROSE) treatment for complications after laser in situ keratomileuisis (LASIK).

Methods:

Retrospective review of clinical and manufacturing records. A database of patients who underwent PROSE treatment from 1992 to 2007 was searched to yield all patients with history of LASIK. Primary indication for PROSE treatment and year of LASIK is reported as well as history of contact lens intolerance and pretreatment and posttreatment best-corrected visual acuity (BCVA).

Results:

From 1992 to 2007, 44 patients (75 eyes) with history of LASIK underwent PROSE treatment. Patients with corneal ectasia (n=23, 52%) comprise the largest group of patients, followed by those with other optical aberrations (n = 14.32%), dry eye (n = 4.9%), and corneal neuralgia (n=3.7%). Thirteen patients (30%) had more than one indication for PROSE treatment. The majority (71%) of patients referred for PROSE treatment had LASIK between 1998 and 2000, including every patient with aberrations as primary indication. Eighty-six percent of all patients had history of contact lens intolerance. Eighty-four percent of eyes showed improvement in BCVA after PROSE treatment, mean −0.3LogMAR, (P < 0.0001, 2-tailed paired t test, n = 75).

Conclusions:

PROSE treatment is an effective option for management of ectasia, cornea first surface aberrations, dry eye, and corneal neuralgia after LASIK, even in patients who are contact lens intolerant.
Vaccines against major ICU pathogens: where do we stand?
Authors: Pletz Mathias W. , Uebele Julia , Götz Karen , Hagel Stefan , Bekeredjian-Ding Isabelle
Published: July 2016

Purpose of review

Multidrug resistance of bacterial pathogens has confronted physicians around the world with the threat of inefficacy of the antibiotic regime, which is particularly important for patients with sepsis. Antibiotic resistance has revived search for alternative nonantibiotic strategies. Among them, prophylaxis by vaccination is an appealing concept.

Recent findings

This review provides a compact overview on available vaccines against community-acquired pathogens such as pneumococci (in synergy with influenza) and meningococci and provides an overview on the ongoing developments of vaccines targeting typical nosocomial pathogens such as Clostridium difficile, Staphylococcus aureus, Acintetobacter baumannii, Klebsiella pneumonia, and Pseudomonas aeruginosa.

The effects achieved by some conjugated vaccines (e.g. against Haemophilus influenzae B and Streptococcus pneumoniae) are encouraging. Their widespread use has resulted in a decrease or almost elimination of invasive diseases by the covered pneumococcal serotypes or Haemophilus influenzae B, respectively. These vaccines confer not only individual protection but also exploit herd protection effects. However, a multitude of failures reflects the obstacles on the way to effective and well tolerated bacterial vaccines. Regional differences in strain prevalence and variability of antigens that limit cross-protectivity remain major obstacles. However, promising candidates are in clinical development.
Critical care for dengue in adult patients: an overview of current knowledge and future challenges
Authors: Pang Junxiong , Leo Yee-Sin , Lye David C.
Published: July 2016

Purpose of review

This review aims to update and summarize the current knowledge about clinical features, management, and risk factors of adult dengue patients requiring intensive care with consequently higher risk of mortality.

Recent findings

Increasingly, there are more adult dengue patients who require intensive care. This may be due to a shift in epidemiology of dengue infection from mainly a pediatric disease toward adult disease. In addition, multiorgan dysfunction was observed to be a key risk factor for ICU admission and mortality. This may be due to older adults having preexisting comorbidities that potentially predispose to have multiple severe organ impairment. Interventions remain largely supportive but also require more evidence-based trials and treatment protocols.

These findings highlight the common clinical manifestations of adult dengue patients and the challenges of clinical management in ICU. Risk factors for prediction of adult dengue patients who require ICU are available, but they lack validation and consistent study design for meta-analysis in future. Early recognition of these risk factors, with close monitoring and prompt clinical management, remains critical to reduce mortality.
Community-acquired pneumonia: still a major burden of disease
Authors: Feldman Charles , Anderson Ronald
Published: July 2016

Purpose of review

Describe recent studies that may impact on the management of community-acquired pneumonia (CAP).

