bluuebunny/crossref_metadata_2025 huggingface dataset:
MRI-Arthroscopy Correlation of the Rotator Cuff: A Case-based Review
Authors: Buerba Rafael A. , Arshi Armin , Lee Kim M. , Levine Benjamin D. , Petrigliano Frank A.
Published: October 2017

With significant advancements over recent decades, magnetic resonance imaging (MRI) and shoulder arthroscopy are important complementary tools in guiding orthopedic surgeons to diagnosis, decision making, and treatment of rotator cuff pathology. The objective of this article is to review the basic principles and pearls of MRI-arthroscopy correlation of the rotator cuff through an overview of our approach to reading shoulder MRI followed by a case-based review of selected conditions. By understanding and comparing the subtleties of these modalities, radiologists and clinicians can better appreciate both the utility and limitations of MRI in predicting operative findings.
MRI Arthroscopy Correlations: Ligaments of the Knee
Authors: Ruzbarsky Joseph J. , Konin Gabrielle , Mehta Naaman , Marx Robert G.
Published: October 2017

Magnetic resonance imaging and a thorough understanding of its interpretation in the diagnosis and management of injuries to the ligaments about the knee is an essential skill for orthopedists. The goal of this review is to provide a description of the native and injured anatomy through magnetic resonance imaging and its correlations, when appropriate, as seen through the arthroscope at the time of surgery. The ligaments of focus include the anterior cruciate ligament, the posterior cruciate ligament, the medial collateral ligament, the posterolateral corner, the anterolateral ligament, and the medial patellofemoral ligament.
MRI and Arthroscopic Evaluation of Meniscal Injuries
Authors: Blake Matthew H. , Lattermann Christian , Johnson Darren L.
Published: October 2017

There has been an increasing awareness of the importance of the meniscus in maintaining the health and function of the knee. When injured, magnetic resonance imaging (MRI) has become the gold standard to diagnose meniscal tears. The information obtained from the MRI helps determine the need for surgical intervention. To achieve the best patient outcome a surgeon must be able to diagnose a meniscal injury by MRI as well as identify the injury at time of arthroscopy. This article aims to illustrate meniscal pathology utilizing side by side comparison of MRI identified meniscal injuries to its arthroscopic correlate as well as describe treatment options for the injury.
Ankle MRI and Arthroscopy Correlation With Cartilaginous Defects and Symptomatic Os Trigonum
Authors: Powell Brian D. , Cooper Minton T.
Published: October 2017

Arthroscopic intervention of the foot and ankle is used for a growing number of procedures. Magnetic resonance imaging (MRI) can be a helpful technique while detecting pathology before surgical intervention. A common use of MRI is detecting osteochondral lesion of the talus; however, other pathology can be detected including but not limited to symptomatic Os trigonum and subtalar osteochondral defects. An MRI sensitivity and specificity for detecting these pathologies vary. Correlating findings on MRI with arthroscopy is helpful in determining its accuracy and will be discussed in the following case examples.
MRI and Arthroscopy Correlation in the Patellofemoral Joint
Authors: Friedman Lisa G.M. , White Melissa S. , Carroll Patrick F. , Macalena Jeffrey A. , Arendt Elizabeth A. , Ellermann Jutta M. , Tompkins Marc
Published: October 2017

The patellofemoral joint is an articulation between the patella and the femoral trochlea, which serves to increase the lever arm of the extensor mechanism. The stability of the patella within the trochlear groove is supported statically by the bony confines of the groove itself, as well as the medial patellofemoral ligament, and dynamically by the vastus musculature. Pathologic changes seen on magnetic resonance imaging (MRI) are frequently well correlated with findings found by arthroscopy at the time of surgery. Degenerative changes to the articular cartilage, osteochondral lesions and loose bodies, tears in the retinaculum, and the medial patellofemoral ligament can be seen in MRI and are well correlated with arthroscopy. In addition, other findings that may predispose an individual to injury or degenerative changes over time, such as patella alta and trochlear dysplasia, can also be assessed by MRI and observed arthroscopically.
Feasibility of a 3D Printed Patient-Specific Model System to Determine Hemodynamic Energy Delivery During Extracorporeal Circulation
Authors: Ahn Chi Bum , Lee Seok In , Choi Chang Hyu , Park Chul Hyun , Park Kook Yang , Lee Jin Woo , Son Kuk Hui
Published: October 2017

Although many have studied the effects of pulsatile flow on extracorporeal circulation, its advantages remain controversial. One reason for this situation is that in most studies, pulsatility was evaluated using an in vitro model system. The most serious disadvantage of such model systems is that they lack consideration of anatomical variations due to the use of a straight tubing line to mimic the aorta. In the current study, the authors constructed and tested the feasibility of a three-dimensional (3D) printed, patient-specific, silicone aortic model to determine whether aortic cannula tip positional changes affect energy equivalent pressure (EEP) and surplus hemodynamic energy (SHE) in carotid arteries. Donovan model systems were connected to a pulsatile pump (Korea hybrid ventricular assist device [KH-VAD]; Korea Artificial Organ Center, Seoul, Korea) and a 3D printed silicone model of the ascending aorta. The KH-VAD mimicked the heart, and another pulsatile pump (Twin-Pulse Life Support [T-PLS]; Newheartbio Co., Seoul, Korea) was connected to an aortic cannula, which was inserted at three different tip positions. Using this 3D printed silicone model of the ascending aorta, it was found that EEP and SHE of both right and left carotid arteries were significantly affected by aortic cannula tip position. The authors suggest that the described 3D printed, patient-specific, aorta model provides a feasible option to measure hemodynamic energy accurately given the considerable anatomical differences of model circuits.
Atrial Fibrillation Should Guide Prophylactic Tricuspid Procedures During Left Ventricular Assist Device Implantation
Authors: Anwer Lucman A. , Tchantchaleishvili Vakhtang , Poddi Salvatore , Daly Richard C. , Joyce Lyle D. , Kushwaha Sudhir S. , Topilsky Yan , Stulak John M. , Maltais Simon
Published: October 2017

