bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural and hydrodynamic properties of an intrinsically disordered region of a germ cell-specific protein on phase separation
Authors: Brady Jacob P. , Farber Patrick J. , Sekhar Ashok , Lin Yi-Hsuan , Huang Rui , Bah Alaji , Nott Timothy J. , Chan Hue Sun , Baldwin Andrew J. , Forman-Kay Julie D. , Kay Lewis E.
Published: September 2017

Significance

The cell is divided into compartments where specific biochemical functions are performed. These compartments can be delineated by membranes or through phase separation of proteins or protein and nucleic acids to form membraneless organelles. The latter situation occurs with an intrinsically disordered region of Ddx4, a major constituent of germ granules. The nature of the interior of membraneless organelles is poorly understood. Here, we use NMR to show that the intrinsically disordered Ddx4 region remains disordered and highly dynamic in the phase-separated state, while diffusing as slowly as a particle the size of a bacterial cell. Ddx4 molecules form a network of interactions on phase separation, providing an alternative environment to that found in membrane-encapsulated organelles.
Nanoswitch-linked immunosorbent assay (NLISA) for fast, sensitive, and specific protein detection
Authors: Hansen Clinton H. , Yang Darren , Koussa Mounir A. , Wong Wesley P.
Published: September 2017

Significance

Basic research and medical diagnostics rely on the ability to detect and quantify specific proteins in biological fluids. While numerous current detection techniques exist, these are often limited by trade-offs between ease of use, sensitivity, and cost. Here, we present the nanoswitch-linked immunosorbent assay (NLISA), an accessible, sensitive, and low-cost detection platform that is based upon nanoscale devices that change confirmation upon binding a target protein. NLISA is surface-free and includes a kinetic-proofreading purification step, enabling both enhanced sensitivity and the ability to accurately distinguish between similar proteins from different strains of the same virus or that differ by only a single mutation. Our method is also readily transferable to point-of-care devices due to an easy readout and few hands-on steps.
Cryo-EM structure of the bacteriophage T4 isometric head at 3.3-Å resolution and its relevance to the assembly of icosahedral viruses
Authors: Chen Zhenguo , Sun Lei , Zhang Zhihong , Fokine Andrei , Padilla-Sanchez Victor , Hanein Dorit , Jiang Wen , Rossmann Michael G. , Rao Venigalla B.
Published: September 2017

Significance

The WT bacteriophage T4 head is prolate with icosahedral T=13 ends closing the central cylindrical section. The structure of a T=13 icosahedral head assembly, in which the major capsid protein of T4 phage had a single mutation at a residue in the interface between neighboring subunits, has been determined to 3.3-Å resolution. The structure shows the extensive network of interactions between the major capsid proteins gp23 and the vertex proteins gp24 and the stabilizing Soc proteins. We show that the angle between hexameric and pentameric capsomers helps to determine the triangulation number (T number) and suggests how other viruses assemble consistently with a predetermined T number.
RABIF/MSS4 is a Rab-stabilizing holdase chaperone required for GLUT4 exocytosis
Authors: Gulbranson Daniel R. , Davis Eric M. , Demmitt Brittany A. , Ouyang Yan , Ye Yihong , Yu Haijia , Shen Jingshi
Published: September 2017

Significance

Rab GTPases are central regulators of vesicle-mediated cargo transport. They are switched from the GDP-bound inactive conformation to the GTP-bound active state by guanine nucleotide exchange factors (GEFs). Rab-interacting factor (RABIF)/mammalian suppressor of Sec4 (MSS4) and its yeast homolog DSS4 are the first putative GEFs isolated for Rabs, but their biological function and molecular mechanism remained unclear. In this work, we demonstrate that RABIF plays a crucial role in exocytosis. Unexpectedly, we discovered that RABIF does not function as a GEF, as previously assumed. Instead, RABIF is a Rab-stabilizing holdase chaperone, a previously unrecognized mode of Rab regulation independent of its GDP-releasing activity. We suggest that a requirement for holdase chaperones is likely a general feature of Rab GTPases.
Screening, Brief Intervention, and Referral to Treatment (SBIRT) Curriculum Integration and Sustainability: Social Work and Nursing Faculty Perspectives
Authors: Belfiore M. Nicole , Blinka Marcela D. , BrintzenhofeSzoc Karlynn , Shields Joseph
Published: September 2017

Background

The Substance Abuse and Mental Health Services Administration (SAMHSA) has funded grants to universities to provide training and conduct research on the dissemination of Screening, Brief Intervention, and Referral to Treatment (SBIRT) to health care professionals. However, when it comes to integrating SBIRT content into an existing curriculum, difficulties can arise. When there is so much content already in the curriculum, adding more can be challenging. Additionally, some faculty believe that course curricula should be driven by the expertise and knowledge of faculty, not by opportunities afforded because of grant funding.

Methods

Using qualitative semi-structured faculty interviews and thematic data analysis, this study explored the process and content issues surrounding the integration of SBIRT content into the Masters of Social Work (MSW) and Masters of Science in Nursing (MSN) curricula at one university.