Recent findings

CAP continues to be associated with a considerable burden of disease. Diagnosis remains problematic, and various biomarkers are neither accurate in the diagnosis of the presence of CAP nor superior to standard severity of illness scores in predicting outcome. Current evidence indicates that patients with nonsevere CAP can be effectively treated with antibiotic monotherapy, whereas those with severe infection, particularly ICU cases, do best with early initiation of combination antibiotic therapy. Several studies have investigated anti-inflammatory, adjunctive therapies for severe CAP, with corticosteroids appearing to be most promising. It is well recognized that cardiac complications occur during the course of CAP, being associated with poorer short-term and long-term outcomes, prompting considerable interest in the adjunctive potential of statins and antiplatelet therapies. In addition to evaluating these adjunctive therapies, attention has also focused on identifying strategies that predict the need for ICU admission in patients with CAP.

Although questions remain, particularly with regard to prediction of outcome, recent studies of CAP, both clinical and experimental, have contributed novel insights into disease pathogenesis that may enable improvement of current treatment strategies.
Sequential Crohn’s Ileitis, Ileosigmoidal Fistula, Segmental Sigmoid Polyposis, and Sigmoid Stricture
Authors: Korelitz Burton I. , Kesar Vivek , Taunk Raja , Schneider Judy
Published: July 2016

Background:

We have previously recognized segmental sigmoid polyps as an indicator of a fistula from Crohn’s ileitis to the sigmoid or the proximal rectum. In the course of this study, we realized that many patients with this fistula had no sigmoid polyps, but the sigmoid was the site of marked inflammation and early or late stricture formation. Furthermore, in some patients with a stricture, the fistula was not recognized until the surgeon (or the pathologist) dissected an inflammatory peri-ileal and/or a perisigmoidal mass.

In this study, we have sought to clarify the sequence of events by focusing on the segmental inflammation and the stricturing of the sigmoid so that its significance can be recognized as a local complication of the ileitis and the progression of its severity as opposed to arising sui generis.

Materials and Methods:

From our database of >3000 patients with inflammatory bowel disease at Lenox Hill Hospital, we identified 45 patients with Crohn’s ileitis and ileosigmoid fistula (ISF): 24 had segmental sigmoid polyps and 18 had segmental inflammatory sigmoid strictures. The fistula was first seen by imaging in 36 patients, but not until resection by the surgeon or dissection by the pathologist in 7 patients.

Results:

The method of diagnosis for the initial recognition of the ISF and the sigmoid stricture is presented in Table 1. In 36 of the 45 cases, the ISF was recognized by radiologic imaging. In total, 31 of the 36 cases required surgical intervention, not because of the fistula, but because of small-bowel obstruction due to the ileitis. In 7 of the 31 (22%) cases, the fistula was recognized only by dissection of the inflammatory ileosigmoid mass by the surgeon or examination of the surgical specimen by the pathologist. The sequence of events from the originating ileitis to the ISF to the segmental sigmoid polyposis and stricture, with the resulting sigmoid obstruction, is shown in Figures 1A–E.

Conclusions:

We emphasize the natural history of the ISF so that its recognition will lead to earlier medical management of the originating ileitis. Furthermore, it adds evidence of the recognition that the causative agent of Crohn’s disease is carried by the fecal stream.
Mechanism of Increased Intestinal Permeability in Acute Pancreatitis
Authors: Sonika Ujjwal , Goswami Pooja , Thakur Bhaskar , Yadav Rajni , Das Prasenjit , Ahuja Vineet , Saraya Anoop
Published: July 2016

Background and Aims:

Intestinal permeability (IP) has been shown to be increased in acute pancreatitis (AP) and is considered to be responsible for development of septic complications. However, the mechanism of increase in IP is not well studied. We studied whether alteration in tight junction proteins (TJP) has any role in altered IP in patients with AP.

Materials and Methods:

This is a prospective study conducted at a tertiary care referral center. Twenty consecutive moderate and severe AP patients fulfilling the study criteria were included along with 20 controls that underwent gastroduodenoscopy for dyspepsia. IP was measured with lactulose mannitol (LM) ratio and TJP were studied by measuring expression of claudin-2 and claudin-4 in duodenal biopsy samples. Statistical analysis was done with STATA 13.0.

Results:

IP as depicted by LM ratio was significantly higher in AP patients as compared with controls (4.659±10.4 vs. 0.101±0.297; P<0.001). Claudin-4 expression was reduced in duodenal biopsies in AP patients (P<0.001 for crypt intercellular junction and P=0.007 for crypt cytoplasm). However, LM ratio was not associated with either mortality (P=0.12) or development of infected pancreatic necrosis (P=0.3).