Atrial fibrillation (AF) and tricuspid regurgitation (TR) are common in patients undergoing left ventricular assist device (LVAD) implantation. TR progression is associated with the presence of AF, and questions remain as to who benefits from tricuspid valve procedures (TVPs). We examined the impact of preoperative AF on TR progression after LVAD implantation. From February 2007 to May 2014, 250 patients underwent LVAD implantation at our institution. Patients with concomitant TVP were excluded from this analysis (113 patients). The indication for LVAD was destination therapy in 80 patients (58%) and the etiology of heart failure was ischemic in 73 (53%). Follow-up was available in all early survivors for a total of 393 patient-years of support. Of the 137 non-TVP patients, 52 (38%) had AF preoperatively. Observed overall survival at 1, 3, and 5 years was 82%, 67%, and 55%, respectively. Median grade of TR increased from 2 preoperatively to 3 (p = 0.04) in the AF group and 2.2 (p = 0.75) in the non-AF group at 5 years of follow-up. We also observed a significant difference in the degree of TR between groups at 3 months (p = 0.03) and 12 months (p = 0.01) postimplantation, and a trend toward significance at 18 (p = 0.06) and 24 (p = 0.07) months. The presence of AF is associated with early progression of TR after LVAD implantation. Addition of concomitant TVP in patients with preoperative AF may be considered in patients with less than severe TR. The impact of these findings on right ventricular failure/remodeling remains to be evaluated.
Modern Management of Pancreatic Fluid Collections
Authors: Andalib Iman , Dawod Enad , Kahaleh Michel
Published: October 2017

The last decade has seen dramatic shift in paradigm in the management of pancreatic fluid collections with the rise of endoscopic therapy over radiologic or surgical management. Endosonographic drainage is now considered the gold standard therapy for pancreatic pseudocyst. Infected pancreatic necroses are being offered endoscopic necrosectomy that has been facilitated by the arrival on the market of large diameter lumen-apposing metal stent. Severe pancreatitis or failure to thrive should receive enteral nutrition while pancreatic ductal disruption or strictures are best treated by pancreatic stenting.
Pancreatic Cystic Lesions
Authors: Vilas-Boas Filipe , Macedo Guilherme
Published: October 2017

The diagnosis of incidental pancreatic cystic lesions is increasing in the general population because of the routine use of cross-sectional imaging modalities. Not all cysts are neoplastic, and the majority of cystic neoplasms have a low overall likelihood of progression to malignancy. Current management is based on imaging and cyst fluid analysis, but we are not able to diagnose the specific type of cyst and its malignant potential in a significant number of patients. Better diagnostic tools are required to avoid unnecessary surgical resections that carry an important risk of morbidity and mortality. Herein we review current evidence concerning the use of new endoscopic modalities for the evaluation of pancreatic cystic lesions. We focus our discussion on the new cyst fluid markers, and the advancements on modalities such as confocal endomicroscopy, contrast-enhanced endoscopic ultrasound, and the use of Spyglass. We also discuss the use of new devices to improve the cellular yield from cyst fluid and to obtain cyst-wall tissue, namely the cytology brush, the fine needle biopsy, and forceps for cyst-wall biopsy.
Preventing Hospitalization in Mild Acute Pancreatitis Using a Clinical Pathway in the Emergency Department
Authors: Kothari Darshan , Babineau Matthew , Hall Matthew , Freedman Steven D. , Shapiro Nathan I. , Sheth Sunil G.
Published: October 2017

Goals:

We created an observation pathway with close outpatient follow-up for patients with mild acute pancreatitis (AP) to determine its effect on admission rates, length of stay (LOS), and costs.

Background:

AP is a common reason for hospitalization costing $2.6 billion annually. Majority have mild disease and improve quickly but have unnecessarily long hospital stays.

Study:

We performed a pilot prospective cohort study in patients with AP at a tertiary-care center. In total, 90 patients with AP were divided into 2 groups: observation cohort and admitted cohort. Exclusion criteria from observation included end-organ damage, pancreatic complications, and/or severe cardiac, liver, and renal disease. Patients in observation received protocolized hydration and periodic reassessment in the emergency department and were discharged with outpatient follow-up. Using similar exclusion criteria, we compared outcomes with a preintervention cohort composed of 184 patients admitted for mild AP in 2015. Our primary outcome was admission rate, and secondary outcomes were LOS, patient charges, and 30-day readmission.

