bluuebunny/crossref_metadata_2025 huggingface dataset:
Can Emergency Department, Hospital Discharge, and Death Data Be Used to Monitor Burden of Drug Overdose in Rhode Island?
Authors: Jiang Yongwen , McDonald James V. , Koziol Jennifer , McCormick Meghan , Viner-Brown Samara , Alexander-Scott Nicole
Published: December 2016

Context:

Drug overdoses are a growing public health problem in the United States. Rhode Island is also confronted with a serious epidemic of drug overdose deaths and ranks sixth worst in the United States for age-adjusted drug overdose death rate.

Objective:

To monitor trends of drug overdose-related emergency department (ED) visits, hospitalizations, and deaths and classify the drug overdoses by demographics, discharge status, intent, and specific drug involved to plan for health care resource allocation, mental health services, drug abuse treatment, prevention, and policies.

Design:

Cross-sectional study.

Setting:

The 2005-2014 ED, hospital discharge, and death data were used for this study.

Main Outcome Measure:

Age-adjusted rates were calculated by using age-specific Rhode Island 2010 standard population. Healthcare Cost and Utilization Project cost-to-charge ratios were used to convert total hospital charges to costs. The descriptive analysis was performed.

Results:

Hospitalizations generally represent the most severe cases; there are substantially fewer cases than are seen in the ED, and their characteristics are different from ED visits. More than half of the ED cases were an unintentional injury by drug overdose, but more than half of the hospital discharge data cases were a suicide/self-inflicted injury by drug overdose. There were typically much more females than males that result in a hospital admission. In Rhode Island, there were 249 drug overdose deaths in 2014. Drug overdose fatalities were more likely to be young, male, white, and those who reside in suburban regions.

Implications:

Nonfatal and fatal drug overdose data are important for understanding the scope, incidence, and breadth of this public health epidemic and can guide overdose intervention efforts. In Rhode Island, policy makers can use drug overdose data to target high-risk subpopulations to reduce overdose injuries and fatalities. The Rhode Island study can be shared with other states.

Conclusions:

Regardless of the type of drug, overdoses remain a public health crisis in Rhode Island. It is a dynamic epidemic and needs partnership among public health, behavioral health, public safety, clinic, pharmacy, and communities. The ability to track drug overdose in real time will be an essential tool to respond to the constantly evolving drug overdose epidemic in Rhode Island quickly and effectively.
Disparities in Female Breast Cancer Stage at Diagnosis in New Jersey: A Spatial-Temporal Analysis
Authors: Roche Lisa M. , Niu Xiaoling , Stroup Antoinette M. , Henry Kevin A.
Published: December 2016

Background:

Despite improvements in early detection of breast cancer, disparities persist in stage at diagnosis, which is an important prognostic factor.

Methods:

We used the space-time scan statistic in SaTScan to identify geographic areas and time periods with significantly elevated proportions of female breast cancer diagnosed at the in situ or distant stage in New Jersey. The analyses were conducted with census tracts as the geographic unit of analysis, elliptical spatial windows, 3-year temporal windows, and Poisson models. Statistical significance was determined by 999 Monte Carlo simulations (P < .05); significant clusters were mapped in ArcMap. Breast cancer cases within the clusters were compared with breast cancer cases outside the clusters on demographic, socioeconomic, and clinical factors using the Pearson chi-square test (P < .05). In addition, populations within the clusters were compared with the population outside the clusters on demographic and socioeconomic factors.

Results:

After exclusions, 126 756 cases of primary female breast cancer diagnosed in 1997 to 2011 from the New Jersey State Cancer Registry were included in the analysis. One distant stage breast cancer cluster was identified in northeastern New Jersey from 1997 through 2011 (n = 26 244, relative risk [RR] = 1.42, P < .001). Two in situ breast cancer clusters were found in northeastern New Jersey from 2004 through 2011 (n = 12 496, RR = 1.35, P < .001) and in central New Jersey from 2006 through 2011 (n = 29 319, RR = 1.24, P < .001). The distant stage cluster contained relatively high percentages of minority and lower socioeconomic status (SES) breast cancer cases and populations, whereas the in situ clusters had relatively low percentages of minority and lower SES breast cancer cases and populations.

Conclusion:

Although there have been improvements since an earlier study of distant stage breast cancer diagnosed in 1995 to 1997, disparities in stage at diagnosis continue. These findings can be used by our local cancer control partners to target specific populations for interventions such as breast cancer education and mammography screening, as well as by state legislative and public health authorities for resource allocation.
Positive and Negative Affect Is Related to Experiencing Chest Pain During Exercise-Induced Myocardial Ischemia
Authors: Stébenne Philippe , Bacon Simon L. , Austin Anthony , Paine Nicola J. , Arsenault André , Laurin Catherine , Meloche Bernard , Gordon Jennifer , Dupuis Jocelyn , Lavoie Kim L.
Published: December 2016

Objective

Silent myocardial ischemia is thought to be associated with worse cardiovascular outcomes due to a lack of perception of pain cues that initiate treatment seeking. Negative affect (NA) has been associated with increased pain reporting and positive affect (PA) with decreased pain reporting, but these psychological factors have not been examined within the context of myocardial ischemia. This study evaluated the associations between PA, NA, and chest pain reporting in patients with and without ischemia during exercise testing.

