bluuebunny/crossref_metadata_2025 huggingface dataset:
Institutional Substance Use Disorder Intervention Improves General Internist Preparedness, Attitudes, and Clinical Practice
Authors: Wakeman Sarah E. , Kanter Genevieve Pham , Donelan Karen
Published: April 2017

Objective:

To assess the impact of hospital substance use disorder (SUD) initiative, which, beginning in October 2014, implemented an inpatient addiction consult team, a postdischarge addiction clinic, recovery coaches, and SUD treatment within primary care on general internists’ attitudes, clinical practice, and preparedness to care for SUD.

Methods:

Pre and postintervention survey of general internal medicine physicians at Massachusetts General Hospital, in Boston, Massachusetts, in September 2014 (n = 290) and 2015 (n = 296) was conducted.

Results:

There were 149 respondents for the pre and 143 respondents for the post survey. There were no significant differences between groups. In the follow-up group, 66% of physicians had a patient receive care from the initiative. These physicians were significantly more likely to have favorable attitudes towards SUD; 44% report caring for patients with SUD is as satisfying as other clinical activities versus 9% of physicians without experience with the initiative. These physicians were significantly more likely to feel very prepared to screen for SUD (27% vs 9%), diagnose SUD (23% vs 9%), deliver a brief intervention (16% vs 5%), refer to treatment (36% vs 14%), discuss medication treatments (22% vs 5%), discuss overdose prevention and naloxone (33% vs 5%), and discuss harm reduction (22% vs 7%). They were also significantly more likely to frequently prescribe naloxone (11% vs 0%), prescribe addiction pharmacotherapy (15% vs 2%), and provide addiction treatment themselves (18% vs 5%).

Conclusion:

General internists’ attitudes, preparedness, and clinical practice related to SUD significantly improved after having a patient receive care from new clinical services implemented through a hospital-wide SUD initiative.
Effects of Single Nucleotide Polymorphisms on Surgical and Postsurgical Opioid Requirements
Authors: Choi Siu-Wai , Lam David M.H. , Wong Stanley S.C. , Shiu Haydn H.C. , Wang Amy X.M. , Cheung Chi-Wai
Published: April 2017

Objectives:

There is great heterogeneity in the way individuals respond to medications. Inherited differences, such as single nucleotide polymorphisms (SNP), can influence the efficacy and toxicity of drugs. This meta-analysis aims to collate data from studies investigating the effect of SNPs on postoperative and/or intraoperative opioid requirements.

Materials and Methods:

A meta-analysis was conducted following PRISMA guidelines. Eligibility criteria for studies included were reporting amount of postoperative and/or intraoperative opioid used as the primary outcome and genotyping patients for SNPs in one of the following genes; OPRM1, CYP2D6, CYP3A4, CYP3A5, COMT, UGT2B7, or ABCB1. A comprehensive systematic search for articles using keywords “opioid-sensitivity,” “polymorphisms,” “post-operative opioid,” “post-surgical opioid,” “post-operative pain,” and “post-surgical pain” was performed.

Results:

Fifty-one studies were included. Individuals homozygous for AA at the OPRMI (rs1799971) polymorphisms required less postsurgical opioid compared with those homozygous for GG (Hedges g, −0.270; 95% confidence interval, −0.433 to −0.108; P=0.001). Polymorphisms in CYP2D6, CYP3A4, CYP3A5, COMT, UGT2B7, and ABCB1 did not affect opioid requirements.

Discussion:

Investigation of single changes in 1 gene can only yield limited information regarding genetic effects on opioid requirements. Rapid development of whole genome sequencing enables information on all genetic modifications that may affect analgesic response to be collected. The information collected must include data on the individual’s metabolic enzymes, as well as information on drug receptors and enzymes responsible for drug degradation, so that a personal profile can be built up which will predict individual response to drugs, and guide clinicians on the type and dosage of drug to use.
Patients With Knee Osteoarthritis Who Score Highly on the PainDETECT Questionnaire Present With Multimodality Hyperalgesia, Increased Pain, and Impaired Physical Function
Authors: Moss Penny , Benson Heather A.E. , Will Rob , Wright Anthony
Published: April 2017

Objectives:

PainDETECT is a self-report questionnaire that can be used to identify features of neuropathic pain. A proportion of patients with knee osteoarthritis (OA) score highly on the PainDETECT questionnaire. This study aimed to determine whether those with a higher “positive neuropathic” score on the PainDETECT questionnaire also had greater pain, hypersensitivity, and reduced function compared with individuals with knee OA with lower PainDETECT scores.

Materials and Methods:

In total, 130 participants with knee OA completed the PainDETECT, Western Ontario and McMaster Universities Arthritis Index (WOMAC), and Pain Quality Assessment Scale questionnaires. Quantitative sensory testing was carried out at 3 sites (both knees and elbow) using standard methods. Cold and heat pain thresholds were tested using a Peltier thermode and pressure pain thresholds using a digital algometer. Physical function was assessed using 3 timed locomotor function tests.