Results:

Admitted and preintervention cohorts had longer LOS compared with the observation cohort (89.7 vs. 22.6 h,P<0.01 and 72.0 vs. 22.6 h,P<0.01). The observation cohort admission rate was 22.2% lower than the preintervention cohort (P<0.01) and had 43% lower patient charges ($5281 vs. $9279,P<0.01). Moreover there were significantly fewer imaging studies performed (25 vs. 49 images,P=0.03) in the observation cohort. There were no differences in readmission rates and mortality.

Conclusions:

In this feasibility study, we demonstrate that a robust pathway can prevent hospitalization in those with AP and may reduce resource utilization without a detrimental impact on safety.
Rolling-out Screening Volume Affecting Compliance Rate and Waiting Time of FIT-based Colonoscopy
Authors: Jen Hsiao-Hsuan , Hsu Chen-Yang , Chen Sam Li-Sheng , Yen Amy Ming-Fang , Chiu Sherry Yueh-Hsia , Fann Jean Ching-Yuan , Lee Yi-Chia , Wu Ming-Shiang , Hsu Wen-Feng , Peng Szu-Min , Chen Hsiu-Hsi , Chiu Han-Mo
Published: October 2017

Background and Study Aims:

The population-based colorectal cancer screening program with fecal immunochemical test (FIT) from the inaugural period to the rolling-out period may create a higher demand for colonoscopies, but such a change has not been quantified. We intended to assess the change in the compliance rate and the waiting time (WT) for a colonoscopy and the associated geographic and institutional variations across the 2 periods.

Materials and Methods:

Data from the Taiwanese nationwide colorectal cancer screening program were analyzed. The data included a total of 46,235 FIT-positive cases of 1,258,560 tests in the inaugural period (2004 to 2009) and 270,700 FIT-positive cases of 3,723,789 tests in the rolling-out period (2010 to 2013). The compliance rate and WT for colonoscopy after positive FIT was ascertained and compared between the 2 periods.

Results:

The rolling-out period resulted in a decline of 16.0% for compliance rate and yielded an additional 1,778,499 waiting days with variation across geography and institution. After adjusting for relevant factors, a decrease in compliance rate by 8.5% and an increase of 714,648 waiting days were still noted. In the rolling-out period, a remarkable decline in compliance rate by 9.8% was found in middle Taiwan, and the longest WT (1,260,109 d) was observed in southern Taiwan. Screening at public health centers led to a 19% decrease in compliance rate and an increase of 2,546,746 waiting days.

Conclusions:

The decrease in compliance rate and an increase in the WT with variation across geography and institution resulting from the increased volume of rolling-out FIT screening provide an insight into optimal resource allocation of clinical capacity for colonoscopy.
Clinical Implications of Pediatric Colonic Eosinophilia
Authors: Mark Jacob , Fernando Shahan D. , Masterson Joanne C. , Pan Zhaoxing , Capocelli Kelley E. , Furuta Glenn T. , de Zoeten Edwin F.
Published: October 2017

Objective:

Pediatric colonic eosinophilia represents a confounding finding with a wide differential. It is often difficult to determine which children may progress to inflammatory bowel disease (IBD), which have an eosinophilic colitis (EC), and which may have no underlying pathology. There is little guidance for the practitioner on the approach to these patients. To define the clinical presentations of colonic eosinophilia and identify factors which may aid in diagnosis we reviewed patients with colonic eosinophilia and the clinicopathologic factors associated with their diagnoses.

Methods:

An 8‐year retrospective chart review of children whose histopathology identified colonic eosinophilia (N = 72) compared to controls with normal biopsies (N = 35).

Results:

Patients with colonic eosinophilia had increased eosinophils/high‐power field compared to controls (P < 0.001) and had 3 clinical phenotypes. Thirty‐six percent had an inflammatory phenotype with elevated erythrocyte sedimentation rate (P < .0001), chronic inflammation on colonic biopsies (P < 0.001), and were diagnosed as having IBD. Thirty‐seven percent were diagnosed as having EC, associated with male sex (P < 0.005) and peripheral eosinophilia (P = 0.041). Twenty‐one percent had no significant colonic pathology. Forty‐three percent of patients had >1 colonoscopy and 68% of these had change from initial diagnoses.

Conclusions:

There are 3 main phenotypes of children with colonic eosinophilia. Signs of chronic systemic inflammation raise suspicion for IBD. Peripheral eosinophilia and male sex are associated with EC. A significant percent of children with colonic eosinophilia do not have colonic disease. Eosinophils/high‐power field is not reliable to differentiate etiologies. Repeat colonoscopies may be required to reach final diagnoses.
Prevalence and Factors Associated With Polypharmacy Use Among Adult Patients in Saudi Arabia
Authors: Balkhi Bander , AlQahtani Nasser , Alwhaibi Monira , Alshammari Thamir M. , Alhawassi Tariq M. , Mahmoud Mansour A. , Almetwazi Mansour , Ata Sondus , Basyoni Mada , Aljadhey Hisham
Published: October 2017

Background

Polypharmacy is very common in clinical practice, especially among adult patients. The use of multiple medications may increase the risk of adverse drug events, medication cost, and medication errors. In addition, polypharmacy exacerbates treatment complexity, which consequently leads to poor patients’ adherence to their medications. Despite being a well-recognized problem, few studies have investigated the prevalence and predictors of polypharmacy in Saudi Arabia.