Conclusions:

IP is increased in AP. Alteration in TJP in the form of reduced claudin-4 expressions could be the possible mechanism for increased IP.
True, true, unrelated? A review of recent evidence for a causal influence of breakfast on obesity
Authors: Dhurandhar Emily J.
Published: July 2016

Purpose of review

It has long been known that breakfast skipping is associated with obesity; however, well controlled clinical trials have only recently been conducted to determine a causative relationship.

Recent findings

Skipping breakfast is likely to be detrimental for insulin sensitivity; however, randomized trials suggest that it does not play a large role in weight gain or weight loss. Specific breakfast strategies such as certain types of breakfast, and consuming more calories in the morning relative to the evening, however, may produce greater weight loss.

The act of eating breakfast, compared to skipping it, does not appear to have a large impact on body weight. More specific strategies regarding the size and type of breakfast may be required for a substantial effect on weight loss, and improving glycemic regulation may be an important reason to consume breakfast rather than skipping it.
The Impact of Socioeconomic Factors on the Outcome of Childhood Acute Lymphoblastic Leukemia (ALL) Treatment in a Low/Middle Income Country (LMIC)
Authors: Jabeen Kishwer , Ashraf Mohammed S. , Iftikhar Sundus , Belgaumi Asim F.
Published: July 2016

Survival for childhood acute lymphoblastic leukemia (ALL) has improved significantly, but these benefits may not be available to many children from low and middle income countries, where reasons for treatment failure may be unique to their environment. We retrospectively reviewed data on pediatric (1 to 18 y or younger) patients with newly diagnosed ALL treated over 5 years at a children’s cancer hospital in Pakistan. Patients were treated with modified Berlin-Frankfurt-Muenster -based therapy without risk stratification. There were 255 children with a median age of 7 years (mean, 7.65 y) and a male preponderance (M:F=1.6:1). 20% had T-ALL, one-third had white blood cells >50×109/L and 13.7% central nervous system disease. A majority (56.5%) was malnourished. In total, 49 (19.2%) died before the end of induction and 21 died in complete remission. Most deaths were infection-related. A total of 50 patients relapsed and 19 abandoned therapy after complete remission. Five-year overall survival is 52.9% with abandonment censored and 45.8% with abandonment as an event. Overall survival was related to socioeconomic status but not to known risk factors. The outcome of ALL at our center is suboptimal and associated with factors not commonly seen in developed countries. Special attention to early diagnosis, infection control, and parental educational are needed to improve the survival.
Optimizing Team Dynamics: An Assessment of Physician Trainees and Advanced Practice Providers Collaborative Practice*
Authors: Foster Cortney B. , Simone Shari , Bagdure Dayanand , Garber Nan A. , Bhutta Adnan
Published: July 2016

Objectives:

The presence of advanced practice providers has become increasingly common in many ICUs. The ideal staffing model for units that contain both advanced practice providers and physician trainees has not been described. The objectives of this study were to evaluate ICU staffing models that include physician trainees and advanced practice providers and their effects on patient outcomes, resident and fellow education, and training experience. A second aim was to assess strategies to promote collaboration between team members.

Data Sources:

PubMed, CINAHL, OVID MEDLINE, and Cochrane Review from 2002 to 2015.

Study Selection:

Experimental study designs conducted in an ICU setting.

Data Extraction:

Two reviewers screened articles for eligibility and independently abstracted data using the identified search terms.

Data Synthesis:

We found 21 articles describing ICU team structure and outcomes. Four articles were found describing the impact of advanced practice providers on resident or fellow education. Two articles were found discussing strategies to promote collaboration between advanced practice providers and critical care fellows or residents.

Conclusions:

Several articles were identified describing the utilization of advanced practice providers in the ICU and the impact of models of care on patient outcomes. Limited data exist describing the impact of advanced practice providers on resident and fellow education and training experience. In addition, there are minimal data describing methods to enhance collaboration between providers. Future research should focus on determining the optimal ICU team structure to improve patient outcomes, education of trainees, and job satisfaction of team members and methods to promote collaboration between advanced practice providers and physicians in training.
Effects of Health Insurance Among Patients on Hepatitis C Treatment Along the Texas–Mexico Border
Authors: Romero Roberta , Campbell Lisa , Song Huaxin , Zuckerman Marc J. , Alozie Ogechika
Published: July 2016