Methods

A total of 246 patients referred for myocardial perfusion single-photon emission computed tomography exercise stress testing completed the positive and negative affect schedule-expanded version, a measure of PA and NA. Presence of chest pain and myocardial ischemia were evaluated using standardized protocols.

Results

Logistic regression analyses revealed that for every 1-point increase in NA, there was a 13% higher chance for ischemic patients (odds ratio [OR] = 1.13; 95% confidence interval [CI] = 1.02 to 1.26) and an 11% higher chance in nonischemic patients (OR = 1.11; 95% CI = 1.03 to 1.19) to report chest pain. A significant interaction of PA and NA on chest pain reporting (β = 0.02; 95% CI = 0.002 to 0.031) was also observed; nonischemic patients with high NA and PA reported more chest pain (57%) versus patients with low NA and low PA (13%), with high NA and low PA (17%), and with high PA and low NA (7%).

Conclusions

Patients who experience higher NA are more likely to report experiencing chest pain. In patients without ischemia, high NA and PA was also associated with a higher likelihood of reporting chest pain. Results suggest that high levels of PA as well as NA may increase the experience and/or reporting of chest pain.
Separate Medication Preparation Rooms Reduce Interruptions and Medication Errors in the Hospital Setting: A Prospective Observational Study
Authors: Huckels-Baumgart Saskia , Baumgart André , Buschmann Ute , Schüpfer Guido , Manser Tanja
Published: December 2016

Background

Interruptions and errors during the medication process are common, but published literature shows no evidence supporting whether separate medication rooms are an effective single intervention in reducing interruptions and errors during medication preparation in hospitals. We tested the hypothesis that the rate of interruptions and reported medication errors would decrease as a result of the introduction of separate medication rooms.

Aim

Our aim was to evaluate the effect of separate medication rooms on interruptions during medication preparation and on self-reported medication error rates.

Methods

We performed a preintervention and postintervention study using direct structured observation of nurses during medication preparation and daily structured medication error self-reporting of nurses by questionnaires in 2 wards at a major teaching hospital in Switzerland.

Results

A volunteer sample of 42 nurses was observed preparing 1498 medications for 366 patients over 17 hours preintervention and postintervention on both wards. During 122 days, nurses completed 694 reporting sheets containing 208 medication errors. After the introduction of the separate medication room, the mean interruption rate decreased significantly from 51.8 to 30 interruptions per hour (P < 0.01), and the interruption-free preparation time increased significantly from 1.4 to 2.5 minutes (P < 0.05). Overall, the mean medication error rate per day was also significantly reduced after implementation of the separate medication room from 1.3 to 0.9 errors per day (P < 0.05).

Conclusions

The present study showed the positive effect of a hospital-based intervention; after the introduction of the separate medication room, the interruption and medication error rates decreased significantly.
Left Atrium Maximal Axial Cross-Sectional Area is a Specific Computed Tomographic Imaging Biomarker of World Health Organization Group 2 Pulmonary Hypertension
Authors: Jivraj Khalil , Bedayat Arash , Sung Yon K. , Zamanian Roham T. , Haddad Francois , Leung Ann N.C. , Rosenberg Jarrett , Guo H. Henry
Published: December 2016

Purpose:

Left heart disease is associated with left atrial enlargement and is a common cause of pulmonary hypertension (PH). We investigated the relationship between left atrium maximal axial cross-sectional area (LA-MACSA), as measured on chest computed tomography (CT), and PH due to left heart disease (World Health Organization group 2) in patients with right heart catheterization–proven PH.

Materials and Methods:

A total of 165 patients with PH who had undergone right heart catheterization with pulmonary artery pressure and pulmonary capillary wedge pressure (PCWP) measurements and nongated chest CTs were included. LA-MACSA, LA anterior-posterior, and LA transverse measurements were independently obtained using the hand-drawn region-of-interest and distance measurement tools on standard PACS by 2 blinded cardiothoracic radiologists. Nonparametric statistical analyses and receiver operating characteristic curve were performed.

Results:

Forty-three patients had group 2 PH (PCWP>15 mm Hg), and 122 had nongroup 2 PH (PCWP≤15 mm Hg). Median LA-MACSA was significantly different between the group 2 PH and nongroup 2 PH patients (2312 vs. 1762 mm2, P<0.001). Interobserver concordance correlation for LA-MACSA was high at 0.91 (P<0.001). At a threshold of 2400 mm2, LA-MACSA demonstrated 93% specificity for classifying group 2 PH (area under the curve, 0.73; P<0.001).