Objectives

The aims of the study were to investigate the prevalence of polypharmacy among adult patients in a tertiary teaching hospital and to determine patients’ characteristics that are associated with polypharmacy.

Methods

This was a retrospective cross-sectional study using data extracted from the electronic health records database for a period of 6 months between January and June 2016 in outpatient setting. Descriptive statistics were used to analyze the study sample. A multivariate logistic regression model was used to examine the association between different variables and polypharmacy. Statistical analysis software (SAS 9.2) was used to analyze the study data.

Results

A total of 17,237 observations (67.2% females) were included in the final analysis. Of these, nearly 54% (n = 9222) of reported observations were found using up to four prescription drugs and the other 46% (n = 8015) were using five or more prescription drugs. Interestingly, the prevalence of polypharmacy use was doubled among adults with hypertension as compared with those without hypertension (odds ratio [OR] = 2.68, 95% confidence interval [CI] = 2.51–2.87). In addition, polypharmacy use was two times more prevalent among adults with diabetes as compared with those without diabetes (OR = 2.31, 95% CI = 1.99–2.28) and five times more prevalent in patient with dementia (OR = 5.57, 95% CI = 1.26–24.7). Moreover, polypharmacy in adult patients was significantly influenced by sex (OR = 1.69, 95% CI = 1.59–1.80) and nationality (OR = 2.15, 95% CI = 2.00–2.31).

Conclusions

Polypharmacy is common among adult patients especially those who are older than 60 years. Polypharmacy may affect the overall process of drug therapy. It can be a risk factor to develop undesirable adverse drug events, especially in those with chronic health conditions. A special care should be taken to manage polypharmacy among adults in Saudi Arabia.
Emerging multidrug-resistant Candida species
Authors: Colombo Arnaldo L. , Júnior João N. de Almeida , Guinea Jesus
Published: October 2017

Purpose of review

To describe the epidemiology, strategies for early detection, and clinical management of infections caused by the most commonly found multidrug-resistant (MDR)Candidaspp.

Recent findings

Increasing numbers of reports describing invasive infections by MDRCandida aurisandCandida glabratahas been reported in medical centers worldwide.

We checked all papers published along the last 10 years describing epidemiological, diagnostic, and clinical aspects of infections by MDRCandidaspp., with emphasis onC. aurisandC. glabrataspp.C. aurishas been reported in 15 countries and multidrug resistance rates is usually above 30%. Horizontal transmission is a great concern regardingC. auris.C. glabrataranks the second most reportedCandidaspp. in deep-seated infections from United States and some European Centers, although multidrug resistance rates above 10% are restricted to some US centers.Candida haemuloniicomplex isolates with poor susceptibility to azoles and amphotericin B have been isolated in superficial and deep-seated infections, whereasCandida guilliiermondiicomplex isolates with poor susceptibility to azoles and echinocandins have been recovered from catheter-related bloodstream infections. Other potential MDRCandidaspecies areCandida krusei,Candida lusitaniae,Candida kefyr,Yarrowia(Candida)lypolitica,andCandidarugosa.
Quantum phase slips: from condensed matter to ultracold quantum gases
Authors: D'Errico C. , Abbate S. Scaffidi , Modugno G.
Published: October 2017

Quantum phase slips (QPS) are the primary excitations in one-dimensional superfluids and superconductors at low temperatures. They have been well characterized in most condensed-matter systems, and signatures of their existence have been recently observed in superfluids based on quantum gases too. In this review, we briefly summarize the main results obtained on the investigation of phase slips from superconductors to quantum gases. In particular, we focus our attention on recent experimental results of the dissipation in one-dimensional Bose superfluids flowing along a shallow periodic potential, which show signatures of QPS.

This article is part of the themed issue ‘Breakdown of ergodicity in quantum systems: from solids to synthetic matter’.
Thermal inclusions: how one spin can destroy a many-body localized phase
Authors: Ponte Pedro , Laumann C. R. , Huse David A. , Chandran A.
Published: October 2017

Many-body localized (MBL) systems lie outside the framework of statistical mechanics, as they fail to equilibrate under their own quantum dynamics. Even basic features of MBL systems, such as their stability to thermal inclusions and the nature of the dynamical transition to thermalizing behaviour, remain poorly understood. We study a simple central spin model to address these questions: a two-level system interacting with strength
J
with
N
≫1 localized bits subject to random fields. On increasing
J
, the system transitions from an MBL to a delocalized phase on the
vanishing
scale
J
c
(
N
)∼1/
N
, up to logarithmic corrections. In the transition region, the single-site eigenstate entanglement entropies exhibit bimodal distributions, so that localized bits are either ‘on’ (strongly entangled) or ‘off’ (weakly entangled) in eigenstates. The clusters of ‘on’ bits vary significantly between eigenstates of the
same
sample, which provides evidence for a heterogeneous discontinuous transition out of the localized phase in single-site observables. We obtain these results by perturbative mapping to bond percolation on the hypercube at small
J
and by numerical exact diagonalization of the full many-body system. Our results support the arguments that the MBL phase is unstable in systems with short-range interactions and quenched randomness in dimensions
d
that are high but finite.