Results:

In total, 22.3% of participants scored in the “positive neuropathic” category with a further 35.4% in the unclear category. Participants in the “positive neuropathic” category reported higher levels of pain and more impaired function based on the WOMAC questionnaire (P<0.0001). They also exhibited increased levels of hyperalgesia at the knee and upper limb sites for all stimulation modalities except heat pain thresholds at the OA knee. They were also slower to complete 2 of the locomotion tasks.

Discussion:

This study identified a specific subgroup of people with knee OA who exhibited PainDETECT scores in the “positive neuropathic” category. These individuals experienced increased levels of pain, widespread, multimodality hyperalgesia, and greater functional impairment than the remaining cohort. Identification of OA patients with this pain phenotype may permit more targeted and effective pain management.
Cochlear Implantation in Cases of Unilateral Hearing Loss: Initial Localization Abilities
Authors: Dillon Margaret T. , Buss Emily , Anderson Meredith L. , King English R. , Deres Ellen J. , Buchman Craig A. , Brown Kevin D. , Pillsbury Harold C.
Published: April 2017

Objectives:

The present study evaluated early auditory localization abilities of cochlear implant (CI) recipients with normal or near-normal hearing (NH) in the contralateral ear. The goal of the study was to better understand the effect of CI listening experience on localization in this population.

Design:

Twenty participants with unilateral hearing loss enrolled in a prospective clinical trial assessing outcomes of cochlear implantation (ClinicalTrials.gov Identifier: NCT02203305). All participants received the MED-EL Standard electrode array, were fit with an ear-level audio processor, and listened with the FS4 coding strategy. Localization was assessed in the sound field using an 11-speaker array with speakers uniformly positioned on a horizontal, semicircular frame. Stimuli were 200-msec speech-shaped noise bursts. The intensity level (52, 62, and 72 dB SPL) and sound source were randomly interleaved across trials. Participants were tested preoperatively, and 1, 3, and 6 months after activation of the audio processor. Performance was evaluated in two conditions at each interval: (1) unaided (NH ear alone [NH-alone] condition), and (2) aided, with either a bone conduction hearing aid (preoperative interval; bone conduction hearing aid + NH condition) or a CI (postoperative intervals; CI + NH condition). Performance was evaluated by comparing root-mean-squared (RMS) error between listening conditions and between measurement intervals.

Results:

Mean RMS error for the soft, medium, and loud levels were 66°, 64°, and 69° in the NH-alone condition and 72°, 66°, and 70° in the bone conduction hearing aid + NH condition. Participants experienced a significant improvement in localization in the CI + NH condition at the 1-month interval (38°, 35°, and 38°) as compared with the preoperative NH-alone condition. Localization in the CI + NH condition continued to improve through the 6-month interval. Mean RMS errors were 28°, 25°, and 28° in the CI + NH condition at the 6-month interval.

Conclusions:

Adult CI recipients with normal or near-normal hearing in the contralateral ear experienced significant improvement in localization after 1 month of device use, and continued to improve through the 6-month interval. The present results show that binaural acclimatization in CI users with unilateral hearing loss can progress rapidly, with marked improvements in performance observed after only 1 month of listening experience.
Biological fixation of pelvic ring and acetabular fractures: a pilot study with anatomical validation
Authors: Saoud Abdelfattah Mohamed Fathy , Sallam Ahmed Mohamed , Morsey Ahmed Mohamed
Published: April 2017

Background:

The middle window of the ilioinguinal approach described by Letournel requires dissection through important structures (inguinal part). We developed a less invasive anterior approach consisting of a medial window (Pfannenstiel) combined with the lateral window of the ilioinguinal approach.

Methods:

Initially, anatomical validation on two cadaver specimens proved the feasibility of the assumption. Between 2007 and 2012, 15 patients with acetabular fractures and 35 patients with pelvic ring injuries were consecutively operated on using the modified technique. The patients were prospectively followed clinically and by standard radiographs for at least 1 yr.

Results:

Fifty patients with a fractured pelvis or acetabulum managed to complete at least 1 yr follow-up. Anatomical reduction was achieved in 21 pelvic fractures (60% of pelvic fractures) and in 10 acetabular fractures (67% of acetabular fractures). Satisfactory reduction was achieved in 14 pelvic fractures (40% of pelvic fractures) and in five acetabular fractures (33% of acetabular fractures).

Conclusions:

The modified approach allows reduction of the anterior column and pelvic ring fractures without requiring dissection through the inguinal neurovascular structures. Our results demonstrate that safe reduction and stable fixation of selected acetabular and pelvic ring fractures is possible with this approach.