Conclusions:

LA-MACSA is a readily obtainable and reproducible measurement of left atrial enlargement on CT and can distinguish between group 2 and nongroup 2 PH with high specificity.
Teamwork Assessment Tools in Obstetric Emergencies
Authors: Onwochei Desire N. , Halpern Stephen , Balki Mrinalini
Published: December 2016

Introduction

Team-based training and simulation can improve patient safety, by improving communication, decision making, and performance of team members. Currently, there is no general consensus on whether or not a specific assessment tool is better adapted to evaluate teamwork in obstetric emergencies. The purpose of this qualitative systematic review was to find the tools available to assess team effectiveness in obstetric emergencies.

Methods

We searched Embase, Medline, PubMed, Web of Science, PsycINFO, CINAHL, and Google Scholar for prospective studies that evaluated nontechnical skills in multidisciplinary teams involving obstetric emergencies. The search included studies from 1944 until January 11, 2016. Data on reliability and validity measures were collected and used for interpretation. A descriptive analysis was performed on the data.

Results

Thirteen studies were included in the final qualitative synthesis. All the studies assessed teams in the context of obstetric simulation scenarios, but only six included anesthetists in the simulations. One study evaluated their teamwork tool using just validity measures, five using just reliability measures, and one used both. The most reliable tools identified were the Clinical Teamwork Scale, the Global Assessment of Obstetric Team Performance, and the Global Rating Scale of performance. However, they were still lacking in terms of quality and validity.

Conclusions

More work needs to be conducted to establish the validity of teamwork tools for nontechnical skills, and the development of an ideal tool is warranted. Further studies are required to assess how outcomes, such as performance and patient safety, are influenced when using these tools.
Improving the support of the suddenly bereaved
Authors: Mayer Dorothy “Dale” M.
Published: December 2016

Purpose of review

It is recognized that death is inevitable but rarely are we prepared for the death of significant persons in our lives. Sudden death is by its nature unexpected and thus shocking for family members and friends of the decedent. Sudden deaths have customarily been divided into four categories based on the cause of death, including natural, accidental, suicidal, or homicidal (NASH) deaths. Supporting the suddenly bereaved can be stressful, for both novice and experienced professionals; this review provides information important to healthcare professionals (HCP) who are often in a position to support family members after a sudden death.

Recent findings

Evidence suggests that supportive actions for those suddenly bereaved include HCPs conveying empathy, answering questions about the cause of death, allowing family members an opportunity to say goodbye, and providing follow-up over time. Bereaved individuals appreciate ongoing connections with healthcare professionals after the death, and HCPs need to recognize that the bereaved are at increased risk of illness in the months after a sudden death.

Supporting those bereaved after a sudden unexpected death is not easy, even for experienced professionals. This review identifies supportive strategies to use with individuals and family members who are suddenly bereaved. The suggestions in this review can be used in emergency departments and other settings involved with death notifications. Also provided is information that HCPs can use to support bereaved family members.
A review of cognitive screening tools in cancer
Authors: Isenberg-Grzeda Elie , Huband Helen , Lam Henry
Published: December 2016

Purpose of review

Cancer-related cognitive impairment (CRCI) is highly prevalent, and assessment of cognition is crucial in providing optimal cancer care. Neuropsychological assessment (NPA) can be lengthy and expensive. Cognitive screening tools are plenty but validity has not been thoroughly studied for use in cancer patients.

Recent findings

Our search of the recent literature revealed that the Montreal Cognitive Assessment, Mini–Mental State Examination, and Clock Draw Test were the most frequently studied objective screening tools. The Functional Assessment of Cancer Therapy-Cognitive Function and the Cognitive Symptom Checklist-Work 21 were the most commonly studied subjective measures of perceived cognitive impairment. Evidence supports using the Montreal Cognitive Assessment or the Clock Draw Test over the Mini–Mental State Examination to screen for cognitive impairment within specific patient populations. In addition, adding a subjective measure of cognitive impairment (e.g., Functional Assessment of Cancer Therapy-Cognitive Function) may increase diagnostic sensitivity.

These suggest that cognitive screening tools may have a role in screening for CRCI, particularly when full NPA is not feasible. Researchers must continue to conduct high-quality studies to build an evidence to guide best practices in screening for CRCI.
Cancer-related cognitive impairment in children
Authors: Hutchinson Amanda D. , Pfeiffer Susan M. , Wilson Carlene
Published: December 2016

Purpose of review

To review recent research on cancer-related cognitive impairment (CRCI) in children, including correlational studies and interventions in which outcomes have included cognitive test performance, neuroimaging or academic performance.

Recent findings

Impairments in processing speed, working memory, executive function and attention continue to be demonstrated in survivors of childhood cancers. Children receiving radiation treatment for their cancer demonstrate greater impairment than those who undergo surgery and/or chemotherapy without radiation. However, CRCI still occurs in the absence of radiation treatment, particularly in the domain of attention. Recent neuroimaging studies highlight atypical connectivity of white matter and its associations with cognitive performance. Given impairments in cognitive function and associated neuroanatomical factors, it is not surprising that survivors of childhood cancers experience academic difficulties. However, early intervention may provide one means of improving cognitive and academic outcomes.

