bluuebunny/crossref_metadata_2025_split huggingface dataset:
EBSeq-HMM: a Bayesian approach for identifying gene-expression changes in ordered RNA-seq experiments
Authors: Leng Ning , Li Yuan , McIntosh Brian E. , Nguyen Bao Kim , Duffin Bret , Tian Shulan , Thomson James A. , Dewey Colin N. , Stewart Ron , Kendziorski Christina 
Published: April 2015

AbstractMotivation: With improvements in next-generation sequencing technologies and reductions in price, ordered RNA-seq experiments are becoming common. Of primary interest in these experiments is identifying genes that are changing over time or space, for example, and then characterizing the specific expression changes. A number of robust statistical methods are available to identify genes showing differential expression among multiple conditions, but most assume conditions are exchangeable and thereby sacrifice power and precision when applied to ordered data.Results: We propose an empirical Bayes mixture modeling approach called EBSeq-HMM. In EBSeq-HMM, an auto-regressive hidden Markov model is implemented to accommodate dependence in gene expression across ordered conditions. As demonstrated in simulation and case studies, the output proves useful in identifying differentially expressed genes and in specifying gene-specific expression paths. EBSeq-HMM may also be used for inference regarding isoform expression.Availability and implementation: An R package containing examples and sample datasets is available at Bioconductor.Contact: kendzior@biostat.wisc.eduSupplementary information: Supplementary data are available at Bioinformatics online.
Sleep Disruption
Authors: Brody David L 
Published: April 2015

You have to get this right; everything else hinges on it. The patient will get worse over time, not better, if they accumulate more and more sleep deficit from chronic insomnia. The hierarchy for sleep is as follows: Best is good quality natural sleep, second best is pharmacologically enhanced good quality sleep, worst is insufficient or poor quality sleep. The tools: sleep hygiene; pain control; psychological counseling and training, for example, cognitive behavioral therapy for insomnia; and sleep medications such as zolpidem (Ambien), Eszopiclone (Lunesta) Melatonin, and trazodone, which are helpful and relatively safe in concussion patients. Avoid whenever possible medications that can impair recovery and cognitive function, such as benzodiazepines, anticholinergics, antipsychotics, and alcohol as a sleep aide. If there are concerns, refer to a sleep medicine clinic for consultation and a formal sleep study; patients may not be reliable historians with regard to their own sleep habits.
Anxiety and Depression
Authors: Brody David L 
Published: April 2015

First, assess safety. Severe anxiety and depression can lead to suicide. Second, distinguish between reactive anxiety and depressive symptoms versus an impairing mood disorder. The “treatment” for reactive anxiety and depressive symptoms is education, reassurance, and a good plan to get the patient’s life back on track. If the patient has an impairing (but not immediately dangerous) mood disorder, it can be treated for the most part just like a mood disorder in the absence of concussion. The optimal approach usually involves both nonpharmacological and pharmacological interventions: exercise, treat sleep disturbances, psychological counseling, avoid substances that worsen mood overall such as alcohol and street drugs, consider appropriate long-term antidepressant/antianxiety medications. There are many options, but fluoxetine (Prozac) and venlafaxine (Effexor) may be good choices for patients where low energy is more concerning than anxiety, whereas paroxetine (Paxil) or sertraline (Zoloft) may be preferred when anxiety is a major component.
Memory Impairment
Authors: Brody David L 
Published: April 2015

Many complaints of memory problems after concussion actually turn out to be attention deficit. Take a careful collateral history regarding memory function in everyday life. Consider both bedside testing and formal neuropsychological testing of memory, but treat the patient, not the test results. Reduce barriers to optimal memory function: Optimize sleep; treat chronic pain; taper or stop cognitively impairing medications; stop alcohol and illicit drugs; prescribe moderate cardiovascular exercise; test for vitamin B12 deficiency, hypothyroidism, electrolyte disorders, hypo- or hypergylcemia, renal failure, liver failure, and anemia. Refer to speech therapy and occupational therapy for memory training. Stimulants can allow more intense cognitive rehabilitation when attention or fatigue are limiting. Consider pharmacological enhancers of memory including caffeine, donepezil, or rivastigmine. These have modest benefits, and the nonpharmacological interventions are more important.
Executive Dysfunction
Authors: Brody David L 
Published: April 2015