Results

Guidelines for the successful integration of SBIRT content into MSW and MSN curricula fall into two thematic areas: 1. Encourage buy-in and ownership of SBIRT curriculum development by current faculty. 2. Use a scaffolded approach. SBIRT includes several unique content areas which should be integrated per competencies addressed in each course. SBIRT content areas lend themselves to integration into a range of courses, employing an array of learning techniques and teaching materials. Scaffolding content requires creativity, which serves as the basis of the six subthemes that guide a scaffolded SBIRT integration approach.

Conclusions

SBIRT offers an evidence based intervention that uses a public health approach to reduce harm from substance use. As such, professional nursing and social work education programs should teach SBIRT to their master's level practitioners. This paper proposes guidelines for integrating that content into existing curricula.
Mbd3/NuRD controls lymphoid cell fate and inhibits tumorigenesis by repressing a B cell transcriptional program
Authors: Loughran Stephen J. , Comoglio Federico , Hamey Fiona K. , Giustacchini Alice , Errami Youssef , Earp Eleanor , Göttgens Berthold , Jacobsen Sten Eirik W. , Mead Adam J. , Hendrich Brian , Green Anthony R.
Published: September 2017

Differentiation of lineage-committed cells from multipotent progenitors requires the establishment of accessible chromatin at lineage-specific transcriptional enhancers and promoters, which is mediated by pioneer transcription factors that recruit activating chromatin remodeling complexes. Here we show that the Mbd3/nucleosome remodeling and deacetylation (NuRD) chromatin remodeling complex opposes this transcriptional pioneering during B cell programming of multipotent lymphoid progenitors by restricting chromatin accessibility at B cell enhancers and promoters. Mbd3/NuRD-deficient lymphoid progenitors therefore prematurely activate a B cell transcriptional program and are biased toward overproduction of pro–B cells at the expense of T cell progenitors. The striking reduction in early thymic T cell progenitors results in compensatory hyperproliferation of immature thymocytes and development of T cell lymphoma. Our results reveal that Mbd3/NuRD can regulate multilineage differentiation by constraining the activation of dormant lineage-specific enhancers and promoters. In this way, Mbd3/NuRD protects the multipotency of lymphoid progenitors, preventing B cell–programming transcription factors from prematurely enacting lineage commitment. Mbd3/NuRD therefore controls the fate of lymphoid progenitors, ensuring appropriate production of lineage-committed progeny and suppressing tumor formation.
Chemistry in a vesicle
Authors: Jackson Meyer B.
Published: September 2017

Slow fusion pore expansion could retain molecules within vesicles, enabling a chemical reaction that modifies secreted products.
Temporal probabilistic modeling of bacterial compositions derived from 16S rRNA sequencing
Authors: Äijö Tarmo , Müller Christian L , Bonneau Richard
Published: September 2017

Motivation

The number of microbial and metagenomic studies has increased drastically due to advancements in next-generation sequencing-based measurement techniques. Statistical analysis and the validity of conclusions drawn from (time series) 16S rRNA and other metagenomic sequencing data is hampered by the presence of significant amount of noise and missing data (sampling zeros). Accounting uncertainty in microbiome data is often challenging due to the difficulty of obtaining biological replicates. Additionally, the compositional nature of current amplicon and metagenomic data differs from many other biological data types adding another challenge to the data analysis.

Results

To address these challenges in human microbiome research, we introduce a novel probabilistic approach to explicitly model overdispersion and sampling zeros by considering the temporal correlation between nearby time points using Gaussian Processes. The proposed Temporal Gaussian Process Model for Compositional Data Analysis (TGP-CODA) shows superior modeling performance compared to commonly used Dirichlet-multinomial, multinomial and non-parametric regression models on real and synthetic data. We demonstrate that the nonreplicative nature of human gut microbiota studies can be partially overcome by our method with proper experimental design of dense temporal sampling. We also show that different modeling approaches have a strong impact on ecological interpretation of the data, such as stationarity, persistence and environmental noise models.

Availability and implementation

A Stan implementation of the proposed method is available under MIT license at https://github.com/tare/GPMicrobiome.

Supplementary information

Supplementary data are available at Bioinformatics online.
High dimensional classification with combined adaptive sparse PLS and logistic regression
Authors: Durif Ghislain , Modolo Laurent , Michaelsson Jakob , Mold Jeff E , Lambert-Lacroix Sophie , Picard Franck
Published: September 2017

Motivation

The high dimensionality of genomic data calls for the development of specific classification methodologies, especially to prevent over-optimistic predictions. This challenge can be tackled by compression and variable selection, which combined constitute a powerful framework for classification, as well as data visualization and interpretation. However, current proposed combinations lead to unstable and non convergent methods due to inappropriate computational frameworks. We hereby propose a computationally stable and convergent approach for classification in high dimensional based on sparse Partial Least Squares (sparse PLS).

Results

We start by proposing a new solution for the sparse PLS problem that is based on proximal operators for the case of univariate responses. Then we develop an adaptive version of the sparse PLS for classification, called logit-SPLS, which combines iterative optimization of logistic regression and sparse PLS to ensure computational convergence and stability. Our results are confirmed on synthetic and experimental data. In particular, we show how crucial convergence and stability can be when cross-validation is involved for calibration purposes. Using gene expression data, we explore the prediction of breast cancer relapse. We also propose a multicategorial version of our method, used to predict cell-types based on single-cell expression data.

Availability and implementation

Our approach is implemented in the plsgenomics R-package.