Children with cancer are at risk of impairment in the domains of processing speed, attention, working memory and executive function. Those who receive radiation are likely to experience greater CRCI than those who do not receive this treatment. All survivors of childhood cancers should be carefully monitored to provide support and implement evidence-based interventions to ameliorate cognitive late effects.
A Meta-review of the Safety of Electroconvulsive Therapy in Pregnancy
Authors: Sinha Preeti , Goyal Parth , Andrade Chittaranjan
Published: December 2016

Background

Four systematic reviews have examined the safety of electroconvulsive therapy (ECT) in pregnancy. These have varied widely in methods, findings, and conclusions.

Methods

We compared these reviews with regard to search strategy, study selection criteria, total number of studies identified, total number of patients included, findings related to safety and adverse events, and interpretation of results.

Results

The number of studies (number of cases) included in the reviews ranged from 16 (n = 300) to 67 (n = 169) with only one review stating reasons for exclusion of nonselected studies. We provide comparisons about how the reviews described patient characteristics, illness characteristics, ECT characteristics, confounder characteristics, and outcome characteristics; there was wide variation in these regards. We list adverse outcomes that were identified by some but not other reviews. We provide a detailed breakdown of the adverse maternal and fetal outcomes identified in each review. Finally, we examine how different reviews interpreted their findings; whereas some reviews provided reasons for ruling out ECT as an explanation for an adverse outcome, one review adopted the stance that all adverse outcomes were potentially ECT-related.

Conclusions

Our meta-review provides readers with comparative information on the strengths and limitations of the 4 systematic reviews, their findings, and their conclusions. It can assist with clinical decision making on the use of ECT in pregnancy by providing a more complete description of the available literature.
Electroconvulsive Therapy Considerations for Transgendered Patients
Authors: Tran Billy K. , O’Donnell Stephen E. , Balla Agnes , Adams David C. , Grondin Lydia S. , Tsai Mitchell H.
Published: December 2016

As the transgender patient population continues to grow, health care providers will need to become aware of elements unique to the transgender community in order to provide the highest quality of care. Neuromuscular blockade with succinylcholine is routinely administered to patients undergoing electroconvulsive therapy (ECT). Decreased amounts or activity of pseudocholinesterase in serum can lead to prolonged duration of muscle paralysis. Causes of reduced action by pseudocholinesterase include genetically abnormal enzymes, reduced hepatic production, pregnancy, and various drug interactions. Estrogen supplementation taken by transitioning patients may affect the duration of neuromuscular blockade.

This is a case of a 32-year-old male-to-female transgender patient with prolonged apnea following ECT treatment for severe, refractory depression. Further investigation revealed the patient was on estrogen therapy as a part of her transition and laboratory testing demonstrated reduced serum pseudocholinesterase activity. Further laboratory testing demonstrated reduced serum pseudocholinesterase activity. Succinylcholine dosing was titrated to an appropriate level to avoid prolonged apnea in subsequent ECT treatments. Physicians and other health care providers are faced with a unique population in the transgender community and must be aware of distinctive circumstances when providing care to this group. Of specific interest, many transitioning and transitioned patients can be on chronic estrogen supplementation. Neuromuscular blockade in those patients require attention from the anesthesiology care team as estrogen compounds may decrease pseudocholinesterase levels and lead to prolonged muscle paralysis from succinylcholine.
The Treatment of Disruptive Vocalization in Dementia (Behavioral and Psychological Symptoms of Dementia) With Electroconvulsive Therapy
Authors: Lau Timothy Edwin , Babani Prakash Kishor , McMurray Lisa Anne
Published: December 2016

Objective

There is emerging evidence that electroconvulsive therapy (ECT) can help with the behavioral and psychological symptoms of dementia. One of the most distressing behavioral symptoms of dementia is disruptive vocalization. Previous small case series have suggested that antidepressants and ECT can be beneficial for this distressing condition. The aim of this study was to describe the successful use of ECT in treating 5 patients with disruptive vocalization.

Methods

A retrospective chart review of 5 patients with dementia of mixed etiologies was conducted comparing pretreatment and posttreatment scores on the Cohen-Mansfield Agitation Inventory. All 5 patients had unsuccessful treatments with nonpharmacological methods and pharmacotherapy including antidepressants.

Results

After completion of a series of ECT, the mean verbal agitation score decreased from 6.8 (95% confidence interval, 6.3–7.3) to 2.3 (95% confidence interval, 1.3–3.3), with both clinical and statistical significance (P < 0.001).

Conclusions

Although further research is needed, these findings support considering the use of ECT for disruptive vocalization in dementia.
ECT-Related Anxiety
Authors: Obbels Jasmien , Verwijk Esmée , Bouckaert Filip , Sienaert Pascal
Published: December 2016

Background

A significant proportion of electroconvulsive therapy (ECT)–treated patients experience anxiety anticipating the treatment, often to such an extent that they refuse or discontinue a much-needed treatment. Despite its great impact on treatment adherence, anxiety in patients receiving ECT is underexposed in the scientific literature.