Level of Evidence:

This is considered a level IV evidence study (case series).
Effects of long-term high-load exercise on the anatomy of the hip joints: a preliminary report
Authors: Song Yawei , Zhang Xiyuan , Rong Ke
Published: April 2017

The aim of this study was to assess the impact of different sports on hip joint anatomic parameters in athletes. This was a cross-sectional study of eight male trampolinists, eight male weightlifters, and eight male volunteers enrolled in July 2014. Hip joint anatomic parameters were measured from plain radiographs taken at the level of the lesser trochanter center. Data were compared between groups using the χ
2-test or one-way analysis of variance with the Bonferroni post-hoc test. There were no significant differences among groups in age, height, or weight. Compared with the controls, trampolinists showed higher pelvic width, femoral neck length, metaphyseal width (T0), width 20 mm above T0 (T+20), width 20 mm below T0 (T−20) and center edge (CE) angle, and lower head–trochanter ratio, joint space, neck-shaft angle, and articular cartilage angle (P<0.05). Compared with the controls, weightlifters showed lower pelvic femoral index, joint space, length of femoral neck, eccentricity, neck-shaft, and AC angle, and higher pelvic width, femoral head radius, and CE angle (P<0.05). Compared with trampolinists, weightlifters showed higher head–trochanter ratio and femoral head radius, and lower pelvic femoral index, femoral neck length, eccentricity, T0, T+20, T−20, neck-shaft angle, CE angle, and articular cartilage angle (P<0.05). Long-term high-intensity training causes adaptive changes in the hip joint structure that differ between trampolinists and weightlifters.
Recent lung cancer mortality trends in Europe: effect of national smoke-free legislation strengthening
Authors: López-Campos Jose L. , Ruiz-Ramos Miguel , Fernandez Esteve , Soriano Joan B.
Published: April 2017

The impact of smoke-free legislation within European Union (EU) countries on lung cancer mortality has not been evaluated to date. We aimed to determine lung cancer mortality trends in the EU-27 by sex, age, and calendar year for the period of 1994 and 2012, and relate them with changes in tobacco legislation at the national level. Deaths by Eurostat in each European country were analyzed, focusing on ICD-10 codes C33 and C34 from the years 1994 to 2012. Age-standardized mortality rates (ASR) were estimated separately for women and men in the EU-27 total and within country for each one of the years studied, and the significance of changing trends was estimated by joinpoint regression analysis, exploring lag times after initiation of smoke-free legislation in every country, if any. From 1994 to 2012, there were 4 681 877 deaths from lung cancer in Europe (3 491 607 in men and 1 190 180 in women) and a nearly linear decrease in mortality rates because of lung cancer in men from was observed1994 to 2012, mirrored in women by an upward trend, narrowing the sex gap during the study period from 5.1 in 1994 to 2.8 in 2012. Joinpoint regression analysis identified a number of trend changes over time, but it appears that they were unrelated to the implementation of smoke-free legislations. A few years after the introduction of smoke-free legislations across Europe, trends of lung cancer mortality trends have not changed.
Immunoresponsive Autonomic Neuropathy in Sjögren Syndrome—Case Series and Literature Review
Authors: Goodman Brent P.
Published: April 2017

Background:

Sjögren syndrome (SS) is one of the most common autoimmune disorders that classically affects exocrine glands, resulting in keratoconjunctivitis sicca and xerostomia, and frequently is associated with other systemic symptoms. SS appears to have a particular predilection for involving the autonomic nervous system.

Study Question:

Does immunotherapy improve signs and symptoms of autonomic nervous system impairment in SS?

Study Design:

This is a retrospective review of patients seen in the autonomic clinic at our institution who underwent an evaluation for a suspected autonomic disorder that ultimately was attributed to SS. SS patients who were treated with immunotherapy and completed autonomic testing before and after treatment were included in this review.

Results:

A total of 4 patients were identified who were treated for SS-related autonomic dysfunction with immunotherapy and underwent repeat autonomic testing after treatment. Marked clinical and functional improvement was seen after treatment with intravenous immunoglobulin in all patients and adjunctive rituximab therapy in 1 patient. The clinical improvement with immunotherapy in these patients correlated with markedly improved findings on autonomic testing in all.

Measures and Outcomes:

Clinical symptoms and results of autonomic testing prior to and following immunotherapy were assessed.

Conclusions:

Autonomic signs and symptoms in SS are potentially immunoresponsive, but immunotherapy in these patients may require repeated, ongoing, or adjunctive therapy for optimal and sustained improvement.
Combination Steroid and Test‐based Food Elimination for Eosinophilic Esophagitis
Authors: Constantine Gregory , Seth Neha , Chokshi Niti , Minard Charles G. , Guffey Danielle , Olive Anthony P. , Davis Carla M.
Published: April 2017

Objectives:

Eosinophilic esophagitis (EoE) is a clinicopathologic disorder characterized by infiltration of eosinophils into the esophagus. Primary treatment approaches include topical corticosteroids and/or food elimination. The aim of the present study was to compare the effectiveness of combination therapy (topical corticosteroid plus test‐based food elimination [FS]) with single therapy (topical corticosteroid [S] or test‐based food elimination [F]).