Problems with organization, planning, strategy decisions, mental flexibility, optimizing risk/reward relationships, prioritizing, and goal setting are often called executive dysfunction. Collateral history and neuropsychological testing will help sort out the nature of the impairment, but treat the patient, not the test results. Reduce barriers to optimal cognitive function: Optimize sleep; treat chronic pain; taper or stop cognitively impairing medications; stop alcohol and illicit drugs; prescribe moderate cardiovascular exercise; refer to speech therapy and occupational therapy for executive function training. There are no specific pharmacological treatments for executive function. Consider trials of caffeine, stimulants, donepezil or rivastigmine, modafinil, or dopaminergic agents.
Seizures
Authors: Brody David L 
Published: April 2015

Concussion rarely causes recurrent seizures. A patient with a brief seizure that occurs within the first 30 minutes of concussion does not need to be treated with antiepileptics or have driving restrictions. However, a seizure occurring later than 30 minutes after the injury, a seizure that lasts more than one minute, or a seizure after concussion in a patient with a previous seizure disorder requires a different approach. Consider hospital observation, brain MRI, EEG, laboratory studies, assessment for infection, and a screen for drug and alchohol use or withdrawal. If seizures need to be treated, often the best approach includes mood stabilizing medications with minimal cognitively impairing side effects. An oxcarbazepine (Trileptal) bridge during lamotrigine (Lamictal) titration is a reasonable choice. Carbamazepine generic is a good option when cost is an issue.
Return to Contact Sports
Authors: Brody David L 
Published: April 2015

Published guidelines on return to play apply to simple concussions: (1) No return to play in the same 24-hour period as the concussion. (2) Graded, stepwise increases in activity guided by symptoms over 6–10 days. (3) No difference in return to play for elite versus nonelite athletes. (4) Brief convulsions or posturing at the time of concussion does not indicate higher than normal risk of seizures and requires no specific management. For more complex concussions, discourage the patient from returning to contact sports until all of the following are true: The symptoms are all in the mild range or resolved, the collateral source verifies that the patient’s behavior is back to normal, the patient has been able to successfully return to school or work, balance is back to normal, and the patient passes a physical therapist-directed moderate exercise test.
Special Topics in Adolescents
Authors: Brody David L 
Published: April 2015

Adolescents may be less able to make good judgments about their own abilities than adults. The collateral source becomes even more important than usual. Address questions about drug and alchohol use privately and give advice without the parents present. Peer influences may have a big impact on decision-making. Obtain collateral history from peers and educate peers as well as parents. Preexisting attention deficit, learning disabilities, and mood instability can get substantially worse after concussion and may require intensified treatment. For patients at the cusp of starting to drive, consider advising extra caution: go back to the beginning of driver’s education and get a professional driving evaluation. Consider preemptively addressing questions that the adolescent may be afraid to ask or cannot formulate accurately.
Factors contributing to elder abuse in Ethiopia
Authors: Chane Samson , Adamek Margaret E. 
Published: April 2015

Purpose
– The purpose of this paper is to increase understanding of elder abuse in Ethiopia by considering the perspectives of abused elders.

Design/methodology/approach
– A phenomenological study was conducted to investigate the lived experience of 15 elders (six men, nine women) in Ethiopia who experienced domestic abuse. Data were collected using unstructured interviews and were analyzed using interpretive phenomenological analysis. The results described here focus on Ethiopian elders’ perceptions of factors contributing to abuse.

Findings
– Themes identified in elders’ statements about the factors contributing to elder abuse included: declining respect for elders, conflicts of interest, poor health, mutual dependency and other economic issues, and loss of support providers. Abject poverty was evident as an underlying influence contributing to abuse. One elder stated, “Life is meaningless without food and without a caregiver. I am ready to welcome death.”

Research limitations/implications
– Documentation of elder abuse is needed to bring recognition to abuse as a problem deserving public attention and response.

Practical implications
– Given the apparent influence of poverty-related factors on the occurrence of elder abuse among the study's participants, policy initiatives are needed to enhance the economic well-being of older adults in Ethiopia.