Objectives

We aimed to review the prevalence and specific subjects of ECT-related anxiety and therapeutic interventions to reduce it.

Methods

We performed a computerized search (EMBASE, MEDLINE, and PsycINFO) for articles meeting the following inclusion criteria: (1) qualitative (interview) studies, quantitative (questionnaire) studies, or experimental (interventional) studies that (2) report on anxiety that is related to a planned, ongoing, or past ECT treatment.

Results

Of 1160 search results, 31 articles were included. Electroconvulsive therapy–related anxiety is estimated to be present in 14% to 75% of patients and is most often linked to worries about memory impairment or brain damage. Only a few interventions (chlorpromazine, meprobamate, propofol, a talking-through technique, an information leaflet, and animal-assisted therapy) have been proposed to reduce patients’ ECT-related anxiety.

Conclusions

Electroconvulsive therapy–related anxiety is a highly prevalent phenomenon, and the literature provides little guidance for its clinical management. Most studies are of a low methodological quality and suffer from significant limitations, thereby hampering generalized conclusions. Given the clinical importance of ECT-related anxiety, further study on its nature and evolution through the course of treatment and on anxiety-reducing interventions is warranted.
diffloop: a computational framework for identifying and analyzing differential DNA loops from sequencing data
Authors: Lareau Caleb A. , Aryee Martin J.
Published: December 2016

The three-dimensional architecture of DNA within the nucleus is a key determinant of interactions between genes, regulatory elements, and transcriptional machinery. As a result, differences in loop structure are associated with differences in gene expression and cell state. Here, we introducediffloop, an R/Bioconductor package for identifying differential DNA looping between samples. The package additionally provides a suite of functions for the quality control, statistical testing, annotation and visualization of DNA loops. We demonstrate this functionality by detecting differences in DNA loops between ENCODE ChIA-PET datasets and relate looping to differences in epigenetic state and gene expression.
RealTime Heart Rate Monitoring Using Photoplethysmographic (PPG) Signals During Intensive Physical Exercises
Authors: Farhadi Majid , Boloursaz Mashhadi Mahdi , Essalat Mahmoud , Marvasti Farokh
Published: December 2016

Heart Rate (HR) is a fundamental vital sign, monitoring which provides essential information for automated healthcare systems. The emerging technology of Photoplethysmograph (PPG) is shown as a feasible candidate for such applications; however, Motion Artifacts (MA) hinder efficient HR estimation using PPG, especially in situations involving physical activities. It is previously shown that even in the presence of sever MA, HR is still traceable with the help of simultaneous acceleration data although at high computational expenses. In this paper, we propose a novel framework, that not only improves the accuracy in HR estimation, but also achieves realtime performance by significantly reducing the complexity of system; mainly due to alleviation of the need for computationally demanding MA cancellation methods. Utilizing an spectrum estimation model (autoregressive) that suits well to the inherent PPG generation process, and benefiting from further intrinsic properties of the environment (e.g., the venous pulsation phenomenon); our framework achieves realtime and delayed (post-processed) Average Absolute Errors (AAE) of 1.19 and 0.99 Beats Per Minute (BPM) respectively, on the 12 benchmark recordings in which subjects run at speeds of up to 15km/hmaximum. Moreover, the system makes standalone implementation feasible by processing input frames (2 channel PPG and 3D ACC) in < 0.004 times of the frame duration, operating on a 3.2 GHz processor. This study provides wearable healthcare technologies with a robust framework for accurate HR monitoring; at considerably low computational costs.
Improving Gene Regulatory Network Inference by Incorporating Rates of Transcriptional Changes
Authors: Desai Jigar S. , Sartor Ryan C. , Lawas Lovely Mae , Jagadish SV Krishna , Doherty Colleen J.
Published: December 2016

Organisms respond to changes in their environment through transcriptional regulatory networks (TRNs). The regulatory hierarchy of these networks can be inferred from expression data. Computational approaches to identify TRNs can be applied in any species where quality RNA can be acquired, However, ChIP-Seq and similar validation methods are challenging to employ in non-model species. Improving the accuracy of computational inference methods can significantly reduce the cost and time of subsequent validation experiments. We have developed ExRANGES, an approach that improves the ability to computationally infer TRN from time series expression data. ExRANGES utilizes both the rate of change in expression and the absolute expression level to identify TRN connections. We evaluated ExRANGES in five data sets from different model systems. ExRANGES improved the identification of experimentally validated transcription factor targets for all species tested, even in unevenly spaced and sparse data sets. This improved ability to predict known regulator-target relationships enhances the utility of network inference approaches in non-model species where experimental validation is challenging. We integrated ExRANGES with two different network construction approaches and it has been implemented as an R package available here:http://github.com/DohertyLab/ExRANGES.To install the package type:devtools::install_github(“DohertyLab/ExRANGES”)
Dorsal hippocampus contributes to model-based planning
Authors: Miller Kevin J. , Botvinick Matthew M. , Brody Carlos D.
Published: December 2016