Supplementary information

Supplementary data are available at Bioinformatics online.
Genome-scale fluxes predicted under the guidance of enzyme abundance using a novel hyper-cube shrink algorithm
Authors: Xie Zhengwei , Zhang Tianyu , Ouyang Qi
Published: September 2017

Motivation

One of the long-expected goals of genome-scale metabolic modelling is to evaluate the influence of the perturbed enzymes on flux distribution. Both ordinary differential equation (ODE) models and constraint-based models, like Flux balance analysis (FBA), lack the capacity to perform metabolic control analysis (MCA) for large-scale networks.

Results

In this study, we developed a hyper-cube shrink algorithm (HCSA) to incorporate the enzymatic properties into the FBA model by introducing a pseudo reaction V constrained by enzymatic parameters. Our algorithm uses the enzymatic information quantitatively rather than qualitatively. We first demonstrate the concept by applying HCSA to a simple three-node network, whereby we obtained a good correlation between flux and enzyme abundance. We then validate its prediction by comparison with ODE and with a synthetic network producing voilacein and analogues in Saccharomyces cerevisiae. We show that HCSA can mimic the state-state results of ODE. Finally, we show its capability of predicting the flux distribution in genome-scale networks by applying it to sporulation in yeast. We show the ability of HCSA to operate without biomass flux and perform MCA to determine rate-limiting reactions.

Availability and implementation

Algorithm was implemented by Matlab and C ++. The code is available at https://github.com/kekegg/HCSA.

Supplementary information

Supplementary data are available at Bioinformatics online.
LinkageMapView—rendering high-resolution linkage and QTL maps
Authors: Ouellette Lisa A , Reid Robert W , Blanchard Steven G , Brouwer Cory R
Published: September 2017

Motivation

Linkage and quantitative trait loci (QTL) maps are critical tools for the study of the genetic basis of complex traits. With the advances in sequencing technology over the past decade, linkage map densities have been increasing dramatically, while the visualization tools have not kept pace. LinkageMapView is a free add-on package written in R that produces high resolution, publication-ready visualizations of linkage and QTL maps. While there is software available to generate linkage map graphics, none are freely available, produce publication quality figures, are open source and can run on all platforms. LinkageMapView can be integrated into map building pipelines as it seamlessly incorporates output from R/qtl and also accepts simple text or comma delimited files. There are numerous options within the package to build highly customizable maps, allow for linkage group comparisons, and annotate QTL regions.

Availability and implementation

https://cran.r-project.org/web/packages/LinkageMapView/
Disablement in Context: Neighborhood Characteristics and Their Association With Frailty Onset Among Older Adults
Authors: Caldwell Julia T , Lee Haena , Cagney Kathleen A
Published: September 2017

Objectives

Frailty, an aggregate expression of risk resulting from age- or disease-associated physiologic accumulation, is responsible for large economic and societal costs. Little is known about how the context in which older adult’s live may contribute to differences in frailty. This study clarifies the role of neighborhood structural characteristics and social processes for understanding declines in health status.

Method

Data from two waves of the National Social Life, Health and Aging Project were linked to tract-level information from the 2000 Census (n = 1,925). Frailty was measured with in-home assessments and self-report. Ordered logistic regressions were employed to estimate the role of tract-level structural and social process indicators at baseline on frailty at follow-up.

Results

Living in a neighborhood characterized with a higher density of African Americans and with more residential instability was associated with higher odds of frailty. Adults in neighborhoods with increasing levels of physical disorder had higher odds of frailty (adjusted odds ratio [AOR]: 1.20, 95% confidence interval [CI]: 1.03, 1.39), while those exposed to more social cohesion had lower odds (AOR: 0.87, CI: 0.78, 0.97).

Discussion

For older adults, both neighborhood structural and social process characteristics appear to be independently associated with frailty.
Serial Daily Organ Failure Assessment Beyond ICU Day 5 Does Not Independently Add Precision to ICU Risk-of-Death Prediction
Authors: Holder Andre L. , Overton Elizabeth , Lyu Peter , Kempker Jordan A. , Nemati Shamim , Razmi Fereshteh , Martin Greg S. , Buchman Timothy G. , Murphy David J.
Published: September 2017

Objectives:

To identify circumstances in which repeated measures of organ failure would improve mortality prediction in ICU patients.

Design:

Retrospective cohort study, with external validation in a deidentified ICU database.

Setting:

Eleven ICUs in three university hospitals within an academic healthcare system in 2014.

Patients:

Adults (18 yr old or older) who satisfied the following criteria: 1) two of four systemic inflammatory response syndrome criteria plus an ordered blood culture, all within 24 hours of hospital admission; and 2) ICU admission for at least 2 calendar days, within 72 hours of emergency department presentation.

Intervention:

None

Measurements and Main Results:

Data were collected until death, ICU discharge, or the seventh ICU day, whichever came first. The highest Sequential Organ Failure Assessment score from the ICU admission day (ICU day 1) was included in a multivariable model controlling for other covariates. The worst Sequential Organ Failure Assessment scores from the first 7 days after ICU admission were incrementally added and retained if they obtained statistical significance (p < 0.05). The cohort was divided into seven subcohorts to facilitate statistical comparison using the integrated discriminatory index. Of the 1,290 derivation cohort patients, 83 patients (6.4%) died in the ICU, compared with 949 of the 8,441 patients (11.2%) in the validation cohort. Incremental addition of Sequential Organ Failure Assessment data up to ICU day 5 improved the integrated discriminatory index in the validation cohort. Adding ICU day 6 or 7 Sequential Organ Failure Assessment data did not further improve model performance.