This article is part of the themed issue ‘Breakdown of ergodicity in quantum systems: from solids to synthetic matter’.
Atypical energy eigenstates in the Hubbard chain and quantum disentangled liquids
Authors: Veness Thomas , Essler Fabian H. L. , Fisher Matthew P. A.
Published: October 2017

We investigate the implications of integrability for the existence of quantum disentangled liquid (QDL) states in the half-filled one-dimensional Hubbard model. We argue that there exist finite energy-density eigenstates that exhibit QDL behaviour in the sense of Grover & Fisher (2014
J. Stat. Mech.
2014
, P10010. (
doi:10.1088/1742-5468/2014/10/P10010
)). These states are atypical in the sense that their entropy density is smaller than that of thermal states at the same energy density. Furthermore, we show that thermal states in a particular temperature window exhibit a weaker form of the QDL property, in agreement with recent results obtained by strong-coupling expansion methods in Veness
et al.
(2016 (
http://arxiv.org/abs/1611.02075
)).

This article is part of the themed issue ‘Breakdown of ergodicity in quantum systems: from solids to synthetic matter’.
Functional reorganisation and recovery following cortical lesions: A study in macaque monkeys
Authors: Ainsworth Matthew , Browncross Helen , Mitchell Daniel J , Mitchell Anna S , Passingham Richard E , Buckley Mark J , Duncan John , Bell Andrew H
Published: October 2017

Damage following traumatic brain injury or stroke can often extend beyond the boundaries of the initial insult and can lead to maladaptive cortical reorganisation. On the other hand, beneficial cortical reorganisation leading to recovery of function can also occur. Here, we used resting state FMRI (rsFMRI) to examine how functional connectivity in the macaque brain changed across time in response to lesions to the prefrontal cortex, and how this reorganisation correlated with changes in behaviour. Two monkeys were trained to perform location-based and object-based delayed match-to-sample tasks. We also collected rsFMRI data under general anaesthesia at two pre-lesion time-points, separated by 3-4 weeks. After two cycles of testing and scanning, the animals received a principal sulcus lesion followed by an additional 4 cycles of testing and scanning. Later, the same animals received a second lesion to the opposite hemisphere and additional cycles of testing and scanning.

Both animals showed a marked behavioural impairment following the first lesion, which was associated with a decrease in functional connectivity, predominantly within frontal-frontal networks in both hemispheres. Approximately 8 weeks following the lesion, performance improved, as did functional connectivity within these networks. Following the second lesion, functional connectivity again decreased and this was associated with a marginal behavioural deficit that did not recover.

Our data show that behavioural impairments reflect not just the removal of the lesioned area, but also disturbance to an extensive cortical network. This network can recover by restoring and/or strengthening pre-existing connections, leading to improvement in behaviour.
Cross talk between photo-pigments and graphene electron cloud - Designing a biodiode
Authors: Ray Sanhita , Sen Sayantani , Das Alakananda , Bose Anirban , Bhattacharya Anirban , Das Avishek , Chattopadhyay Sanatan , Patra Hirak , Singha Shib Shankar , Singha Achintya , Dasgupta Anjan Kr.
Published: October 2017

We report emergence of a new electrical material by growing photosynthetic biofilm on a Dirac material, graphene. The material showed new conducting as well as semiconducting properties. Frequency dependent capacitive spectra further indicated presence of electrical isosbestic points(at 0.8 and 9MHz), implying two state dieletric transitions at critical frequencies. A notable reult was a Schottky diode like behavior in the IV curve. Voltage dependent conductance with conductance peaks near the Schottky diode threshold was observed. We obtained facilitated growth of photosynthetic biofilm in presence of graphene. Lastly higher bacterial metabolism was seen in graphene incorporated biofilm. For this zero band gap Dirac material this can only be interpreted as coupling of the electron transport chain of the bacterial biofilm and the graphene electron cloud.
Reproducibility and repeatability of six high-throughput 16S rDNA sequencing protocols for microbiota profiling
Authors: Raju Sajan C. , Lagström Sonja , Ellonen Pekka , de Vos Willem M. , Eriksson Johan G. , Weiderpass Elisabete , Rounge Trine B.
Published: October 2017

Culture-independent molecular techniques and advances in next generation sequencing (NGS) technologies make large-scale epidemiological studies on microbiota feasible. A challenge using NGS is to obtain high reproducibility and repeatability, which is mostly attained through robust amplification. We aimed to assess the reproducibility of saliva microbiota by comparing triplicate samples. The microbiota was produced with simplified in-house 16S amplicon assays taking advantage of large number of barcodes. The assays included primers with Truseq (TS-tailed) or Nextera (NX-tailed) adapters and either with dual index or dual index plus a 6-nt internal index. All amplification protocols produced consistent microbial profiles for the same samples. Although, in our study, reproducibility was highest for the TS-tailed method. Five replicates of a single sample, prepared with the TS-tailed 1-step protocol without internal index sequenced on the HiSeq platform provided high alpha-diversity and low standard deviation (mean Shannon and Inverse Simpson diversity was 3.19 ± 0.097 and 13.56 ± 1.634 respectively). Large-scale profiling of microbiota can consistently be produced by all 16S amplicon assays. The TS-tailed-1S dual index protocol is preferred since it provides repeatable profiles on the HiSeq platform and are less labour intensive.
Contribution of non-coding mutations to RPGRIP1-mediated inherited retinal degeneration
Authors: Jamshidi Farzad , Place Emily M. , Mehrotra Sudeep , Navarro-Gomez Daniel , Maher Mathew , Valkanas Elise , Cherry Timothy J. , Lek Monkol , MacArthur Daniel , Pierce Eric A. , Bujakowska Kinga M.
Published: October 2017