Planning can be defined as a process of action selection that leverages an internal model of the environment. Such models provide information about the likely outcomes that will follow each selected action, and their use is a key function underlying complex adaptive behavior. However, the neural mechanisms supporting this ability remain poorly understood. In the present work, we adapt for rodents recent advances from work on human planning, presenting for the first time a task for animals which produces many trials of planned behavior per session, allowing the experimental toolkit available for use in trial-by-trial tasks for rodents to be applied to the study of planning. We take advantage of one part of this toolkit to address a perennially controversial issue in planning research: the role of the dorsal hippocampus. Although prospective representations in the hippocampus have been proposed to support model-based planning, intact planning in hippocampally damaged animals has been observed in a number of assays. Combining formal algorithmic behavioral analysis with muscimol inactivation, we provide the first causal evidence directly linking dorsal hippocampus with planning behavior. The results reported, and the methods introduced, open the door to new and more detailed investigations of the neural mechanisms of planning, in the hippocampus and throughout the brain.
rAmpSeq: Using repetitive sequences for robust genotyping
Authors: Buckler Edward S. , Ilut Daniel C. , Wang Xiaoyun , Kretzschmar Tobias , Gore Michael , Mitchell Sharon E.
Published: December 2016

Repetitive sequences have been used for DNA fingerprinting and genotyping for more than a quarter century. Now, with our knowledge of whole genome sequences, repetitive sequences can be used to identify polymorphisms that can be mapped and scored in a systematic manner. We have developed a simple, robust platform for designing primers, PCR amplification, and high throughput cloning that allows hundreds to thousands of markers to be scored for less than $5 per sample. Conserved regions were used to design PCR primers for amplifying thousands of middle repetitive regions of the maize (Zea maysssp.mays) genome. Bioinformatic scans were then used to identify DNA sequence polymorphisms in the low copy intervening sequences. When used in conjunction with simple DNA preps, optimized PCR conditions, high multiplex Illumina indexing and a bioinformatic marker calling platform tailored for repetitive sequences, this methodology provides a cost effective genotyping strategy for large-scale genomic selection projects. We show detailed results from four maize primer sets that produced between 1,335-3,225 good coverage loci with 1056 that segregated appropriately in a bi-parental family. This approach could have wide applicability to breeding and conservation biology, where hundreds of thousands of samples need to be genotyped for very minimal cost.
Inferring weighted gene annotations from expression data
Authors: Cary Michael , Kenyon Cynthia
Published: December 2016

Annotating genes with information describing their role in the cell is a fundamental goal in biology, and essential for interpreting data-rich assays such as microarray analysis and RNA-Seq. Gene annotation takes many forms, from Gene Ontology (GO) terms, to tissues or cell types of significant expression, to putative regulatory factors and DNA sequences. Almost invariably in gene databases, annotations are connected to genes by a Boolean relationship, e.g., a GO term eitherisorisn’tassociated with a particular gene. While useful for many purposes, Boolean-type annotations fail to capture the varying degrees by which some annotations describe their associated genes and give no indication of the relevance of annotations to cellular logistical activities such as gene expression. We hypothesized that weighted annotations could prove useful for understanding gene function and for interpreting gene expression data, and developed a method to generate these from Boolean annotations and a large compendium of gene expression data. The method uses an independent component analysis-based approach to find gene modules in the compendium, and then assigns gene-specific weights to annotations proportional to the degree to which they are shared among members of the module, with the reasoning that the more an annotation is shared by genes in a module, the more likely it is to be relevant to their function and, therefore, the higher it should be weighted. In this paper, we show that analysis of expression data with module-weighted annotations appears to be more resistant to the confounding effect of gene-gene correlations than non-weighted annotation enrichment analysis, and show several examples in which module-weighted annotations provide biological insights not revealed by Boolean annotations. We also show that application of the method to a simple form of genetic regulatory annotation, namely, the presence or absence of putative regulatory words (oligonucleotides) in gene promoters, leads to module-weighted words that closely match known regulatory sequences, and that these can be used to quickly determine key regulatory sequences in differential expression data.
An image processing method for metagenomic binning: multi-resolution genomic binary patterns
Authors: Kouchaki Samaneh , Tapinos Avraam , Robertson David L
Published: December 2016

Bioinformatics methods typically use textual representations of genetic information, represented computationally as strings or sub-strings of the characters A, T, G and C. Image processing methods offer a rich source of alternative descriptors as they are designed to work in the presence of noisy data without the need for exact matching. We introduce a method, multi-resolution local binary patterns (MLBP) from image processing to extract local ‘texture’ changes from nucleotide sequence data. We apply this feature space to the alignment-free binning of metagenomic data. The effectiveness of MLBP is demonstrated using both simulated and real human gut microbial communities. The intuition behind our method is the MLBP feature vectors permit sequence comparisons without the need for explicit pairwise matching. Sequence reads or contigs can then be represented as vectors and their ‘texture’ compared efficiently using state-of-the-art machine learning algorithms to perform dimensionality reduction to capture eigengenome information and perform clustering (here using RSVD and BH-tSNE). We demonstrate this approach outperforms existing methods based onk-mer frequency. The image processing method, MLBP, thus offers a viable alternative feature space to textual representations of sequence data. The source code for our Multi-resolution Genomic Binary Patterns method can be found athttps://github.com/skouchaki/MrGBP.
K-mer Motif Multinomial Mixtures, a scalable framework for multiple motif discovery
Authors: Trippe Brian L. , Prabhakaran Sandhya , Bussemaker Harmen J.
Published: December 2016