Conclusions:

Serial organ failure data improve prediction of ICU mortality, but a point exists after which further data no longer improve ICU mortality prediction of early sepsis.
Upper-Limb Prostheses: Perspectives Involving the Veteran Population
Authors: Fantini Christopher , Yancosek Kathleen E.
Published: September 2017

Evidence-based practice has been described as the conscientious, explicit, and judicious use of current best evidence in making decisions about the care of individual patients. Clinical practice guidelines are statements of recommended practice based on a systematic review of the best available evidence and expert opinion. A systematic review evaluates research studies in a particular area and produces a summary of overall results. Recent publications to inform evidence-based prescription of upper-limb prostheses, including a 2014 systematic review of the differences in myoelectric and body-powered systems by Carey et al. showing a lack of empirical evidence. This lack of evidence makes it challenging to determine the most effective and appropriate prosthetic interventions for individuals with upper-limb amputations, including those who are veterans. There is, however, a substantial amount of practice-based evidence (expert opinion) available to help guide clinical care. In 2008, in response to the current and future need to advance the clinical care for veterans with amputation, the Department of Veterans Affairs (VA) rolled out its Amputation System of Care (ASoC) model. Its mission is to incorporate the latest practices in medical rehabilitation, including therapy services and prosthetic technology, to enhance the quality and consistency of amputation care for US veterans. Furthermore, the VA and Department of Defense (DoD) have collaborated to address the need for clinical guidance specifically regarding upper-limb amputation and rehabilitation with the 2014 publication of the “VA/DoD Clinical Practice Guideline for the Management of Upper Extremity Amputation Rehabilitation” (UEAR-CPG). The purpose of this paper is to introduce and describe the ASoC as well as the UEAR-CPG and offer perspectives of the authors in their respective roles as clinicians in each, the VA and the DoD environments.
MELD Stratified Outcomes Among Recipients With Diabetes or Hypertension
Authors: Singal Ashwani K. , Hasanin Mohsen , Kaif Mohamed , Wiesner Russell W. , Kuo Yong-Fang
Published: September 2017

Background and Aim:

Data are scanty on allocating simultaneous liver kidney (SLK) based on model for end-stage disease (MELD) score. Diabetes mellitus (DM) and hypertension (HTN) are frequent in cirrhosis patients. We analyzed transplant recipients with DM and/or HTN to compare MELD-based outcomes of SLK to liver transplantation alone (LTA).

Materials and Methods:

Of 13,584 first deceased donor liver transplantation among patients with DM and/or HTN (1530 or 11.2% SLK), MELD score predicted SLK [1.02 (1.01-1.03)]. SLK was beneficial for 5-year patient survival at MELD score ≥43 (78.6% vs. 62.6%, P=0.017), but not at MELD score <29 (74.8% vs. 76.2%, P=0.63). Among 11,405 recipients (976 SLK) at MELD score <29, SLK (n=816) was beneficial compared with 706 LTA [75% vs. 64%, P<0.001; 0.71 (0.55-0.91)] at serum creatinine (SC) ≥2 but not at SC<2 [73% vs. 76%, P=0.32; 0.85 (0.60-1.2)]. Among patients with MELD score 29 to 42, SLK (n=484) and LTA (n=1403) had similar survival [69% vs. 69%, P=0.58; 0.9 (0.7-1.5)]. Among patients with MELD score ≥43, SLK (n=70) was associated with 35% improved patient survival at 5 years compared with 222 LTA [0.65 (0.46-0.93)].

Conclusions:

Among patients with DM and/or HTN, SLK is useful at: (a) MELD score <29 and SC≥2 and (b) MELD score ≥43. Prospective studies are needed to confirm these findings as basis to optimize use of SLK.
Novel Method Enabling the Use of Cryopreserved Primary Acute Myeloid Leukemia Cells in Functional Drug Screens
Authors: Degnin Michelle , Agarwal Anupriya , Tarlock Katherine , Meshinchi Soheil , Druker Brian J. , Tognon Cristina E.
Published: September 2017

The ability to assess antileukemic drug activity on primary patient samples is a powerful tool in determining potential drug targets and selection of therapeutic agents with biological and functional rationale. We previously established small molecule inhibitor screens for use on freshly isolated leukemia cells for this purpose. Here we describe a method that produces functional small molecule inhibitor screening results using cryopreserved primary acute myeloid leukemia cells. This method was established to take advantage of biorepositories containing archival material, such as those established by the Children’s Oncology Group, and to enable validation of potential pathway dependencies uncovered by genomic analysis. Various conditions used to thaw and culture cryopreserved specimens were assessed for effect on viability, differentiation, and the ability to recapitulate sensitivity results obtained on fresh samples. The most reproducible results were obtained by quick-thawing and culturing samples in cytokine rich media before performing drug screens. Our data suggest that cytokine-enriched media aids in maintaining the viability and numbers required to perform functional analysis on cryopreserved leukemia cells. This method can aid in producing informative data on therapeutic targeting and precision medicine efforts in leukemia by making use of biorepositories and bio banks.
Increased Risk of Acute Kidney Injury in Critically Ill Children Treated With Vancomycin and Piperacillin/Tazobactam*
Authors: Holsen Maya R. , Meaney Calvin J. , Hassinger Amanda B. , Fusco Nicholas M.
Published: September 2017

Objectives:

Compare the rates of acute kidney injury in critically ill children treated with vancomycin and piperacillin-tazobactam versus vancomycin and ceftriaxone.

