bluuebunny/crossref_metadata_2025 huggingface dataset:
Embedding Nursing Interventions into the World Health Organization’s International Classification of Health Interventions (ICHI)
Authors: Fortune Nicola , Hardiker Nicholas R , Strudwick Gillian
Published: November 2016

Objective: The International Classification of Health Interventions, currently being developed, seeks to span all sectors of the health system. Our objective was to test the draft classification’s coverage of interventions commonly delivered by nurses, and propose changes to improve the utility and reliability of the classification for aggregating and analyzing data on nursing interventions.

Materials and methods: A 2-phase content mapping method was used: (1) three coders independently applied the classification to a dataset comprising 100 high-frequency nursing interventions; (2) the coders reached consensus for each intervention and identified reasons for initial discrepancies.

Results: A consensus code was found for 80 of the 100 source terms; for 34% of these, the code was semantically equivalent to the source term, and for 64% it was broader. Issues that contributed to discrepancies in Phase 1 coding results included concepts in source terms not captured by the classification, ambiguities in source terms, and uncertainty of semantic matching between “action” concepts in source terms and classification codes.

Discussion: While the classification generally provides good coverage of nursing interventions, there remain a number of content gaps and granularity issues. Further development of definitions and coding guidance is needed to ensure consistency of application.

Conclusion: This study has produced a set of proposals concerning changes needed to improve the classification. The novel method described here will inform future health terminology and classification content coverage studies.
Occupational Differences in BMI, BMI Trajectories, and Implications for Employment Status among Older U.S. Workers
Authors: Burgard Sarah A , Sonnega Amanda
Published: November 2016

We examined associations between employment and obesity, arguing that risk for unhealthy weight may vary across occupational groups because they shape workplace exposures, social class standing, material resources, and norms and expectations about healthy behaviors and weight. We used a large sample of 51–61-year-old workers from the Health and Retirement study, tracking their body mass index (BMI) over time while accounting for potentially confounding influences of socioeconomic status and gender and exploring whether gender modified associations between occupational group, BMI, and retirement timing. Compared with women in professional occupations, women managers were less likely to be obese at baseline and were less likely to be in the obese upward trajectory class, while female professionals and operators and laborers were less likely than women in farm and precision production to be in the normal stable trajectory. Male professionals were less likely than men in sales, service, and operator and laborer positions to be obese at baseline and more often followed the normal upward trajectory than most other groups, though they and farm and precision production men were more likely to be in the overweight to obese trajectory than men in service occupations. Adjustment for sociodemographic and lifestyle characteristics reduced associations more for men than for women. While retirement risk differed across occupational groups, most of these differences were explained by socioeconomic, demographic, and lifestyle characteristics, especially for men. Obesity at baseline was an independent predictor of retirement but did not further explain differences in the timing of retirement by occupational group.
Comparative Proteomics Reveals the Potential Targets of BcNoxR, a Putative Regulatory Subunit of NADPH Oxidase of Botrytis cinerea
Authors: Li Hua , Zhang Zhanquan , He Chang , Qin Guozheng , Tian Shiping
Published: November 2016

The NADPH oxidase (NOX) complex has been shown to play a crucial role in stress response and in the virulence of various fungal pathogens. The underlying molecular mechanisms of NOX, however, remain largely unknown. In the present study, a comparative proteomic analysis compared changes in protein abundance in wild-type Botrytis cinerea and ΔbcnoxR mutants in which the regulatory subunit of NOX was deleted. The ΔbcnoxR mutants exhibited reduced growth, sporulation, and impaired virulence. A total of 60 proteins, representing 49 individual genes, were identified in ΔbcnoxR mutants that exhibited significant differences in abundance relative to wild-type. Reverse transcription-quantitative polymerase chain reaction analysis demonstrated that the differences in transcript levels for 36 of the genes encoding the identified proteins were in agreement with the proteomic analysis, while the remainder exhibited reverse levels. Functional analysis of four proteins that decreased abundance in the ΔbcnoxR mutants indicated that 6-phosphogluconate dehydrogenase (BcPGD) played a role in the growth and sporulation of B. cinerea. The Δbcpgd mutants also displayed impaired virulence on various hosts, such as apple, strawberry, and tomato fruit. These results suggest that NOX can influence the expression of BcPGD, which has an impact on growth, sporulation, and virulence of B. cinerea.
Reduced Sensitivity to Azoxystrobin of Monilinia fructicola Isolates From Brazilian Stone Fruits is Not Associated With Previously Described Mutations in the Cytochrome b Gene
Authors: Pereira Wagner V. , Primiano Isabela V. , Morales Rafael G. F. , Peres Natalia A. , Amorim Lilian , May De Mio Louise L.
Published: November 2016