The incidence and prevalence of hepatitis C virus (HCV) is steadily increasing across the world. Increasing morbidity and mortality rates associated with HCV are influencing research on treatment outcomes. The purpose of this project was to examine the effect of health insurance status and office visit compliance on sustained virologic response (SVR) in adult patients living along the Texas–Mexico border treated for HCV and who received dual or triple medication therapy between January 2010 and August 2013. The objective of this project was to determine whether there is an association between health insurance status, and/or office visit compliance, and SVR. We conducted a longitudinal retrospective chart review pilot study of patients who underwent treatment with dual and triple therapy in a border community in Texas. Results revealed that lack of insurance did not affect SVR in the Texas Tech University Health Sciences Center El Paso-based clinic setting due to enrollment into a managed healthcare program. Providing a financial benefit may improve treatment compliance of HCV-infected individuals, reduce overall cost, and improve the patient's quality of life.
Intralesional Injection of Bevacizumab for the Treatment of an Apical Orbital Cavernous Venous Malformation
Authors: Sweeney Adam R. , Chappell Michael , Khorsand Derek A. , Jian-Amadi Arash , Francis Courtney E.
Published: July 2016

Surgical excision of orbital cavernous venous malformations located in the orbital apex is challenging due to difficulty obtaining surgical exposure and higher risk of morbidity. Intralesional bevacizumab injection has been utilized for the treatment of choroidal and intracranial cavernous venous malformations. A 52-year-old woman with an orbital apical mass consistent with a cavernous venous malformation causing decreased visual acuity, diminished color vision, and visual field loss was treated with intralesional bevacizumab injected under direct surgical visualization. Subsequently, she demonstrated improved visual acuity, color vision, and slow but dramatic visual field improvement over one year. Injection of bevacizumab may be a viable alternative treatment for orbital cavernous venous malformations.
Nonglaucomatous Cupping: Fundus Photography and Spectral Domain Optical Coherence Tomography Imaging Features
Authors: Aboobakar Inas F. , Mettu Pradeep , El-Dairi Mays A.
Published: July 2016

Nonglaucomatous cupping is commonly encountered in neuro-ophthalmic practice. However, the progression of clinical and imaging findings over time has not been well described. We present serial fundus photographs and spectral domain optical coherence tomography from a pediatric patient with neuromyelitis optic spectrum disorder, which demonstrated progression of both cupping and optic atrophy in the setting of normal intraocular pressure.
Force and torque on spherical particles in micro-channel flows using computational fluid dynamics
Authors: Suo Jin , Edwards Erin E. , Anilkumar Ananyaveena , Sulchek Todd , Giddens Don P. , Thomas Susan N.
Published: July 2016

To delineate the influence of hemodynamic force on cell adhesion processes, model
in vitro
fluidic assays that mimic physiological conditions are commonly employed. Herein, we offer a framework for solution of the three-dimensional Navier–Stokes equations using computational fluid dynamics (CFD) to estimate the forces resulting from fluid flow near a plane acting on a sphere that is either stationary or in free flow, and we compare these results to a widely used theoretical model that assumes Stokes flow with a constant shear rate. We find that while the full three-dimensional solutions using a parabolic velocity profile in CFD simulations yield similar translational velocities to those predicted by the theoretical method, the CFD approach results in approximately 50% larger rotational velocities over the wall shear stress range of 0.1–5.0 dynes cm
−2
. This leads to an approximately 25% difference in force and torque calculations between the two methods. When compared with experimental measurements of translational and rotational velocities of microspheres or cells perfused in microfluidic channels, the CFD simulations yield significantly less error. We propose that CFD modelling can provide better estimations of hemodynamic force levels acting on perfused microspheres and cells in flow fields through microfluidic devices used for cell adhesion dynamics analysis.
Shared songs are of lower performance in the dark-eyed junco
Authors: Cardoso Gonçalo C. , Atwell Jonathan W.
Published: July 2016

Social learning enables the adjustment of behaviour to complex social and ecological tasks, and underlies cultural traditions. Understanding when animals use social learning versus other forms of behavioural development can help explain the dynamics of animal culture. The dark-eyed junco (
Junco hyemalis
) is a songbird with weak cultural song traditions because, in addition to learning songs socially, male juncos also invent or improvise novel songs. We compared songs shared by multiple males (i.e. socially learned) with songs recorded from only one male in the population (many of which should be novel) to gain insight into the advantages of social learning versus invention or improvisation. Song types shared by multiple males were on average of lower performance, on aspects of vocal performance that have been implicated in agonistic communication in several species. This was not explained by cultural selection among socially learned songs (e.g. selective learning) because, for shared song types, song performance did not predict how many males shared them. We discuss why social learning does not maximize song performance in juncos, and suggest that some songbirds may add novel songs to culturally inherited repertoires as a means to acquire higher-quality signals.
Plant–soil feedbacks promote negative frequency dependence in the coexistence of two aridland grasses
Authors: Chung Y. Anny , Rudgers Jennifer A.
Published: July 2016