Originality/value
– Since elder abuse is generally not viewed as a societal problem in Ethiopia, there have been very few studies documenting its existence. Research on elder abuse in Ethiopia and other developing nations can help to bring the issue to the attention of communities and authorities.
Rocket launcher: A novel reduction technique for posterior hip dislocations and review of current literature
Authors: Dan Michael , Phillips Alfred , Simonian Marcus , Flannagan Scott 
Published: April 2015

AbstractObjectiveWe provide a review of literature on reduction techniques for posterior hip dislocations and present our experience with a novel technique for the reduction of acute posterior hip dislocations in the ED, ‘the rocket launcher’ technique.MethodsWe present our results with six patients with prosthetic posterior hip dislocation treated in our rural ED. We recorded patient demographics. The technique involves placing the patient's knee over the shoulder, and holding the lower leg like a ‘Rocket Launcher’ allow the physician's shoulder to work as a fulcrum, in an ergonomically friendly manner for the reducer. We used Fisher's t‐test for cohort analysis between reduction techniques.ResultsOf our patients, the mean age was 74 years (range 66 to 85 years). We had a 83% success rate. The one patient who the ‘rocket launcher’ failed in, was a hemi‐arthroplasty patient who also failed all other closed techniques and needed open reduction. When compared with Allis (62% success rate), Whistler (60% success rate) and Captain Morgan (92% success rate) techniques, there was no statistically significant difference in the successfulness of the reduction techniques. There were no neurovascular or periprosthetic complications.ConclusionWe have described a reduction technique for posterior hip dislocations. Placing the patient's knee over the shoulder, and holding the lower leg like a ‘Rocket Launcher’ allow the physician's shoulder to work as a fulcrum, thus mechanically and ergonomically superior to standard techniques.
Identification of the Mamestra configurata (Lepidoptera: Noctuidae) peritrophic matrix proteins and enzymes involved in peritrophic matrix chitin metabolism
Authors: Toprak Umut , Erlandson Martin , Baldwin Doug , Karcz Steve , Wan Lianglu , Coutu Cathy , Gillott Cedric , Hegedus Dwayne D. 
Published: April 2015

AbstractThe peritrophic matrix (PM) is essential for insect digestive system physiology as it protects the midgut epithelium from damage by food particles, pathogens, and toxins. The PM is also an attractive target for development of new pest control strategies due to its per os accessibility. To understand how the PM performs these functions, the molecular architecture of the PM was examined using genomic and proteomic approaches in Mamestra configurata (Lepidoptera: Noctuidae), a major pest of cruciferous oilseed crops in North America. Liquid chromatography‐tandem mass spectrometry analyses of the PM identified 82 proteins classified as: (i) peritrophins, including a new class with a CBDIII domain; (ii) enzymes involved in chitin modification (chitin deacetylases), digestion (serine proteases, aminopeptidases, carboxypeptidases, lipases and α‐amylase) or other reactions (β‐1,3‐glucanase, alkaline phosphatase, dsRNase, astacin, pantetheinase); (iii) a heterogenous group consisting of polycalin, REPATs, serpin, C‐Type lectin and Lsti99/Lsti201 and 3 novel proteins without known orthologs. The genes encoding PM proteins were expressed predominantly in the midgut. cDNAs encoding chitin synthase‐2 (McCHS‐2), chitinase (McCHI), and β‐N‐acetylglucosaminidase (McNAG) enzymes, involved in PM chitin metabolism, were also identified. McCHS‐2 expression was specific to the midgut indicating that it is responsible for chitin synthesis in the PM, the only chitinous material in the midgut. In contrast, the genes encoding the chitinolytic enzymes were expressed in multiple tissues. McCHS‐2, McCHI, and McNAG were expressed in the midgut of feeding larvae, and NAG activity was present in the PM. This information was used to generate an updated model of the lepidopteran PM architecture.
A Survey of Nitrate and Nitrite Concentrations in Conventional and Organic‐Labeled Raw Vegetables at Retail
Authors: Nuñez de González Maryuri T. , Osburn Wesley N. , Hardin Margaret D. , Longnecker Michael , Garg Harsha K. , Bryan Nathan S. , Keeton Jimmy T. 
Published: April 2015