Design:

Retrospective cohort study.

Setting:

A large tertiary care children’s hospital in an urban setting.

Patients:

Children greater than or equal to 2 months old admitted to the PICU who received greater than or equal to 48 consecutive hours of vancomycin and piperacillin-tazobactam or vancomycin and ceftriaxone.

Interventions:

None.

Measurements and Main Results:

Acute kidney injury was defined as a minimum 50% increase in serum creatinine, adjusted for total fluid balance, from baseline over a 48-hour period. Bivariate analysis compared treatment groups and acute kidney injury groups. A multivariable logistic regression model was fit for acute kidney injury including covariable analysis. The study included 93 children. There were no differences between treatment groups in terms of age, severity of illness, baseline renal function, vancomycin dosing, or vancomycin trough concentrations. Children who received vancomycin and piperacillin-tazobactam had a higher cumulative frequency of acute kidney injury than those who received vancomycin and ceftriaxone 915/58 [25.9%] vs 3/35 [8.6%]; p = 0.041). After controlling for vancomycin trough concentration, age, concurrent nephrotoxin exposure, and use of vasopressors, exposure to piperacillin-tazobactam significantly increased the risk of acute kidney injury (adjusted odds ratio, 4.55; 95% CI [1.11–18.7]; p = 0.035) compared with ceftriaxone. Use of vasopressors (adjusted odds ratio, 3.73 [95% CI, 1.14–12.3]) and a vancomycin trough greater than or equal to 15 mg/dL (adjusted odds ratio, 4.12 [95% CI, 1.12–15.2)] was also associated with acute kidney injury. Length of stay was longer in children with acute kidney injury (median, 18.0 days; interquartile range, 7.76–29.7) compared with those without acute kidney injury (median, 6.21 days; interquartile range, 2.92–15.6; p = 0.017).

Conclusions:

In critically ill children, acute kidney injury occurred more in patients treated with vancomycin and piperacillin-tazobactam versus vancomycin plus ceftriaxone. After controlling for covariates, exposure to piperacillin-tazobactam was associated with an increased odds of acute kidney injury development.
Propranolol 18F-FDG PET/CT
Authors: Ciappuccini Renaud , Bardet Stéphane , Aide Nicolas
Published: September 2017

A 76-year-old woman was referred for 18F-FDG PET/CT assessment of a colorectal cancer. A 9-cm 18F-FDG–avid fatty mass was depicted in the right thigh, suggesting either hibernoma or liposarcoma. Because MRI could not rule out well-differentiated liposarcoma, and biopsy was difficult, surveillance was decided. Follow-up PET/CT showed an increase of 18F-FDG uptake in the fatty mass. We repeated PET/CT after oral administration of 60 mg of propranolol 1 hour before 18F-FDG injection. A dramatic decrease in 18F-FDG uptake was observed, strongly supporting the diagnosis of hibernoma.
Crohn Disease
Authors: Epelboym Yan , Shyn Paul B. , Chick Jeffrey Forris Beecham , Hamilton Matthew J. , O'Connor Stacy D. , Silverman Stuart G. , Kim Chun K.
Published: September 2017

Purpose

Clinical assessments of Crohn disease activity are limited in their capacity to assess treatment response to biologic therapy. The purpose of this study was to determine if changes in FDG activity between baseline PET and repeat PET performed prior to the second dose of induction anti–tumor necrosis factor (TNF) therapy correlate with clinical response.

Methods

In this prospective, institutional review board–approved, Health Insurance Portability and Accountability Act–compliant pilot study of 8 adult patients with active Crohn disease, FDG activity before and 2 weeks after initiation of anti-TNF therapy was assessed using low-dose PET/CT. FDG activity was measured in the most inflamed bowel loop using an SUVratio (SUVmax/liver SUVmean). Changes in SUVratio were compared with a blinded gastroenterologist assessment of clinical response and steroid-free remission, as well as C-reactive protein (CRP), during a 12-month follow-up period.

Results

Of 8 patients, 7 showed FDG activity decline at 2 weeks, 5 of whom achieved a clinical response and steroid-free remission at 8, 26, and 52 weeks. The remaining 2 patients with FDG activity decline did not achieve a clinical response or steroid-free remission at these time points, but there were reductions in CRP. The 1 patient without FDG activity decline was a clinical nonresponder, had no reduction in CRP, and did not achieve steroid-free remission.

Conclusions

A change in FDG activity at FDG PET/CT performed prior to the second induction dose of anti-TNF therapy has the potential to predict clinical response and steroid-free remission in patients with Crohn disease.
Outcomes of Consistent Conservative Management for Acute Cholecystitis Followed by Delayed Cholecystectomy
Authors: Komatsu Shohei , Tsuchida Shinobu , Wakahara Tomoyuki , Ueno Nozomi , Toyokawa Akihiro , Watanabe Akihiko , Sugahara Atsushi , Mukai Hidekazu
Published: September 2017

Objective:

This study’s objective was to assess outcomes of a totally conservative strategy for acute cholecystitis (AC) followed by delayed elective cholecystectomy.