Understanding the mechanisms of species coexistence is key to predicting patterns of species diversity. Historically, the ecological paradigm has been that species coexist by partitioning resources: as a species increases in abundance, self-limitation kicks in, because species-specific resources decline. However, determining coexistence mechanisms has been a particular puzzle for sedentary organisms with high overlap in their resource requirements, such as plants. Recent evidence suggests that plant-associated microbes could generate the stabilizing self-limitation (negative frequency dependence) that is required for species coexistence. Here, we test the key assumption that plant–microbe feedbacks cause such self-limitation. We used competition experiments and modelling to evaluate how two common groups of soil microbes (rhizospheric microbes and biological soil crusts) influenced the self-limitation of two competing desert grass species. Negative feedbacks between the dominant plant competitor and its rhizospheric microbes magnified self-limitation, whereas beneficial interactions between both plant species and biological soil crusts partly counteracted this stabilizing effect. Plant–microbe interactions have received relatively little attention as drivers of vegetation dynamics in dry land ecosystems. Our results suggest that microbial mechanisms can contribute to patterns of plant coexistence in arid grasslands.
Mapping the spatio-temporal risk of lead exposure in apex species for more effective mitigation
Authors: Mateo-Tomás Patricia , Olea Pedro P. , Jiménez-Moreno María , Camarero Pablo R. , Sánchez-Barbudo Inés S. , Rodríguez Martín-Doimeadios Rosa C. , Mateo Rafael
Published: July 2016

Effective mitigation of the risks posed by environmental contaminants for ecosystem integrity and human health requires knowing their sources and spatio-temporal distribution. We analysed the exposure to lead (Pb) in griffon vulture
Gyps fulvus
—an apex species valuable as biomonitoring sentinel. We determined vultures' lead exposure and its main sources by combining isotope signatures and modelling analyses of 691 bird blood samples collected over 5 years. We made yearlong spatially explicit predictions of the species risk of lead exposure. Our results highlight elevated lead exposure of griffon vultures (i.e. 44.9% of the studied population, approximately 15% of the European, showed lead blood levels more than 200 ng ml
−1
) partly owing to environmental lead (e.g. geological sources). These exposures to environmental lead of geological sources increased in those vultures exposed to point sources (e.g. lead-based ammunition). These spatial models and pollutant risk maps are powerful tools that identify areas of wildlife exposure to potentially harmful sources of lead that could affect ecosystem and human health.
Object size determines the spatial spread of visual time
Authors: Fulcher Corinne , McGraw Paul V. , Roach Neil W. , Whitaker David , Heron James
Published: July 2016

A key question for temporal processing research is how the nervous system extracts event duration, despite a notable lack of neural structures dedicated to duration encoding. This is in stark contrast with the orderly arrangement of neurons tasked with spatial processing. In this study, we examine the linkage between the spatial and temporal domains. We use sensory adaptation techniques to generate after-effects where perceived duration is either compressed or expanded in the opposite direction to the adapting stimulus' duration. Our results indicate that these after-effects are broadly tuned, extending over an area approximately five times the size of the stimulus. This region is directly related to the size of the adapting stimulus—the larger the adapting stimulus the greater the spatial spread of the after-effect. We construct a simple model to test predictions based on overlapping adapted versus non-adapted neuronal populations and show that our effects cannot be explained by any single, fixed-scale neural filtering. Rather, our effects are best explained by a self-scaled mechanism underpinned by duration selective neurons that also pool spatial information across earlier stages of visual processing.
False Negatives Are a Significant Feature of Next Generation Sequencing Callsets
Authors: Bobo Dean , Lipatov Mikhail , Rodriguez-Flores Juan L. , Auton Adam , Henn Brenna M.
Published: July 2016