Purpose

With the advent of gene therapies for inherited retinal degenerations (IRDs), genetic diagnostics will have an increasing role in clinical decision-making. Yet the genetic cause of disease cannot be identified using exon-based sequencing for a significant portion of patients. We hypothesized that non-coding mutations contribute significantly to the genetic causality of IRDs and evaluated patients with single coding mutations in RPGRIP1 to test this hypothesis.

Methods

IRD families underwent targeted panel sequencing. Unsolved cases were explored by whole exome and genome sequencing looking for additional mutations. Candidate mutations were then validated by Sanger sequencing, quantitative PCR, and in vitro splicing assays in two cell lines analyzed through amplicon sequencing.

Results

Among 1722 families, three had biallelic loss of function mutations in RPGRIP1 while seven had a single disruptive coding mutation. Whole exome and genome sequencing revealed potential non-coding mutations in these seven families. In six, the non-coding mutations were shown to lead to loss of function in vitro.

Conclusion

Non-coding mutations were identified in 6 of 7 families with single coding mutations in RPGRIP1. The results suggest that non-coding mutations contribute significantly to the genetic causality of IRDs and RPGRIP1–mediated IRDs are more common than previously thought.
Behavioral and neural evidence of the rewarding value of exercise behaviors: A systematic review
Authors: Cheval Boris , Radel Rémi , Neva Jason L. , Boyd Lara A. , Swinnen Stephan P. , Sander David , Boisgontier Matthieu P.
Published: October 2017

Background

In a time of physical inactivity pandemic, attempts to better understand the factors underlying the regulation of exercise behavior are important. The dominant neurobiological approach to exercise behavior considers physical activity to be a reward. However, negative affective responses during exercise challenge this idea.

Objective

Our objective was to systematically review studies testing the automatic reactions triggered by stimuli associated with different types of exercise behavior (e.g., physical activity, sedentary behaviors) and energetic cost variations (e.g., decreased energetic cost, irrespective of the level of physical activity).

Methods

Two authors systematically searched, screened, extracted, and analyzed data from articles in the MEDLINE database.

Results

We included 26 studies. Three outcomes of automatic processes were tested: Affective reactions, attentional capture, and approach tendencies. Behavioral results show that physical activity can become attention-grabbing, automatically trigger positive affect, and elicit approach behaviors. These automatic reactions explain and predict exercise behaviors. However, the use of a wide variety of measures prevents drawing solid conclusions about the specific effects of automatic processes. Brain imaging results are scarce but show that stimuli associated with physical activity and, to a lesser extent, sedentary behaviors activate regions involved in reward processes. Studies investigating the rewarding value of behaviors driving energetic cost variations such as behaviors minimizing energetic cost are lacking.

Conclusion

Reward is an important factor in exercise behavior. The literature based on the investigation of automatic behaviors seems in line with the suggestion that physical activity is rewarding, at least for physically active individuals. Results suggest that sedentary behaviors could also be rewarding, although this evidence remains weak due to a lack of investigations. Finally, from an evolutionary perspective, behaviors minimizing energetic cost are likely to be rewarding. However, no study has investigated this hypothesis. In sum, additional studies are required to establish a strong and complete framework of the reward processes underlying automatic exercise behavior.

Key points

- Behavioral and brain imaging studies using different outcomes of automatic behavior show that physical activity and, to a weaker extent, sedentary behaviors are rewarding.

- Behaviors minimizing energetic cost have been essential to evolutionary survival and are likely to be rewarding. However, experimental evidence is still lacking.

- The dominant neuropsychological approaches to exercise behavior are incomplete, which may partly explain our current inability to counteract the pandemic of physical inactivity.
Quantitative proteomic analysis of auxin signaling during seedling development
Authors: Kelley Dior R. , Shen Zhouxin , Walley Justin W. , Chapman Elisabeth J. , Briggs Steven P. , Estelle Mark
Published: October 2017

Auxin induces rapid gene expression changes throughout plant development. How these transcriptional responses relate to changes in protein abundance is not well characterized. We have identified auxin regulated proteins in whole seedlings, roots and hypocotyls and at three different time points (30 min, 120 min and 3 hours) using an iTRAQ (isobaric tags for relative and absolute quantification) based quantitative proteomics approach. These profiling experiments detected 4,701 proteins from seedling tissue, 6,740 proteins from root tissue and 3,925 proteins from hypocotyl tissue. Comparisons between the differentially expressed proteins data sets showed little overlap, suggesting that auxin proteomes exhibit both temporal and spatial specificity. Numerous proteins showed significant changes in abundance following auxin treatment independent of changes in cognate transcript abundance. This includes several well characterized proteins with various roles in auxin pathways, suggesting that complex gene regulation mechanisms follow auxin signaling events. Specifically, regulation of translation may play a role as inferred from MapMan categorization analyses and protein interaction networks comprised of auxin regulated proteins. Additionally, functional categorization of auxin regulated proteins indicates rapid and complex metabolic changes occur in both roots and hypocotyls in response to auxin which are not apparent from transcriptome analyses. Altogether these data describe novel auxin-regulated proteomes and are an excellent resource for identifying new downstream signaling components related to auxin-mediated plant growth and development.
INFERNO - INFERring the molecular mechanisms of NOncoding genetic variants
Authors: Amlie-Wolf Alexandre , Tang Mitchell , Mlynarski Elisabeth E. , Kuksa Pavel P. , Valladares Otto , Katanic Zivadin , Tsuang Debby , Brown Christopher D. , Schellenberg Gerard D. , Wang Li-San
Published: October 2017