Methods:

Chart review of patients with EoE at Texas Children's Hospital (age <21 years) was performed. Clinical and histological statuses were evaluated after a 3‐month treatment with either single or combination therapy. Comparisons were analyzed using Fisher exact test, Kruskal‐Wallis tests, and multiple logistic regression models.

Results:

Among 670 charts, 63 patients (1–21 years, median 10.3 years) with clinicopathologic diagnoses of EoE were identified. Combination FS therapy was provided to 51% (n = 32) and single treatment (S, F) to 27% (n = 17) or 22% (n = 14) of patients, respectively. Clinical responses were noted in 91% (n = 29), 71% (n = 12), and 64% (n = 14) of patients in the FS, S, and F groups, respectively. The odds of clinically improving were 4.6 times greater (95% confidence interval: 1.1–18.8) with combination versus single therapy. The median peak number of eosinophils per high‐power field after 3‐month therapy was not significantly different in the S, F, and FS groups.

Conclusions:

The combination of topical corticosteroids with specific food elimination is as effective in achieving clinical and histological remissions as the single‐treatment approaches. Responses were achieved with the combination in patients who had previously failed single‐agent therapy. Prospective research of this combination approach in young patients with EoE is needed.
A Systematic Review of Measurement Tools for the Proactive Assessment of Patient Safety in General Practice
Authors: Lydon Sinéad , Cupples Margaret E. , Murphy Andrew W. , Hart Nigel , O'Connor Paul
Published: April 2017

Background

Primary care physicians have reported a difficulty in understanding how best to measure and improve patient safety in their practices.

Objectives

The aims of the study were to identify measures of patient safety suitable for use in primary care and to provide guidance on proactively monitoring and measuring safety.

Methods

Searches were conducted using Medline, Embase, CINAHL and PsycInfo in February 2016. Studies that used a measure assessing levels of or attitudes toward patient safety in primary care were considered for inclusion. Only studies describing tools focused on the proactive assessment of safety were reviewed. Two independent reviewers extracted data from articles and applied the Quality Assessment Tool for Studies with Diverse Designs.

Results

More than 2800 studies were screened, of which 56 were included. Most studies had used healthcare staff survey or interviews to assess patient safety (n = 34), followed by patient chart audit (n = 14) or use of a practice assessment checklist (n = 7). Survey or interview of patients, active monitoring systems, and simulated patients were used with less frequency.

Conclusions

A lack of appropriate measurement tools has been suggested to limit the ability to monitor patient safety in primary care and to improve patient care. There is no evident “best” method of measuring patient safety in primary care. However, many of the measures are readily available, quick to administer, do not require external involvement, and are inexpensive. This synthesis of the literature suggests that it is possible for primary care physicians to take a proactive approach to measuring and improving safety.
Cause-specific Mortality in a Population-based Cohort of 9799 Women Treated for Ductal Carcinoma In Situ
Authors: Elshof Lotte E. , Schmidt Marjanka K. , Rutgers Emiel J.Th. , van Leeuwen Flora E. , Wesseling Jelle , Schaapveld Michael
Published: April 2017

Objective:

To assess cause-specific mortality in women treated for ductal carcinoma in situ (DCIS).

Background:

From screening and treatment perspective, it is relevant to weigh the low breast cancer mortality after DCIS against mortality from other causes and expected mortality in the general population.

Methods:

We conducted a population-based cohort study comprising 9799 Dutch women treated for primary DCIS between 1989 and 2004 and estimated standardized mortality ratios (SMRs).

Results:

After a median follow up of 9.8 years, 1429 patients had died of whom 284 caused by breast cancer (2.9% of total cohort). DCIS patients <50 years experienced higher mortality compared with women in the general population (SMR 1.7; 95% confidence interval, CI: 1.4–2.0), whereas patients >50 had significantly lower mortality (SMR 0.9; 95% CI: 0.8–0.9). Overall, the risk of dying from general diseases and cancer other than breast cancer was lower than in the general population, whereas breast cancer mortality was increased. The SMR for breast cancer decreased from 7.5 (95% CI: 5.9–9.3) to 2.8 (95% CI: 2.4–3.2) for women aged <50 and >50 years, respectively. The cumulative breast cancer mortality 10 years after DCIS was 2.3% for women <50 years and 1.4% for women >50 years treated for DCIS between 1999 and 2004.

Conclusions:

DCIS patients >50 years had lower risk of dying from all causes combined compared with the general female population, which may reflect differences in health behavior. Women with DCIS had higher risk of dying from breast cancer than the general population, but absolute 10-year risks were low.
The role of topiceuticals in cancer pain
Authors: Paisley Peter , Serpell Michael
Published: April 2017

Purpose of review

Pain is one of the most common and feared symptoms associated with a new diagnosis of cancer and its subsequent treatment. Unfortunately, it remains undertreated in around one third of patients. It has been recently postulated that one mechanism for this could be failure to recognize neuropathic pain. One attractive option in both the case of neuropathic pain and pain associated with intolerable side effects of prescribed opioids is the use of ‘topiceuticals’, as a means of targeted pain relief with potentially fewer side effects. The present review summarizes the evidence base for the various topiceuticals available for the treatment of localized neuropathic pain.