Short-read, next-generation sequencing (NGS) is now broadly used to identify rare orde novomutations in population samples and disease cohorts. However, NGS data is known to be error-prone and post-processing pipelines have primarily focused on the removal of spurious mutations or “false positives” for downstream genome datasets. Less attention has been paid to characterizing the fraction of missing mutations or “false negatives” (FN). Here we interrogate several publically available human NGS autosomal variant datasets using corresponding Sanger sequencing as a truth-set. We examine both low-coverage Illumina and high-coverage Complete Genomics genomes. We show that the FN rate varies between 3%-18% and that false-positive rates are considerably lower (<3%) for publically available human genome callsets like 1000 Genomes. The FN rate is strongly dependent on calling pipeline parameters, as well as read coverage. Our results demonstrate that missing mutations are a significant feature of genomic datasets and imply additional fine-tuning of bioinformatics pipelines is needed. To address this, we design a phylogeny-aware tool [PhyloFaN] which can be used to quantify the FN rate for haploid genomic experiments, without additional generation of validation data. Using PhyloFaN on ultra-high coverage NGS data from both Illumina HiSeq and Complete Genomics platforms derived from the 1000 Genomes Project, we characterize the false negative rate in human mtDNA genomes. The false negative rate for the publically available mtDNA callsets is 17-20%, even for extremely high coverage haploid data.
Genomic divergence, introduction history and latitudinal adaptation of grass carp
Authors: Wang Le , Shen Yubang , Fu Jianjun , Xu Xiaoyan , Yue Gen Hua , Li Jiale
Published: July 2016

Understanding the genomic signatures of population differentiation is fundamental to obtain a comprehensive view of the evolutionary process of organisms. Grass carp is one of the most important fish species in the world due to its significant value in aquaculture and world-wide vegetation biocontrol. However, little is known about the contemporary population structure and also the genetic basis of adaptation to a wide range of latitudinal environments. Using 43310 SNPs generated by genotyping by sequencing in 197 grass carps from nine populations, we examined the patterns of population differentiation, historical introduction and evidence of local selection. The overall genetic differentiation across all native populations was unexpectedly low. Nevertheless, these native populations were clearly differentiated into three genetic clusters, corresponding to the Yangtze River, the Pearl River and the Heilongjiang River System, respectively. Populations in Malaysia, India and Nepal, with the earliest introduction records, most likely have an origin from the Pearl River System. Using conceptually different approaches, 451 loci were detected under potential local selection, among which 84 were annotated to have a gene feature. 19.0% of the genes under putative selection were involved in immune responses, while 42.9% of the annotated loci showed a signature of latitudinal variation. This study provides valuable information for application of genomic tools in addressing questions concerning population differentiation that was influenced by both neutral and adaptive forces, as well as human activities.
The fail-safe mechanism of post-transcriptional silencing of unsplicedHAC1mRNA
Authors: Di Santo Rachael , Aboulhouda Soufiane , Weinberg David E.
Published: July 2016

HAC1encodes a transcription factor that is the central effector of the unfolded protein response (UPR) in budding yeast. When the UPR is inactive,HAC1mRNA is stored as an unspliced isoform in the cytoplasm and no Hac1 protein is detectable. Intron removal is both necessary and sufficient to relieve the post-transcriptional silencing ofHAC1mRNA, yet the precise mechanism by which the intron prevents Hac1 protein accumulation has remained elusive. Here, we show that a combination of inhibited translation initiation and accelerated protein degradation—both dependent on the intron—prevents the accumulation of Hac1 protein when the UPR is inactive. Functionally, both components of this fail-safe silencing mechanism are required to prevent ectopic production of Hac1 protein and concomitant activation of the UPR. Our results provide a mechanistic understanding ofHAC1regulation and reveal a novel strategy for complete post-transcriptional silencing of a cytoplasmic mRNA.
Diamond beamline I07: a beamline for surface and interface diffraction
Authors: Nicklin Chris , Arnold Tom , Rawle Jonathan , Warne Adam
Published: July 2016

Beamline I07 at Diamond Light Source is dedicated to the study of the structure of surfaces and interfaces for a wide range of sample types, from soft matter to ultrahigh vacuum. The beamline operates in the energy range 8–30 keV and has two endstations. The first houses a 2+3 diffractometer, which acts as a versatile platform for grazing-incidence techniques including surface X-ray diffraction, grazing-incidence small- (and wide-) angle X-ray scattering, X-ray reflectivity and grazing-incidence X-ray diffraction. A method for deflecting the X-rays (a double-crystal deflector) has been designed and incorporated into this endstation, extending the surfaces that can be studied to include structures formed on liquid surfaces or at liquid–liquid interfaces. The second experimental hutch contains a similar diffractometer with a large environmental chamber mounted on it, dedicated toin situultrahigh-vacuum studies. It houses a range of complementary surface science equipment including a scanning tunnelling microscope, low-energy electron diffraction and X-ray photoelectron spectroscopy ensuring that correlations between the different techniques can be performed on the same sample, in the same chamber. This endstation allows accurate determination of well ordered structures, measurement of growth behaviour during molecular beam epitaxy and has also been used to measure coherent X-ray diffraction from nanoparticles during alloying.
Structure of the lutein-binding domain of human StARD3 at 1.74 Å resolution and model of a complex with lutein
Authors: Horvath Martin P. , George Evan W. , Tran Quang T. , Baumgardner Kody , Zharov Gabe , Lee Sarah , Sharifzadeh Hassan , Shihab Saeed , Mattinson Ty , Li Binxing , Bernstein Paul S.
Published: July 2016