1

Motivation

The advent of inexpensive high-throughput sequencing (HTS) places new demands on motif discovery algorithms. To confront the challenges and embrace the opportunities presented by the growing wealth of information tied up in HTS datasets, we developed K-mer motif multinomial mixtures (KMMMs), a flexible class of Bayesian models for identifying multiple motifs in sequence sets using K-mer tables. Advantages of this framework are inference with time and space complexities that only scale with K, and the ability to be incorporated into larger Bayesian models.

Results

We derived a class of probabilistic models of K-mer tables generated from sequence containing multiple motifs. KMMMs model the K-mer table as a multinomial mixture, with motif and background components, which are distributions over K-mers overlapping with each of the latent motifs and over K-mers that do not overlap with any motif, respectively. The framework casts motif discovery as a posterior inference problem, and we present several approximate inference methods that provide accurate reconstructions of motifs in synthetic data. Finally we apply the method to discover motifs in DNAse hypersensitive sites and ChIP-seq peaks obtained from the ENCODE project.
Short‐term effect of scalpel debridement of plantar callosities versus treatment with salicylic acid patches: The EMEDESCA randomized controlled trial
Authors: Gijón‐Noguerón Gabriel , García‐Paya Irene , Morales‐Asencio José Miguel , Jiménez‐Cebrián Ana , Ortega‐Ávila Ana Belén , Cervera‐Marín José Antonio
Published: December 2016

This study compares scalpel debridement versus salicylic acid patches in the treatment of plantar callosities. A randomized clinical trial (ACTRN12614000591651) was performed with 62 patients, divided into two intervention groups. Group A received treatment with salicylic acid patches (Callívoro Marthand®) and group B underwent scalpel debridement of plantar callosities. Pain was measured on a visual analog scale, and foot pain and disability were evaluated using the Manchester Foot Pain Disability Index (MFPDI) questionnaire (Spanish version). Significant differences were observed in pain measured immediately after treatment (P < 0.001) and at 15 days and 6 weeks after treatment. For some components, the MFPDI questionnaire revealed significantly better outcomes by scalpel debridement at 15 days after treatment. The scalpel debridement of plantar callosities relieves pain more effectively than salicylic acid patches, and patients achieve greater functionality in the initial weeks after debridement.
Incidence of serum antibody titers against varicella zoster virus in Japanese patients with herpes zoster
Authors: Miyachi Motoko , Ihara Honoka , Imafuku Shinichi
Published: December 2016

Herpes zoster is an internal reactivation of varicella zoster virus following establishment of latent infection in the dorsal root ganglia during primary infection, which presents as chickenpox. Therefore, serologically, herpes zoster patients already have anti‐varicella zoster virus immunoglobulin G at the onset of disease. Hence, positive serum antibody does not confirm the diagnosis of herpes zoster. We retrospectively investigated the incidence of varicella zoster virus‐specific complement fixation in 865 zoster patients at initial presentation to a dermatology clinic. As a result, 66% of patients showed negative complement fixation, with patient numbers decreasing as titer increased. Paired complement fixation tests conducted within a short period showed a marked elevation in titer, and complement fixation titer gradually decreased after a year. Furthermore, incidence showed no correlation with patient age. These observations indicate that the complement fixation titer at first visit is mainly influenced by the duration from onset to presentation at clinic. Our findings indicate that a positive complement fixation result by single‐point testing confirms at least recent onset of herpes zoster, while paired tests can confirm disease when primary tests are negative.
Tree species functional group is a more important driver of soil properties than tree species diversity across major European forest types
Authors: Dawud Seid Muhie , Raulund‐Rasmussen Karsten , Ratcliffe Sophia , Domisch Timo , Finér Leena , Joly François‐Xavier , Hättenschwiler Stephan , Vesterdal Lars
Published: December 2016

The influence of tree species diversity and functional group on soil properties (carbon stock, pH and C/N ratio) has not been explored across major European forest types.

We evaluated the relative importance of tree species diversity and functional group for soil carbon (C) stocks, C/N ratio and pH in major European forest types in the six regions Finland, Poland, Germany, Romania, Italy and Spain. We sampled soils in 209 permanent plots along a species diversity gradient from monocultures to five‐species mixtures.