Recent findings

The recent evidence base for established treatments such as capsaicin and lignocaine is examined. A variety of novel and previously used therapies are considered.

The use of topiceuticals in localized neuropathic pain associated with malignancy remain a valuable option with many advantages over systemic treatments. In addition to anecdotal reports of efficacy, there is a growing body of evidence to consider the early use of topical lignocaine and capsaicin in this context. The authors’ have proposed a guideline including the use of topiceuticals to aid in the management of neuropathic pain.
Accelerating the carbon cycle: the ethics of enhanced weathering
Authors: Lawford-Smith H. , Currie A.
Published: April 2017

Enhanced weathering, in comparison to other geoengineering measures, creates the possibility of a reduced cost, reduced impact way of decreasing atmospheric carbon, with positive knock-on effects such as decreased oceanic acidity. We argue that ethical concerns have a place alongside empirical, political and social factors as we consider how to best respond to the critical challenge that anthropogenic climate change poses. We review these concerns, considering the ethical issues that arise (or would arise) in the large-scale deployment of enhanced weathering. We discuss post-implementation scenarios, failures of collective action, the distribution of risk and externalities and redress for damage. We also discuss issues surrounding ‘dirty hands’ (taking conventionally immoral action to avoid having to take action that is even worse), whether enhanced weathering research might present a moral hazard, the importance of international governance and the notion that the implementation of large-scale enhanced weathering would reveal problematic hubris. Ethics and scientific research interrelate in complex ways: some ethical considerations caution against research and implementation, while others encourage them. Indeed, the ethical perspective encourages us to think more carefully about how, and what types of, geoengineering should be researched and implemented.
Simulating carbon capture by enhanced weathering with croplands: an overview of key processes highlighting areas of future model development
Authors: Taylor Lyla L. , Beerling David J. , Quegan Shaun , Banwart Steven A.
Published: April 2017

Enhanced weathering (EW) aims to amplify a natural sink for CO2by incorporating powdered silicate rock with high reactive surface area into agricultural soils. The goal is to achieve rapid dissolution of minerals and release of alkalinity with accompanying dissolution of CO2into soils and drainage waters. EW could counteract phosphorus limitation and greenhouse gas (GHG) emissions in tropical soils, and soil acidification, a common agricultural problem studied with numerical process models over several decades. Here, we review the processes leading to soil acidification in croplands and how the soil weathering CO2sink is represented in models. Mathematical models capturing the dominant processes and human interventions governing cropland soil chemistry and GHG emissions neglect weathering, while most weathering models neglect agricultural processes. We discuss current approaches to modelling EW and highlight several classes of model having the potential to simulate EW in croplands. Finally, we argue for further integration of process knowledge in mathematical models to capture feedbacks affecting both longer-term CO2consumption and crop growth and yields.
Perceptions of enhanced weathering as a biological negative emissions option
Authors: Pidgeon Nick F. , Spence Elspeth
Published: April 2017

This paper addresses the social acceptability of enhanced weathering, a technology that would involve spreading silicate particles over terrestrial surfaces in order to boost the biological processes that currently sequester CO
2
as part of the earth's natural carbon cycle. We present the first exploration of British attitudes towards enhanced weathering, using an online survey (
n
= 935) of a representative quota sample of the public. Baseline awareness of weathering was extremely low. Many respondents remained undecided or neutral about risks, although more people support than oppose weathering. Factors predicting support for weathering and its research included feelings about the technology and trust in scientists. Over half of the sample agrees that scientists should be able to conduct research into effectiveness and risks, but with conditions also placed upon how research is conducted, including the need for scientific independence, small-scale trials, strict monitoring, risk minimization and transparency of results. Public engagement is needed to explore in more detail why particular individuals feel either positive or negative about weathering, and why they believe particular conditions should be applied to research, as part of wider responsible research and innovation processes for biological and other types of negative emissions technologies.
David Edgar Cartwright. 21 October 1926 — 2 December 2015
Authors: Webb David J.
Published: April 2017

David Cartwright was one of the world's leading authorities on the tides. However, when reflecting on his life, Cartwright made the point that his early scientific career was not a success. Indeed in 1953, at the age of 27, he had virtually despaired of any creative scientific future. At the time he was being pressurized to stop his work on the statistics of ship motions but his prospects rapidly changed when he was invited to apply for a post at the new National Institute of Oceanography (NIO) being set up by George Deacon.

At NIO he soon made important contributions to the study of ocean waves, especially the calculation of directional spectrum and wave climate. His earlier involvement with ship motions also culminated in a successful joint study with Louis Rydill on the response of ships to the spectrum of waves. Following this, his use of computer methods for time-series analysis led to an invitation to the Scripps Institution of Oceanography where, with Walter Munk, he developed the response method of analysing tides making use of the very long tidal records collected from Hawaii and Newlyn. He was also made aware of the significant lack of good tidal data from the deep ocean.