A crystal structure of the lutein-binding domain of human StARD3 (StAR-related lipid-transfer protein 3; also known as MLN64) has been refined to 1.74 Å resolution. A previous structure of the same protein determined to 2.2 Å resolution highlighted homology with StARD1 and shared cholesterol-binding character. StARD3 has since been recognized as a carotenoid-binding protein in the primate retina, where its biochemical function of binding lutein with specificity appears to be well suited to recruit this photoprotective molecule. The current and previous structures correspond closely to each other (r.m.s.d. of 0.25 Å), especially in terms of the helix-grip fold constructed around a solvent-filled cavity. Regions of interest were defined with alternate conformations in the current higher-resolution structure, including Arg351 found within the cavity and Ω1, a loop of four residues found just outside the cavity entrance. Models of the complex with lutein generated by rigid-body docking indicate that one of the ionone rings must protrude outside the cavity, and this insight has implications for molecular interactions with transport proteins and enzymes that act on lutein. Interestingly, models with the ∊-ionone ring characteristic of lutein pointing towards the bottom of the cavity were associated with fewer steric clashes, suggesting that steric complementarity and ligand asymmetry may play a role in discriminating lutein from the other ocular carotenoids zeaxanthin andmeso-zeaxanthin, which only have β-ionone rings.
Process reengineering by using the 4PL approach
Authors: Mehmann Jens , Teuteberg Frank
Published: July 2016

Purpose

– Sectors with high transport volumes face the challenge of reengineering existing processes. Furthermore, new models that support transportation processing are required. One possible model would be a fourth party logistics service provider (4PL) approach in order to increase the efficient use of resources. The purpose of this paper is to describe a method for reengineering a transportation handling process using the 4PL approach.

Design/methodology/approach

– Based upon a case study approach existing processes for transportation handling are modelled. Specifications of and definitions for the 4PL approach are compiled and analysed through a literature review. With the help of expert interviews essential functions are identified and the target model is validated.

Findings

– The results of the effort demonstrate that the application of a 4PL approach facilitates an improved transportation process. This may be due to the modification of the IT and communication technology (ICT) that have been applied. Based upon expanded planning horizons an improved planning of orders, a strengthening of the competencies of the involved actors were observed.

Practical implications

– Transportation handling in the agricultural sector is of increasing importance in light of the need to feed a growing global population under the condition of limited productive land for agriculture. This paper describes the alterations in the ICT infrastructure as well as the resulting organisational and technical implications, if a 4PL is used.

Originality/value

– The 4PL approach is an issue that is increasingly discussed in scientific publications. Furthermore, this approach has experienced new opportunities for implementation due to recent developments in ICT.
What contributes to adaptive company resilience? A conceptual and practical approach
Authors: Menéndez Blanco Juan Manuel , Montes Botella José Luis
Published: July 2016

Purpose

This paper aims to explore how companies could adapt to challenges derived from globalization, competitiveness and knowledge-based economy through resiliency as organizational property. It delves to into the factors enhancing the termed nurtured, especially those related to human resources and innovation.

Design/methodology/approach

The research approach is framed within the long run analysis of the internal perspective of resources and business performance (resources-based model) and the theory of complex adaptive systems. According to these approaches, methods and variables for empirically assess company resilience are proposed.

Findings

Main findings indicate a considerable contribution of human resources and innovation to company resilience. Besides, adaptive company resilience requires product diversification and productivity. By strengthening and developing nurtured resilience, a company is equipped to quickly recovering after being adversely affected by a shock, withstand shocks and avoid shocks.

Practical implications

Resilience focus management could be an additional tool for managing the unexpected and also complementary to early warning systems.