AbstractA national survey of the nitrate () and nitrite ( ) concentrations in raw and highly consumed vegetables available at retail in the United States was conducted. A total of 194 samples of fresh broccoli, cabbage, celery, lettuce, and spinach categorized as conventional or organic by label were collected from 5 major cities in different geographic regions of the United States and analyzed to determine and concentrations. There were no differences in the mean values of conventional compared with organic vegetables taken from the 5 metropolitan areas. However, significant differences in mean pairwise comparisons between some conventional and organic vegetables for content were observed. The mean concentration of both conventional and organic vegetables ranged between 0.1 and 1.2 mg/kg of fresh weight (FW) with the exception of conventional spinach that contained 8.0 mg/kg FW. Mean contents of conventional broccoli, cabbage, celery, lettuce, and spinach were 394, 418, 1496, 851, and 2797 mg/kg FW, respectively, while their organic‐labeled counterparts averaged 204, 552, 912, 844, and 1318 mg/kg FW. In most cases, organic vegetables were numerically lower in content than their conventional counterparts. Based on survey results, the finding that low levels were observed in some organic vegetables in different cities may warrant further study to determine if true differences exist, due to production practices, seasonal differences, and the magnitudes of those differences. Furthermore, the geographic differences in content of vegetables may flaw estimates of daily and exposure.
Gender differences in the association between lifestyle behaviors and diabetes distress in a community sample of adults with type 2 diabetes
Authors: Lipscombe Carla , Smith Kimberley J. , Gariepy Geneviève , Schmitz Norbert 
Published: April 2015

AbstractBackgroundThe present study examined the association between moderate and severe diabetes distress (DD) and lifestyle behaviors (physical activity, smoking, alcohol consumption) in a community sample of adults with type 2 diabetes mellitus (T2DM).MethodsA total of 1971 adults with T2DM were recruited using mixed methods sampling. Participants were considered eligible if they had a doctor diagnosis of T2DM (≤10 years), were insulin naïve, aged 40–75 years, and were from Quebec, Canada. Participants provided information on DD, lifestyle behaviors, sociodemographic, and diabetes‐related factors. Multinomial logistic regressions examined the association between moderate and severe DD and each lifestyle behavior, according to gender. Effect estimates can be interpreted as probability ratios (PR).ResultsIn females, physical inactivity was associated with an increased likelihood of moderate distress (PR 2.2; 95% confidence interval [CI] 1.49–3.24) and severe distress (PR 1.80; 95% CI 1.00–3.24). In males, only severe distress was associated with physical inactivity (PR 1.92; 95% CI 1.00–3.66). Current smoking was associated with a greater probability of severe distress in males (PR 3.0; 95% CI 1.54–5.84) and females (PR 1.32; 95% CI 0.67–2.60); however this effect was stronger in males. No association was found between alcohol consumption and DD in females. In males, frequent alcohol consumption was associated with a reduced probability of moderate (PR 0.56; 95% CI 0.34–0.91) and severe distress (PR 0.47; 95% CI 0.21–1.06).ConclusionsThe findings of this study suggest important gender differences in the association between DD and lifestyle behaviors.
Development and validation of panoptic Meso scale discovery assay to quantify total systemic interleukin‐6
Authors: Chaturvedi Shalini , Siegel Derick , Wagner Carrie L. , Park Jaehong , van de Velde Helgi , Vermeulen Jessica , Fung Man‐Cheong , Reddy Manjula , Hall Brett , Sasser Kate 
Published: April 2015

AimInterleukin‐6 (IL‐6), a multifunctional cytokine, exists in several forms ranging from a low molecular weight (MW 20–30 kDa) non‐complexed form to high MW (200–450 kDa), complexes. Accurate baseline IL‐6 assessment is pivotal to understand clinical responses to IL‐6‐targeted treatments. Existing assays measure only the low MW, non‐complexed IL‐6 form. The present work aimed to develop a validated assay to measure accurately total IL‐6 (complexed and non‐complexed) in serum or plasma as matrix in a high throughput and easily standardized format for clinical testing.MethodsCommercial capture and detection antibodies were screened against humanized IL‐6 and evaluated in an enzyme‐linked immunosorbent assay format. The best antibody combinations were screened to identify an antibody pair that gave minimum background and maximum recovery of IL‐6 in the presence of 100% serum matrix. A plate‐based total IL‐6 assay was developed and transferred to the Meso Scale Discovery (MSD) platform for large scale clinical testing.ResultsThe top‐performing antibody pair from 36 capture and four detection candidates was validated on the MSD platform. The lower limit of quantification in human serum samples (n = 6) was 9.77 pg l–1, recovery ranged from 93.13–113.27%, the overall pooled coefficients of variation were 20.12% (inter‐assay) and 8.67% (intra‐assay). High MW forms of IL‐6, in size fractionated serum samples from myelodysplastic syndrome and rheumatoid arthritis patients, were detected by the assay but not by a commercial kit.ConclusionThis novel panoptic (sees all forms) IL‐6 MSD assay that measures both high and low MW forms may have clinical utility.
Bayesian hierarchical regression on clearance rates in the presence of “lag” and “tail” phases with an application to malaria parasites
Authors: Fogarty Colin B. , Fay Michael P. , Flegg Jennifer A. , Stepniewska Kasia , Fairhurst Rick M. , Small Dylan S. 
Published: April 2015