Returning to the UK, he continued these interests, studying the deep-ocean tides of the Atlantic and leading an international collaboration that measured deep-ocean tides. He also investigated the effect of tides on storm surges around the UK. He became assistant director in charge of the Institute of Oceanographic Sciences (IOS) Bidston laboratory, where he continued these activities and started research on estimating the tides using data from the Seasat radar altimeter.

After retirement he successfully extended this work with Richard Ray at the Goddard Space Flight Center. Using Geosat altimeter data they generated accurate global maps of the tides in a set of papers that Cartwright considered to be his best work. He wrote a successful book titled ‘
Tides: a scientific history
’, and later published further work with Ray on the internal tides of the ocean.
SNPs in microRNA target sites and their potential role in human disease
Authors: Moszyńska Adrianna , Gebert Magdalena , Collawn James F. , Bartoszewski Rafał
Published: April 2017

In the post-genomic era, the goal of personalized medicine is to determine the correlation between genotype and phenotype. Developing high-throughput genotyping technologies such as genome-wide association studies (GWAS) and the 1000 Genomes Project (http://www.internationalgenome.org/about/#1000G_PROJECT) has dramatically enhanced our ability to map where changes in the genome occur on a population level by identifying millions of single nucleotide polymorphisms (SNPs). Polymorphisms, particularly those within the coding regions of proteins and at splice junctions, have received the most attention, but it is also now clear that polymorphisms in the non-coding regions are important. In these non-coding regions, the enhancer and promoter regions have received the most attention, whereas the 3′-UTR regions have until recently been overlooked. In this review, we examine how SNPs affect microRNA-binding sites in these regions, and how mRNA stability changes can lead to disease pathogenesis.
Carbon Fiber on Polyimide Ultra-Microelectrodes
Authors: Gillis Winthrop F. , Lissandrello Charles A. , Shen Jun , Pearre Ben W. , Mertiri Alket , Deku Felix , Cogan Stuart , Holinski Bradley J. , Chew Daniel J. , White Alice E. , Gardner Timothy J. , Otchy Timothy M.
Published: April 2017

Most preparations for making neural recordings degrade over time and eventually fail due to insertion trauma and reactive tissue response. The magnitudes of these responses are thought to be related to the electrode size (specifically, the cross-sectional area) and the relative stiffness of the electrode material. Carbon fiber ultramicroelectrodes have a much smaller cross-section than traditional electrodes and thus may enable improved longevity of neural recordings in the central and peripheral nervous systems. Only two carbon fiber array designs have been described previously, each with limited channel densities due to limitations of the fabrication processes or interconnect strategies. Here, we describe a method for assembling carbon fiber electrodes on a flexible polyimide substrate that will facilitate the construction of high-density recording and stimulating arrays for acute use in peripheral nerves. Fibers were aligned using an alignment tool that was 3D-printed with sub-micron resolution using direct laser writing. Indium deposition on the carbon fibers provided a robust and reliable method of electrical connection to the polyimide traces. Spontaneous action potentials and stimulation-evoked compound responses with SNR > 10 and > 120, respectively, were recorded from a small (125 μm) peripheral nerve. We also improved the typically poor charge injection capacity of small diameter carbon fibers can be improved by electrodepositing 100 nm thick iridium oxide films, making the carbon fiber arrays suitable for electrical stimulation as well as recording.
CellView: Interactive exploration of high dimensional single cell RNA-seq data
Authors: Bolisetty Mohan T. , Stitzel Michael L. , Robson Paul
Published: April 2017

Advances in high-throughput single cell transcriptomics technologies have revolutionized the study of complex tissues. It is now possible to measure gene expression across thousands of individual cells to define cell types and states. While powerful computational and statistical frameworks are emerging to analyze these complex datasets, a gap exists between this data and a biologist’s insight. The CellView web application fills this gap by providing easy and intuitive exploration of single cell transcriptome data.
Interactive Visual Exploration and Refinement of Cluster Assignments
Authors: Kern Michael , Lex Alexander , Gehlenborg Nils , Johnson Chris R.
Published: April 2017

Background

With ever-increasing amounts of data produced in biology research, scientists are in need of efficient data analysis methods. Cluster analysis, combined with visualization of the results, is one such method that can be used to make sense of large data volumes. At the same time, cluster analysis is known to be imperfect and depends on the choice of algorithms, parameters, and distance measures. Most clustering algorithms don’t properly account for ambiguity in the source data, as records are often assigned to discrete clusters, even if an assignment is unclear. While there are metrics and visualization techniques that allow analysts to compare clusterings or to judge cluster quality, there is no comprehensive method that allows analysts to evaluate, compare, and refine cluster assignments based on the source data, derived scores, and contextual data.

Results

In this paper, we introduce a method that explicitly visualizes the quality of cluster assignments, allows comparisons of clustering results and enables analysts to manually curate and refine cluster assignments. Our methods are applicable to matrix data clustered with partitional, hierarchical, and fuzzy clustering algorithms. Furthermore, we enable analysts to explore clustering results in context of other data, for example, to observe whether a clustering of genomic data results in a meaningful differentiation in phenotypes.