Patients and Methods:

Consecutive patients who underwent cholecystectomy for AC were divided into the Emergent and Elective cholecystectomy groups. Patients in the elective cholecystectomy group were divided into early, medium, and late groups according to time from symptoms onset.

Results:

The success rate for conservative management reached 97.2%. Increased blood loss and a higher conversion rate were significantly associated with the emergent group. Patients in the late group had significantly lower operative time and tended to have lower blood loss and less frequent conversion to open surgery than those in the early and medium groups.

Conclusions:

Most AC cases could be managed conservatively, and elective cholecystectomy was performed safely regardless of the time. Elective cholecystectomy carried out in late phase was likely to be associated with decreased surgical difficulty.
Time Regained: How the Human Brain Constructs Memory for Time
Authors: Cohn-Sheehy Brendan I. , Ranganath Charan
Published: September 2017

Life’s episodes unfold against a context that changes with time. Recent neuroimaging studies have revealed significant findings about how specific areas of the human brain may support the representation of temporal information in memory. A consistent theme in these studies is that the hippocampus appears to play a central role in representing temporal context, as operationalized in neuroimaging studies of arbitrary lists of items, sequences of items, or meaningful, lifelike events. Additionally, activity in a posterior medial cortical network may reflect the representation of generalized temporal information for meaningful events. The hippocampus, posterior medial network, and other regions—particularly in prefrontal cortex—appear to play complementary roles in memory for temporal context.

Highlights

The hippocampus encodes information about temporal contiguity, order, and event structure.

Posterior medial cortical areas represent order across meaningfully coherent events.

Prefrontal and subcortical contributions to temporal memory deserve further study.
Standing Sentinel during Human Sleep: Continued Evaluation of Environmental Stimuli in the Absence of Consciousness
Authors: Blume Christine , del Giudice Renata , Wislowska Malgorzata , Heib Dominik P. J. , Schabus Manuel
Published: September 2017

While it is a well-established finding that subject’s own names (SON) or familiar voices are salient during wakefulness, we here investigated processing of environmental stimuli during sleep including deep N3 and REM sleep. Besides the effects of sleep depth we investigated how sleep-specific EEG patterns (i.e. sleep spindles and slow oscillations [SOs]) relate to stimulus processing. Using 256-channel EEG we studied processing of auditory stimuli by means of event-related oscillatory responses (de-/ synchronisation, ERD/ERS) and potentials (ERPs) inN= 17 healthy sleepers. We varied stimulus salience by manipulating subjective (SON vs. unfamiliar name) and paralinguistic emotional relevance (familiar vs. unfamiliar voice, FV/UFV). Results reveal that evaluation of voice familiarity continues during all NREM sleep stages and even REM sleep suggesting a ‘sentinel processing mode’ of the human brain in the absence of wake-like consciousness. Especially UFV stimuli elicit larger responses in a 1-15 Hz range suggesting they continue being salient. Beyond this, we find that sleep spindles and the negative slope of SOs attenuate information processing. However, unlike previously suggested they do not uniformly inhibit information processing, but inhibition seems to be scaled to stimulus salience.

Funding

CB is supported by the Konrad-Adenauer-Stiftung e.V. and CB, MW and DPJH are supported by a grant from the Austrian Science Fund FWF (Y-777). CB, RdG, MW and DPJH are also supported by the Doctoral College “Imaging the Mind” (FWF; W1233-G17).
PauparLncRNA Promotes KAP1 Dependent Chromatin Changes And Regulates Subventricular Zone Neurogenesis
Authors: Pavlaki Ioanna , Alammari Farah , Sun Bin , Clark Neil , Sirey Tamara , Lee Sheena , Woodcock Dan J , Ponting Chris P , Szele Francis G , Vance Keith W
Published: September 2017

Many long non-coding RNAs (lncRNAs) are expressed during central nervous system (CNS) development, yet theirin vivoroles and molecular mechanisms of action remain poorly understood.Paupar, a CNS expressed lncRNA, controls neuroblastoma cell growth by binding and modulating the activity of genome-wide transcriptional regulatory elements. We show here thatPaupartranscript directly binds KAP1, an essential epigenetic regulatory protein, and thereby regulates the expression of shared target genes important for proliferation and neuronal differentiation.Pauparpromotes KAP1 chromatin occupancy and H3K9me3 deposition at a subset of distal targets, through formation of a DNA binding ribonucleoprotein complex containingPaupar, KAP1 and the PAX6 transcription factor.Paupar-KAP1 genome-wide co-occupancy reveals a 4-fold enrichment of overlap betweenPauparand KAP1 bound sequences. Furthermore, bothPauparand Kap1 loss of functionin vivoaccelerates lineage progression in the mouse postnatal subventricular zone (SVZ) stem cell niche and disrupts olfactory bulb neurogenesis. These observations provide important conceptual insights into thetrans-acting modes of lncRNA-mediated epigenetic regulation, the mechanisms of KAP1 genomic recruitment and identifyPauparandKap1as regulators of SVZ neurogenesis.
3,3′-(Dodecane-1,12-diyl)bis(1-methylimidazolium) 5,5′-azotetrazolate heptahydrate
Authors: Laus Gerhard , Wurst Klaus , Schottenberger Herwig
Published: September 2017