SummaryWe present a principled technique for estimating the effect of covariates on malaria parasite clearance rates in the presence of “lag” and “tail” phases through the use of a Bayesian hierarchical linear model. The hierarchical approach enables us to appropriately incorporate the uncertainty in both estimating clearance rates in patients and assessing the potential impact of covariates on these rates into the posterior intervals generated for the parameters associated with each covariate. Furthermore, it permits us to incorporate information about individuals for whom there exists only one observation time before censoring, which alleviates a systematic bias affecting inference when these individuals are excluded. We use a changepoint model to account for both lag and tail phases, and hence base our estimation of the parasite clearance rate only on observations within the decay phase. The Bayesian approach allows us to treat the delineation between lag, decay, and tail phases within an individual's clearance profile as themselves being random variables, thus taking into account the additional uncertainty of boundaries between phases. We compare our method to existing methodology used in the antimalarial research community through a simulation study and show that it possesses desirable frequentist properties for conducting inference. We use our methodology to measure the impact of several covariates on Plasmodium falciparum clearance rate data collected in 2009 and 2010. Though our method was developed with this application in mind, it can be easily applied to any biological system exhibiting these hindrances to estimation.
Prostatic arterial embolization for the treatment of lower urinary tract symptoms caused by benign prostatic hyperplasia: a comparative study of medium‐ and large‐volume prostates
Authors: Wang Maoqiang , Guo Liping , Duan Feng , Yuan Kai , Zhang Guodong , Li Kai , Yan Jieyu , Wang Yan , Kang Haiyan 
Published: April 2015

ObjectivesTo compare the outcomes of prostatic arterial embolization (PAE) in treating large (>80 mL) in comparison with medium‐sized prostate glands (50–80 mL) to determine whether size affects the outcome of PAE.Patients and MethodsA total of 115 patients (mean age 71.5 years) diagnosed with lower urinary tract symptoms (LUTS) attributable to benign prostatic hyperplasia (BPH) refractory to medical treatment underwent PAE. Group A (n = 64) included patients with a mean prostate volume of 129 mL; group B (n = 51) included patients with a mean prostate volume of 64 mL. PAE was performed using 100‐μm particles. Follow‐up was performed using the International Prostate Symptom Score (IPSS), quality of life (QoL), peak urinary flow rate (Qmax), post‐void residual urine volume (PVR), the International Index of Erectile Function short form (IIEF‐5), prostate‐specific antigen (PSA) and prostate volume measured by magnetic resonance imaging at 1, 3 and 6 months, and every 6 months thereafter.ResultsThere were no significant differences between groups in baseline IPSS, QoL, Qmax, PVR, PSA level or IIEF‐5 score. The technical success rate was 93.8% in group A and 96.8% in group B (P = 0.7). A total of 101 patients (55 patients in group A and 46 patients in group B) completed the mean (range) follow‐up of 17 (12–33) months. Compared with baseline, there were significant improvements in IPSS, QoL, Qmax, prostate volume and PVR in both groups after PAE. The outcomes in group A were significantly better than in group B with regard to mean ± sd IPSS (−14 ± 6.5 vs −10.5 ± 5.5, respectively), Qmax (6.0 ± 1.5 vs 4.5 ± 1.0 mL/s, respectively), PVR (−80.0 ± 25.0 vs −60.0 ± 20.0 mL, respectively), prostate volume (−54.5 ± 18.0 mL [−42.3%] vs −18.5 ± 5.0 mL [−28.9%], respectively), and QoL score (−3.0 ± 1.5 vs −2.0 ± 1.0) with P values <0.05. The mean IIEF‐5 score was not significantly different from baseline in both groups. No major complications were noted.ConclusionsWe found that PAE is a safe and effective treatment method for patients with LUTS attributable to BPH. The clinical and imaging outcomes of PAE were better in patients with larger prostate glands than medium‐sized ones.