Conclusions

Our methods are integrated into Caleydo StratomeX, a popular, web-based, disease subtype analysis tool. We show in a usage scenario that our approach can reveal ambiguities in cluster assignments and produce improved clusterings that better differentiate genotypes and phenotypes.
Modelling and Interpreting Network Dynamics
Authors: Khambhati Ankit N. , Sizemore Ann E. , Betzel Richard F. , Bassett Danielle S.
Published: April 2017

Recent advances in brain imaging techniques, measurement approaches, and storage capacities have provided an unprecedented supply of high temporal resolution neural data. These data present a remarkable opportunity to gain a mechanistic understanding not just of circuit structure, but also of circuit dynamics, and its role in cognition and disease. Such understanding necessitates a description of the raw observations, and a delineation of computational models and mathematical theories that accurately capture fundamental principles behind the observations. Here we review recent advances in a range of modeling approaches that embrace the temporally-evolving interconnected structure of the brain and summarize that structure in a dynamic graph. We describe recent efforts to model dynamic patterns of connectivity, dynamic patterns of activity, and patterns of activity atop connectivity. In the context of these models, we review important considerations in statistical testing, including parametric and non-parametric approaches. Finally, we offer thoughts on careful and accurate interpretation of dynamic graph architecture, and outline important future directions for method development.
Multimodal neural correlates of cognitive control in the Human Connectome Project
Authors: Lerman-Sinkoff Dov B. , Sui Jing , Rachakonda Srinivas , Kandala Sridhar , Calhoun Vince D. , Barch Deanna M.
Published: April 2017

Cognitive control is a construct that refers to the set of functions that enable decisionmaking and task performance through the representation of task states, goals, and rules. The neural correlates of cognitive control have been studied in humans using a wide variety of neuroimaging modalities, including structural MRI, resting-state fMRI, and task-based fMRI. The results from each of these modalities independently have implicated the involvement of a number of brain regions in cognitive control, including dorsal prefrontal cortex, and frontal parietal and cingulo-opercular brain networks. However, it is not clear how the results from a single modality relate to results in other modalities. Recent developments in multimodal image analysis methods provide an avenue for answering such questions and could yield more integrated models of the neural correlates of cognitive control. In this study, we used multiset canonical correlation analysis with joint independent component analysis (mCCA+jICA) to identify multimodal patterns of variation related to cognitive control. We used two independent cohorts of participants from the Human Connectome Project, each of which had data from four imaging modalities. We replicated the findings from the first cohort in the second cohort using both independent and predictive analyses. The independent analyses identified a component in each cohort that was highly similar to the other and significantly correlated with cognitive control performance. The replication by prediction analyses identified two independent components that were significantly correlated with cognitive control performance in the first cohort and significantly predictive of performance in the second cohort. These components identified positive relationships across the modalities in neural regions related to both dynamic and stable aspects of task control, including regions in both the frontal-parietal and cingulo-opercular networks, as well as regions hypothesized to be modulated by cognitive control signaling, such as visual cortex. Taken together, these results illustrate the potential utility of multi-modal analyses in identifying the neural correlates of cognitive control across different indicators of brain structure and function.
SINAPS: Prediction of microbial traits from marker gene sequences
Authors: Edgar Robert C.
Published: April 2017

Microbial communities are often studied by sequencing marker genes such as 16S ribosomal RNA. Marker gene sequences can be used to assess diversity and taxonomy, but do not directly measure functions arising from other genes in the community metagenome. Such functions can be predicted by algorithms that associate marker genes with experimentally determined traits in well-studied species. Typically, such methods use ancestral state reconstruction. Here I describe SINAPS, a new algorithm that predicts traits for marker gene sequences using a fast, simple word-counting algorithm that does not require alignments or trees. A measure of prediction confidence is obtained by bootstrapping. I tested SINAPS predictions from 16S V4 query sequences for traits including energy metabolism, Gram-positive staining, presence of a flagellum, V4 primer mismatches, and 16S copy number. Accuracy was >90% except for copy number, where a large majority of predictions were within +/−2 of the true value.
The impact of macroeconomic uncertainty on international commodity prices
Authors: Tan Xiaofen , Ma Yongjiao
Published: April 2017

Purpose

The purpose of this paper is to empirically analyze the impact of macroeconomic uncertainty on a large sample of 19 commodity markets.

Design/methodology/approach

The authors rely on Juradoet al.’s (2015) measure of macroeconomic uncertainty based on a wide range of monthly macroeconomic and financial indicators and estimate a threshold VAR model to assess whether the impact of macroeconomic uncertainty on commodity prices differs under the high- or low-uncertainty state.