Originality/value

This paper regards resilience as an integrated and overall framework for developing company internal capabilities balancing efficiency and adaptability (and does not consider it, merely, as an add-on).
How women and men business owners perceive success
Authors: Kirkwood Jodyanne Jane
Published: July 2016

Purpose

– Women and men business owners are often thought to have different success criteria for their businesses, but there is little empirical research to support this. The purpose of this paper is to investigate the nature of self-defined success factors, and to compare women and men’s success criteria.

Design/methodology/approach

– This study surveyed 216 New Zealand business owners’ (78 women, 138 men) self-perceived success criteria for their businesses. Results are based primarily on an open-ended question on their interpretation of what success means to them. In total, 30 main categories of success factors were identified, and the four main factors analyzed in depth.

Findings

– The four most frequently occurring success factors were financial success, personal satisfaction, work-life/work-family balance, and satisfied stakeholders. Women and men business owners described very similar success criteria, which were balanced across financial success and personal and relationship factors. No statistically significant gender differences were found in the incidence of these success factors, suggesting a movement of male business owners to a more holistic view of business success that incorporates financial success, alongside personal and relationship aspects.

Research limitations/implications

– Offers implications for researchers, policy makers, and practitioners. Highlights the need to be careful when designing research studies in multi-faceted areas such as business success, and also in gender comparative studies.

Originality/value

– Uses self-perceived success criteria to assess gender differences.
Measuring entrepreneurial intent? Temporal construal theory shows it depends on your timing
Authors: Hallam Cory , Zanella Gianluca , Dorantes Dosamantes Carlos Alberto , Cardenas Cesar
Published: July 2016

Purpose

– The purpose of this paper is to investigate the influence of temporal construal theory on entrepreneurial intention models using a three-country study. Inclusion of temporal construal theory in intent models would suggest path dependent influence on intent, and more specifically, that intent may be subdivided into temporally based categories, broadly codified as short-term and long-term intent.

Design/methodology/approach

– A quasi-experimental study of 1,046 university students in business and engineering from the USA, Mexico, and Spain was conducted. A temporal construal model of intent is proposed, including measures of short-term and long-term intent. Entrepreneurial self-efficacy (ESE), part of the perceived behavioral control in the theory of planned behavior, is utilized to structure the model antecedents.

Findings

– The results suggest the existence of differences in individual entrepreneurial intent measures depending on the individual’s perception of when the entrepreneurial event is anticipated to occur in their lives. Utilizing an ESE construct, the authors demonstrated that short-term entrepreneurial intent significantly mediates the effect of ESE on long-term entrepreneurial intent. Furthermore, the results identify a mediating model that does not depend on regional country differences, thus supporting the generalizability of the findings.

Originality/value

– The paper bridges temporal construal theory and entrepreneurial intentions to qualify the path dependent effects of this psychological phenomena and its impact on identifying nascent entrepreneurs. The multi-country results indicate the ability to generalize the findings into a more complete theoretical model of entrepreneurial intention and suggests potential improvements in predictive models that currently use single or averaged measures of entrepreneurial intent.
The human development index predicts female entrepreneurship rates
Authors: Maniyalath Narendranathan , Narendran Roshni
Published: July 2016

Purpose

– Past research has identified a negative association between national income and female entrepreneurship rates. Data from Global Entrepreneurship Monitor (GEM) 2012 are analyzed to determine whether the Human Development Index (HDI) predicts female entrepreneurship rates. The purpose of this paper is to indicate how other socioeconomic variables that measure human development interact with national income to predict female entrepreneurship rates.

Design/methodology/approach

– Data were drawn from the 2012 GEM data set, which provides information on female entrepreneurship rates in 61 countries. To test relevant hypotheses, dependent and socio-demographic variables were sourced from international databases to perform quantitative cross-country regression analyses.

Findings

– National income significantly predicted female entrepreneurship rates in the univariate analysis. However, this relationship became non-significant when development indices were added to the model. In contrast, the HDI, the Gender Inequality Index, and national religious composition were robust, significant predictors.

Practical implications

– This study presents evidence that human and gender development indices, and national religious composition, are better predictors of female entrepreneurship rates than national income. Thus, studies on female entrepreneurship rates should account and adjust for human development and gender equality indices. As religiosity continues to be pervasive within multiple nations, policymakers should consider this when developing interventions geared toward promoting female entrepreneurship.

Originality/value

– This paper identifies factors other than economic determinism to explain variance in female entrepreneurship rates and demonstrates that human development and gender inequality indices are better predictors of female entrepreneurship rates.