The title compound, C20H36N4·C2N10·7H2O, was obtained by reaction of 1-methylimidazole with 1,12-dibromododecane, followed by repeated ion metathesis (bromide → sulfate → azotetrazolate). An intricate network of hydrogen bonds is formed between anions and water molecules, leading to a layered arrangement parallel to (101).
Exploring the use of labor and delivery services by women of Haitian nationality in a Dominican Republic border town
Authors: Nelson Adrianne Katrina , Fenwood Marguerite , Burks Courtney , Widner Alexandre , Bah Assiatou B. , Ternier Ralph , F. Franke Molly
Published: September 2017

Purpose

Women of Haitian nationality comprise a sizeable proportion of all women seeking labor and delivery services in a public hospital in Dominican Republic (DR), along the central border of Haiti. The purpose of this paper is to better understand and address the needs of Haitian women receiving labor and delivery services in this border region.

Design/methodology/approach

The authors conducted a mixed-methods study to identify personal motivations, demographic characteristics, and migration history of women seeking labor and delivery services at a public hospital.

Findings

The majority of women (83 percent) were born in Haiti but spoke Spanish (74 percent) and were long-term residents of the DR (mean 7.8 years). While many women reported they felt they had a positive experience delivering at the public hospital, some described feeling unwelcome or resented.

Research limitations/implications

The study sample was small and from one hospital. Future studies could explore the differences in experiences among Haitian women who are long-term residents of the DR and those whose presence is more transient.

Practical implications

Women residing on both sides of the border would likely benefit from coordinated efforts by the Haitian and DR Ministries of Health to strengthen referral services to and from either country.

Social implications

Hospital staff and services in the DR should consider the unique needs of this population, which makes critical contributions to workforce and culture in the DR.

Originality/value

This study is the first to assess labor and delivery service seeking practices and experiences within this population.
Evaluating electronic journal use and access among academic staff at the Faculty of Agriculture, University of Zimbabwe
Authors: Malapela Thembani , de Jager Karin
Published: September 2017

Purpose

The purpose of this paper is to explore issues around access and use of subscription electronic journals by African researchers and seeks to bring to the fore the issues academics and researchers face in accessing electronic databases.

Design/methodology/approach

Donor-funded electronic resources have greatly improved access to essential scientific scholarly information by researchers in developing countries. Yet in Sub-Saharan Africa, researchers and libraries still complain about lack of access to scientific information, and libraries are reported to be struggling to maintain up-to-date scientific information resources. An online survey of academics at the Faculty of Agriculture, University of Zimbabwe was carried out.

Findings

Results indicated that academics rely on approaches other than library facilities to locate electronic information. Google was the most common approach used in locating subscription electronic journals. Furthermore, there was a need for increased awareness of subscription and donated resources. Programmes such as Research4Life, journal schemes by Education Information for Libraries and the International Network for the Availability of Scientific Publications have made an impact on academics’ access to electronic journals. The study established that there was no direct link between access to electronic journals and increased publications.

Originality/value

Work of this kind has not been done in Africa before. The exploration of the complexities inherent in providing access to electronic journals in a developing country presents an opportunity for both librarians and developmental partners to reflect on the challenges as well as the opportunities that exist in current electronic journal access schemes.
Different phylogenetic and environmental controls of first‐order root morphological and nutrient traits: Evidence of multidimensional root traits
Authors: Wang Ruili , Wang Qiufeng , Zhao Ning , Xu Zhiwei , Zhu Xianjin , Jiao Cuicui , Yu Guirui , He Nianpeng
Published: September 2017

Although fine roots are essential for the water and nutrient uptake of plants, there is limited understanding of root trait variation and the underlying mechanism.

Here, six first‐order root morphological and chemical traits were measured for 181 species from eight subtropical and boreal forests to test the hypothesis of different phylogenetic and environmental regulations of root morphological and nutrient traits result in the multidimensions of root traits.

Two independent root trait dimensions between root thickness and nutrient traits were detected at both species and community levels. At the species level, diameter‐related traits were mainly restricted by phylogenetic structure and showed little plasticity to the changing environments, whereas the variation in woody root nutrient was influenced significantly by soil variables. For community‐level traits, the diameter‐related axis scores of principal component analysis were mainly driven by mean annual temperature through shifting species composition, whereas the root nutrient‐related axis scores were strongly influenced by soil P availability.

From both species and community levels, our study confirms, that the root‐thickness‐related dimension and root nutrient dimension represent new support for the multidimensionality of root traits which are driven by different selection pressure. This study also underlines that the community‐aggregated traits might serve as a promising avenue to improve our understanding of community assemblage processes, allowing us to predict changes of vegetation distributions in a changing climate.