Carbon stocks in the topsoil (forest floor (FF), 0–10 cm and FF + 0–10 cm) were positively, but weakly, related to diversity across the regions. While the C/N ratio in the FF + 0–10 cm layer decreased significantly with increasing diversity in the Spanish region, pH was unrelated to species diversity across the regions. Tree species functional group (in terms of conifer proportion, CP) explained a larger proportion of the variability in soil properties than diversity. Conifer admixture increased C stock and C/N ratio, and decreased pH, but the impacts differed between the regions in some layers. Differences in mean annual temperature, actual evapotranspiration and soil texture between the regions were possible driving factors behind the different CP effects in Finland, Spain and Germany.

The results imply that targeted selection of tree species with desired characteristics, e.g. complementary traits for resource use, is a preferred management approach for influencing soil C stock, C/N ratio and pH in mixed forests rather than increasing tree species diversity per se.

A lay summary is available for this article.
Does water shortage generate water stress? An ecohydrological approach across Mediterranean plant communities
Authors: Barkaoui Karim , Navas Marie‐Laure , Roumet Catherine , Cruz Pablo , Volaire Florence
Published: December 2016

The interactions between hydrological and ecological processes are key issues to improve our predictions of ecosystem responses to increasing droughts. However, predicting the dynamics and the impacts of vegetation water stress remains challenging because of complex ecohydrological feedbacks. The ecohydrological optimality approach proposes that functional adjustments within plant communities may buffer the increase in vegetation water stress despite local water shortage.

This study aimed to test whether vegetation water stress may be invariant across contrasting plant communities, reflecting possible optimality processes. We addressed the following question: does a lower soil water storage capacity under the same climate generate greater vegetation water stress over time? We hypothesized that vegetation water stress would be buffered around a low and constant level through the adjustment of vegetation biomass productivity net primary productivity (NPP), evapotranspiration (ET) and/or water‐use efficiency (WUE) in relation with local soil water storage capacity.

We monitored 12 native plant communities distributed along a gradient of soil water storage capacity (ranging from 20 mm to 120 mm) during five successive years. Net primary productivity, ET, WUE as well as soil water dynamics were assessed and modelled for each plant community throughout the 5 years of study. Vegetation water stress was determined for each plant community as the deviation of between actual ET and their maximum ETm rate achieved under non‐limiting conditions.

We found that NPP and ET were together proportionally related to local soil water storage capacity across the 5 years of study while WUE did not differ between plant communities. Vegetation water stress was found quite similar for all plant communities whatever the soil water storage capacity. These results suggested that vegetation water stress was strongly buffered by the community‐level plant growth rates and total water use along the soil gradient, but not by WUE.

Our results suggest that stressful environments rarely exist for plant communities. A dynamic scaling relationship between NPP and ET may underpin the control of vegetation water stress over seasonal and pluriannual time‐scales. Such results could contribute to better understanding processes associated with ecohydrological optimality and improve the predictions of vegetation dynamics under increasing droughts.

A lay summary is available for this article.
Resource selection and landscape change reveal mechanisms suppressing population recovery for the world's most endangered antelope
Authors: Ali Abdullahi H. , Ford Adam T. , Evans Jeffrey S. , Mallon David P. , Hayes Matthew M. , King Juliet , Amin Rajan , Goheen Jacob R.
Published: December 2016

Understanding how bottom‐up and top‐down forces affect resource selection can inform restoration efforts. With a global population size of <500 individuals, the hirola Beatragus hunteri is the world's most endangered antelope, with a declining population since the 1970s. While the underlying mechanisms are unclear, some combination of habitat loss and predation are thought to be responsible for low abundances of contemporary populations.

Efforts to conserve hirola are hindered by a lack of understanding as to why population density remains low, despite eradication of the viral disease, rinderpest. To elucidate factors underlying chronically low numbers, we examined resource selection and landscape change within the hirola's native range. Because hirola are grazers, we hypothesized that the availability of open areas would be linked both to forage and safety from predators. We quantified: (i) changes in tree cover across the hirola's historical range in eastern Kenya over the past 27 years; (ii) how tree cover has influenced resource selection by hirola; and (iii) interactions between tree cover and predation.

Between 1985 and 2012, tree cover increased by 251% across the historical range of hirola. Tree encroachment was associated with a 98% decline of hirola and elephant Loxodonta africana populations, a 74% decline in cattle Bos indicus, an increase in browsing livestock by 327%, and a reduction in rainfall.

Although hirola avoided tree cover, we found no evidence that predation on hirola increased with increasing tree cover.

Synthesis and applications. Hirola may qualify as a refugee species, in which contemporary populations are restricted to suboptimal habitat and exhibit low survival, reproduction or both. The extinction of hirola would be the first of a mammalian genus on the African continent in modern history. We conclude that contemporary low numbers of hirola are due at least partly to habitat loss via tree encroachment, triggered by some combination of elephant extirpation, overgrazing, drought and perhaps fire suppression. We recommend a combination of rangeland restoration efforts (including conservation of elephants, manual clearing of trees, and grass seeding), increased enforcement of an existing protected area (Arawale National Reserve), and reintroductions to enhance recovery for this endangered species. These efforts will rely on enhanced support from the international conservation community and the cooperation of pastoralist communities with which the hirola coexist.