The majority of variants identified by genome-wide association studies (GWAS) reside in the noncoding genome, where they affect regulatory elements including transcriptional enhancers. We propose INFERNO (INFERring the molecular mechanisms of NOncoding genetic variants), a novel method which integrates hundreds of diverse functional genomics data sources with GWAS summary statistics to identify putatively causal noncoding variants underlying association signals. INFERNO comprehensively infers the relevant tissue contexts, target genes, and downstream biological processes affected by causal variants. We apply INFERNO to schizophrenia GWAS data, recapitulating known schizophrenia-associated genes includingCACNA1Cand discovering novel signals related to transmembrane cellular processes.
CoDEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing
Authors: Jiang Yuchao , Wang Rujin , Urrutia Eugene , Anastopoulos Ioannis N. , Nathanson Katherine L. , Zhang Nancy R.
Published: October 2017

High-throughput DNA sequencing enables detection of copy number variations (CNVs) on the genome-wide scale with finer resolution compared to array-based methods, but suffers from biases and artifacts that lead to false discoveries and low sensitivity. We describe CODEX2, a statistical framework for full-spectrum CNV profiling that is sensitive for variants with both common and rare population frequencies and that is applicable to study designs with and without negative control samples. We demonstrate and evaluate CODEX2 on whole-exome and targeted sequencing data, where biases are the most prominent. CODEX2 outperforms existing methods and, in particular, significantly improves sensitivity for common CNVs.
A cryptic Tudor domain links BRWD2/PHIP to COMPASS-mediated histone H3K4 methylation
Authors: Morgan Marc A.J. , Rickels Ryan A. , Collings Clayton K. , He Xiaolin , Cao Kaixiang , Herz Hans-Martin , Cozzolino Kira A. , Abshiru Nebiyu A. , Marshall Stacy A. , Rendleman Emily J. , Sze Christie C. , Piunti Andrea , Kelleher Neil L. , Savas Jeffrey N. , Shilatifard Ali
Published: October 2017

Histone H3 Lys4 (H3K4) methylation is a chromatin feature enriched at gene cis-regulatory sequences such as promoters and enhancers. Here we identify an evolutionarily conserved factor, BRWD2/PHIP, which colocalizes with histone H3K4 methylation genome-wide in human cells, mouse embryonic stem cells, and Drosophila. Biochemical analysis of BRWD2 demonstrated an association with the Cullin-4–RING ubiquitin E3 ligase-4 (CRL4) complex, nucleosomes, and chromatin remodelers. BRWD2/PHIP binds directly to H3K4 methylation through a previously unidentified chromatin-binding module related to Royal Family Tudor domains, which we named the CryptoTudor domain. Using CRISPR–Cas9 genetic knockouts, we demonstrate that COMPASS H3K4 methyltransferase family members differentially regulate BRWD2/PHIP chromatin occupancy. Finally, we demonstrate that depletion of the single Drosophila homolog dBRWD3 results in altered gene expression and aberrant patterns of histone H3 Lys27 acetylation at enhancers and promoters, suggesting a cross-talk between these chromatin modifications and transcription through the BRWD protein family.
Crystal structure of 2,3,5,6-tetrakis(pyridin-2-yl)pyrazine hydrogen peroxide 4.75-solvate
Authors: Navasardyan Mger A. , Bezzubov Stanislav I. , Kuz'mina Lyudmila G. , Prikhodchenko Petr V. , Churakov Andrei V.
Published: October 2017

The structure of the title co-crystal, C24H16N6·4.75H2O2, consists of a 2,3,5,6-tetrakis(pyridin-2-yl)pyrazine coformer and hydrogen peroxide solvent molecules in an overall ratio of 1:4.75. Three of the six H2O2molecules modelled in the structure were found to be cross-orientationally disordered over two positions with occupancy ratios 0.846 (9):0.154 (9), 0.75 (2):0.25 (2), and 0.891 (9):0.109 (9). In the crystal, all of the peroxide molecules are linked into hydrogen-bonded chains that propagate parallel to theaaxis. These chains are further linked by O—H...N hydrogen bonds to the pyridine groups of the main molecule.
Open innovation: on the influence of internal and external collaboration on degree of newness
Authors: Lassen Astrid Heidemann , Laugen Bjørge Timenes
Published: October 2017

Purpose

The purpose of this paper is to test the effect of internal and external collaboration on the degree of newness (incremental/radical) in innovation projects. This adds to the understanding of the particular patterns of open innovation (OI) and what characterizes the innovation emerging through this approach.