A plain language summary is available for this article.
Is This What The Democratic City Looks Like? Local Democracy, Housing Rights and Homeownership in the Portuguese Context
Authors: Drago Ana
Published: September 2017

This article analyses the creation of a normative framework for the democratic city during the regime change in Portugal in 1975—the answers that were given to the question, ‘What should a city be like in a democratic regime?’ While I critically discuss post‐democracy and its use of post‐foundational contributions, I review the post‐revolution Portuguese constitutional debate, contending that the call for democratization brought by urban popular organizations was answered with a political compromise that exchanged expectations of a participatory city for a commitment to a social rights city, enhanced with a promise of homeownership for urban popular segments. In light of this, in this article I question post‐democratic proposals, arguing that when this approach implicitly establishes equivalence between democracy and ‘the political’, it has difficulties in interpreting how the grammar of democracy is ‘organized’ in conflictual and contingent processes of democratic institutionalization. As an alternative, I contend that a critical debate concerning democracy and the urban must address how democratic expectations of emancipation have been translated into institutions and rights through interwoven and situated processes of politicization and depoliticization that allow both politicization of the urban and the production of consent.
Complementary and alternative medicine in US adults with diabetes: Reasons for use and perceived benefits
Authors: Rhee Taeho G. , Westberg Sarah M. , Harris Ila M.
Published: September 2017

Background

Although complementary and alternative medicine (CAM) is increasingly used, little is known about the reasons for CAM use (treatment, wellness, or both), or the self‐reported perceived benefits among US adults with diabetes. In this study we estimated prevalence rates of overall and specific types of CAM, as well as the perceived benefits of CAM, by reason for use among US diabetic adults.

Methods

Cross‐sectional data from the 2012 National Health Interview Survey, which represents non‐institutionalized adults with diabetes (n = 3386 unweighted), were used to estimate prevalence rates of CAM use by reason. Multivariate logistic regression analyses were used to investigate the odds of perceived benefits of CAM by reason for use after controlling for covariates.

Results

Of US diabetic adults, 26.2% reported using some form of CAM in the past year. Of these, 56.7% used CAM for both treatment and wellness, 28.3% used CAM for wellness only, and 15.0% used CAM for treatment only. Regardless of reasons for use, most commonly used CAM were herbal therapies (56.9%), followed by chiropractic (25.3%) and massage (20.2%). Those using CAM for a combination of both treatment and wellness had a higher likelihood of self‐reporting a “better sense of control over their health” (P = 0.011) and “improved overall health and feeling better” (P = 0.014) than those using CAM for treatment only.

Conclusion

Although CAM may be a promising approach to improving health‐related quality of life, future research should address efficacy and patient safety.
Improved Survival for Rural Trauma Patients Transported by Helicopter to a Verified Trauma Center: A Propensity Score Analysis
Authors: Zhu Thein Hlaing , Hollister Lisa , Opoku Dazar , Galvagno Samuel M.
Published: September 2017

Objectives

Recent studies using advanced statistical methods to control for confounders have demonstrated an association between helicopter transport (HT) versus ground ambulance transport (GT) in terms of improved survival for adult trauma patients. The aim of this study was to apply a methodologically vigorous approach to determine if HT is associated with a survival benefit for when trauma patients are transported to a verified trauma center in a rural setting.

Methods

The ascertainment of trauma patients age ≥ 15 years (n = 469 cases) by HT and (n = 580 cases) by GT between 1999 and 2012 was restricted to the scene of injury in a rural area of 10 to 35 miles from the trauma center. The propensity score (PS) was determined using data including demographics, prehospital physiology, intubation, total prehospital time, and injury severity. The PS matching was performed with different calipers to select a higher percentage of matches of HT compared to GT patients. The outcome of interest was survival to discharge from hospital. Identical logistic regression analysis was done taking into account for each matched design to select an appropriate effect estimate and confidence interval (CI) controlling for initial vital signs in the emergency department, the need for urgent surgery, intensive care unit admission, and mechanical ventilation.

Results

Unadjusted mortalities for HT compared to GT were 7.7 and 5.3%, respectively (p > 0.05). The adjusted rates were 4.0% for HT and 7.6% for GT (p < 0.05). In a PS well‐matched data set, HT was associated with a 2.69‐fold increase in odds of survival compared to GT patients (adjusted odds ratio = 2.69; 95% CI = 1.21–5.97).

Conclusions

In a rural setting, we demonstrated improved survival associated with HT compared to GT for scene transportation of adult trauma patients to a verified Level II trauma center using an advanced methodologic approach, which included adjustment for transport distance. The implication of survival benefit to rural population is discussed. We recommend larger studies with multiple trauma systems need to be repeated using similar study methodology to substantiate our findings.
Trends and age, period and cohort effects for marijuana use prevalence in the 1984–2015 US National Alcohol Surveys
Authors: Kerr William C. , Lui Camillia , Ye Yu
Published: September 2017

Background and Aims

Epidemiological trends show marijuana use in the United States to have increased in recent years. Previous research has identified cohort effects as contributing to the rising prevalence, in particular birth cohorts born after 1945. However, given recent policy efforts to regulate marijuana use at the state level, period effects could also play a contributory role. This study aimed to examine whether cohort or period effects play a larger role in explaining trends in marijuana use.

Design

Using data from seven National Alcohol Surveys, we estimated age–period–cohort decomposition models for marijuana use, controlling for socio‐demographic measures.

Setting

United States.

Participants

US general population aged 18 and older from 1984 to 2015.

Measurements

Any past‐year marijuana use.

Findings

Results indicated that period effects were the main driver of rising marijuana use prevalence. Models including indicators of medical and recreational marijuana policies did not find any significant positive impacts.

Conclusions

The steep rise in marijuana use in the United States since 2005 occurred across the population and is attributable to general period effects not linked specifically to the liberalization of marijuana policies in some states.