Findings

The findings show that positive macroeconomic uncertainty shocks affect commodity prices returns negatively on average and the impact of macroeconomic uncertainty is generally higher in high-uncertainty states compared with low-uncertainty states. Besides, although the safe-haven role of precious metals is confirmed, energy and industrial markets are more sensitive to short-run and long-run macroeconomic uncertainty, respectively.

Research limitations/implications

The findings in this study suggest that commodity prices reflect not only the level of economic fundamental but also the volatility of economic fundamental.

Originality/value

This study empirically analyzes and verifies the influence of macroeconomic uncertainty not only on oil prices but also on four groups of 19 raw materials. As for the methodological issues, the authors rely on a structural threshold vector autoregressive specification for modeling commodity price returns to account for potentially different effects depending on the macroeconomic uncertainty states.
Estimating liquidity premium of corporate bonds using the spread information in on- and off-the-run Treasury securities
Authors: Li Haitao , Wu Chunchi , Shi Jian
Published: April 2017

Purpose

The purpose of this paper is to estimate the effects of liquidity on corporate bond spreads.

Design/methodology/approach

Using a systematic liquidity factor extracted from the yield spreads between on- and off-the-run Treasury issues as a state variable, the authors jointly estimate the default and liquidity spreads from corporate bond prices.

Findings

The authors find that the liquidity factor is strongly related to conventional liquidity measures such as bid-ask spread, volume, order imbalance, and depth. Empirical evidence shows that the liquidity component of corporate bond yield spreads is sizable and increases with maturity and credit risk. On average the liquidity spread accounts for about 25 percent of the spread for investment-grade bonds and one-third of the spread for speculative-grade bonds.

Research limitations/implications

The results show that a significant part of corporate bond spreads are due to liquidity, which implies that it is not necessary for credit risk to explain the entire corporate bond spread.

Practical implications

The results show that returns from investments in corporate bonds represent compensations for bearing both credit and liquidity risks.

Originality/value

It is a novel approach to extract a liquidity factor from on- and off-the-run Treasury issues and use it to disentangle liquidity and credit spreads for corporate bonds.
Effect of facilities management components on the quality of life of Chinese elderly in care and attention homes
Authors: Leung Mei-yung , Famakin Ibukun Oluwadara , Olomolaiye Paul
Published: April 2017

Purpose

Quality of life (QoL) for elderly residents of care and attention (C&A) homes has become an important consideration, given the increasingly aging population. Due to the number of hours such residents spend indoors, the quality of the facilities can contribute to their day-to-day QoL. This study aims to investigate the effect of facilities management (FM) on the QoL of Chinese elderly people living in C&A homes.

Design/methodology/approach

A survey of perceived satisfaction with the components of FM and QoL was carried out with a sample of residents. A total of 18 FM components and five QoL domains, including physical health, independence, psychological health, social relationships and living environment, as well as overall QoL, were identified.

Findings

The findings show that physical health is influenced by accessibility, doors and windows and signage; independence can be improved by enhancing accessibility, water supply, lighting and ventilation; accessibility, water supply, distance and doors and windows all predict psychological health; social relationships are improved by lighting and ventilation; distance impacts positively on the living environment; and overall QoL is predicted by lighting, ventilation, accessibility, doors and windows, handrails, recreation and signage.

Originality/value

The study recommends that designers and facilities managers review the micro-climate settings to harness available natural lighting and ventilation, introduce bimetallic strips to the heating systems to maintain a suitable water temperature and install large, easy-to-understand and graphic signage for straightforward wayfinding in C&A homes.
Facility management in Qatar: current state, perceptions and recommendations
Authors: Rybkowski Zofia K. , Shepley Mardelle M. , Bryant John A. , Skelhorn Cynthia , Amato Alex , Kalantari Saleh
Published: April 2017

Purpose

This paper aims to identify the current challenges and opportunities faced by the facility managers (FMs) in Doha, Qatar.

Design/methodology/approach

Researchers queried 40 FMs about their experience working in Qatar, using interviews and workshops.

Findings

Comments gathered followed general patterns. Participants expressed appreciation for their work, but also concern about cultural challenges they faced managing facilities in the region. In general, it was agreed that the low cost of water and energy in Qatar is one of the largest obstacles to conserving resources; however, current consumption is not sustainable.

Research limitations/implications

The sensitive nature of this study made strict demands on the research team to maintain participant anonymity during data collection and reporting. This sensitivity also limited the sample size; a larger sample size for future research would support greater generalizability.

Social implications

Qatar is taking steps to reduce its per capita carbon footprint and energy use, which is among the highest in the world. However, there appears to be a disconnect between Qatar’s expressed intentions and its actions with respect to facility management. To ensure that Qatar manages resources more efficiently, participants recommended that reduced energy use standards be adopted and legally mandated. This action would address many of the challenges, incentivize increased qualifications and training of FM professionals working in Qatar and encourage improvement of the long-term performance of buildings which are energy drains and heavy contributors to greenhouse gas emissions.

Originality/value

Prior to this study, little has been published about current practices of facility management in Doha, Qatar, and the challenges and opportunities that FMs face in this region.