Design/methodology/approach

Tests are performed on the effect of internal and external collaboration on the degree of newness (incremental/radical) in innovation projects. This adds to the understanding of the particular patterns of OI and what characterizes the innovation emerging through this approach. The empirical analysis is based on a data set including responses from 512 Danish engineers.

Findings

The results show that external collaboration has significantly different effects on the degree of newness depending on the type of external partners involved, and they also show that radical innovation output is positively related to involving the R&D department (internal) and universities (external involvement) and negatively related to involving suppliers.

Originality/value

The results provide a more detailed understanding of how different OI patterns affect the development of incremental vs radical innovation in existing organizations. In particular, three findings add new insights into how OI affects innovation to reach the highest degree of newness: high importance of collaboration with external partners with distinct interests and skills; low reliance on existing customers and suppliers for the development of radical innovation; and narrow and focused internal involvement rather than broad internal involvement.
The establishment and simulation of bidirectional Cockcroft-Walton circuit model
Authors: Wu Guozeng , Dong Quanlin
Published: October 2017

Purpose

The purpose of this paper is to improve the stability of high voltage DC power supply and reduce the ripple.

Design/methodology/approach

The study was conducted using the simulation analysis model and numerical calculation.

Findings

By increasing the output arm capacitance, the expression of ripple and times of the output arm capacitance and the auxiliary arm capacitance is derived. The output ripple is determined by the value of the output arm capacitance. Finally, the correctness of the method and the formula are verified using circuit simulation.

Originality value

This paper presents a method to improve the power supply stability.
Strategies for maximizing organizational absorptive capacity
Authors: Baškarada Saša , Koronios Andy
Published: October 2017

Purpose

The purpose of this paper is to discuss strategies for maximizing organizational absorptive capacity.

Design/methodology/approach

The views presented here have been derived from authors’ extensive research and professional experience. Support for the claims made is provided through anecdotal evidence and related literature.

Findings

The viewpoint discusses how organizational absorptive capacity may be maximized through actions and interactions of a wide range of individual, managerial, organizational, and inter-organizational factors.

Originality/value

The viewpoint may assist practitioners with developing strategies for improving vicarious learning. From a theoretical perspective, the claims made in the paper present fertile ground for future empirical testing.
Minority children and academic resilience in the Nordic welfare states
Authors: Johnsen Anja , Ortiz-Barreda Gaby , Rekkedal Guro , Iversen Anette Christine
Published: October 2017

Purpose

The purpose of this paper is to summarise and analyse empirical research on protective factors that promote academic resilience in ethnic minority children mainly aged between 13 and 18 years attending schools in the Nordic countries.

Design/methodology/approach

This paper was opted for a literature review of 23 peer-reviewed quantitative articles published between 1999 and 2014. The analysis entailed protective factors at both the personal and environmental levels in ethnic minority children.

Findings

Some minority children’s school performance may be just as good if not better than majority children when having similar or even lower socioeconomic status than majority children. Protective factors at the personal level included working hard, having a positive attitude towards school, and having high educational aspirations. Protective factors at the environmental level included supportive school systems, supportive schools, and supportive networks including parental qualities and support. The findings are comparable to the findings outside the Nordic countries with one exception; minority children in the Nordic countries performed better than expected despite socioeconomic disadvantages.

Research limitations/implications

Protective factors affecting academic resilience need further attention in a time with an increased global migration. Research implications may be related to how schools and policy makers develop supportive school systems, supportive schools, and supportive networks to contribute to making a difference for minority children’s educational opportunities in the Nordic countries.

Originality/value

Academic resilience is a relatively new research field in the Nordic countries. This review is the first review which has summarised and analysed existing findings on academic resilience in the Nordic countries in minority children.
Fatigue damage detection and prediction of fatigue life on a cantilever beam
Authors: Aenlle Manuel L. , Pelayo F. , Fernandez-Canteli Alfonso
Published: October 2017

Purpose

Fatigue failure is an important criterion to be considered in the design of structures and mechanical components. Catastrophic failure of structures in service conditions can be avoided using adequate techniques to detect and localize fatigue damage. Modal analysis is a tool used in mechanical and structural engineering to estimate dynamic properties and also to monitor the health of structures. If modal analysis is applied periodically to a structure, fatigue damage can be detected and localized and the fatigue life can be extended by means of suitable reinforcement and repairing. The paper aims to discuss these issues.

Design/methodology/approach

The experimental results corresponding to the fatigue tests carried out on a steel S-275 cantilever beam are presented. Operational modal analysis was applied periodically to the beam in order to study the variation of modal parameters during the tests and the stresses were estimated combining a numerical model and the acceleration modal coordinates measured at discrete points of the structure. The experimental results are compared with those predicted applying the S-N model of Eurocode 3.

Findings

A methodology that combines a finite element model and the experimental responses of a structure has been applied to estimate the stress time histories of a cantilever beam clamped to a foundation through a steel plate. The estimated stresses have been used to predict the fatigue damage according to the Eurocode 3. Due to the fact that no information of the scatter is provided by this code (EC3), only the number of cycles corresponding to a probability of failure of 5 percent can be predicted.

Originality/value

The proposed methodology can be applied to real structures in order to know the accumulated fatigue damage in real time.