Quinone-outside inhibitor (QoI) fungicides are effective tools for preharvest control of brown rot of stone fruit. These fungicides have a very specific site of action so the risk of resistance selection is high. The sensitivity of Monilinia fructicola (G. Winter) Honey isolates to azoxystrobin (QoI) was investigated in 143 isolates collected between 2002 and 2011 from four Brazilian states in orchards with different frequencies of fungicide use (0 to 6 fungicides sprays/season). Sensitivity of the isolates to azoxystrobin was determined in vitro, by inhibition of mycelial growth and spore germination on fungicide-amended media or ex vivo by pathogen inoculation in untreated or treated fruit with azoxystrobin. Potential mutations in codons 143, 137, and 129 of the cytochrome b (Cyt b) gene and the occurrence of an intron immediately after codon 143 were analyzed in a subpopulation of the isolates. The M. fructicola population of São Paulo State was less sensitive to the fungicide than the population from the states of Paraná, Santa Catarina, and Rio Grande do Sul. The low sensitivity of the isolates was confirmed also by comparing to the sensitivity of the baseline isolates. Mutations in G143A, F129L, and G137R in Cyt b gene were not found. In addition, 58 isolates tested showed an intron after codon 143 in Cyt b gene. Our results indicate that other mechanisms of selection for low sensitivity to QoI fungicides should be investigated.
Smoking Status and Opioid-related Problems and Concerns Among Men and Women on Chronic Opioid Therapy
Authors: Young-Wolff Kelly C. , Klebaner Daniella , Weisner Constance , Von Korff Michael , Campbell Cynthia I.
Published: November 2016

Objectives:

Smokers on chronic opioid therapy (COT) for noncancer pain use prescription opioids at higher dosages and are at increased risk for opioid misuse and dependence relative to nonsmokers. The current study aims to assess whether smoking is associated with problems and concerns with COT from the perspective of the patient.

Materials and Methods:

In a large sample (N=972) of adult patients prescribed opioids for chronic noncancer pain, we examined sex-specific associations between smoking status and patient perceptions of problems and concerns with COT using regression analyses, adjusting for covariates.

Results:

The sample self-identified as 27% current smokers, 44% former smokers, and 29% never smokers. Current smoking (vs. never smoking) was associated with increased odds of an opioid use disorder among males and females, and higher daily opioid dose among males only. Current and former smokers reported significantly fewer problems with opioids relative to never smokers, and this was driven primarily by lower endorsement of problems that are affected by the stimulant properties of nicotine (eg, difficulties thinking clearly, felt less alert or sleepy).

Discussion:

This study contributes to an understanding of perceived problems and concerns with COT among current, former, and never smokers with chronic noncancer pain. Results suggest that current and former smokers may be a difficult population to target to decrease COT, given that they perceive fewer problems with prescription opioid use, despite higher odds of having an opioid use disorder (males and females) and greater opioid doses (males only).
A Case of Trichogerminoma With Pilomatrical Differentiation and a Unique Immunohistochemical Profile
Authors: Epperson Jonathan , Libow Lester
Published: November 2016

Trichogerminomas are rare adnexal neoplasms first described by Sau et al in 1992. Including the initial report, 20 cases have been reported, all with similar histological features, namely tumor nodules composed of basaloid cells that form densely packed, round nests or “cell balls” and which demonstrate variable degrees of pilosebaceous differentiation. In this study, the authors report a case of a trichogerminoma with pilomatrical differentiation and a unique immunohistochemical profile. The patient is a 71-year-old man with a well-delineated nodule on the top of the scalp. Histologically, the lesion measured 16 mm in greatest dimension and was composed of nodules of basaloid cells with central, compact, slightly eosinophilic cells nests. Immunohistochemically, the tumor nodules diffusely expressed cytokeratins 34βE12, AE1/3, and CK5/6. Diffuse expression of β-catenin and nuclear expression of p63 were also evident. The peripheral basaloid cells, but not the cell balls, expressed CD10, Ber-EP4, BCL-2, and CK7, the latter a previously unreported finding. The histological findings and immunohistochemical profile are compatible with a diagnosis of a trichogerminoma.
Effect of Previous Irradiation on Vascular Thrombosis of Microsurgical Anastomosis: A Preclinical Study in Rats
Authors: Barrera-Ochoa Sergi , Gallardo-Calero Irene , López-Fernández Alba , Romagosa Cleofe , Vergés Ramona , Aguirre-Canyadell Marius , Soldado Francisco , Velez Roberto
Published: November 2016

Background:

The objective of the present investigation was to compare the effect of neoadjuvant irradiation on the microvascular anastomosis in cervical bundle using an experimental model in rats.

Methods:

One hundred forty male Sprague–Dawley rats were allocated into 4 groups: group I, control, arterial microanastomosis; group II, control, venous microanastomosis; group III, arterial microanastomosis with previous irradiation (20 Gy); and group IV, venous microanastomosis with previous irradiation (20 Gy). Clinical parameters, technical values of anastomosis, patency, and histopathological parameters were evaluated.

Results:

Irradiated groups (III and IV) and vein anastomosis groups (II and IV) showed significantly increased technical difficulties. Group IV showed significantly reduced patency rates (7/35) when compared with the control group (0/35). Radiotherapy significantly decreased the patency rates of the vein (7/35) when compared with the artery (1/35). Groups III and IV showed significantly reduced number of endothelial cells and also showed the presence of intimal thickening and adventitial fibrosis as compared with the control group.

Conclusion:

Neoadjuvant radiotherapy reduces the viability of the venous anastomosis in a preclinical rat model with a significant increase in the incidence of vein thrombosis.
Free Medial Plantar Flap Connection with a Posterior Tibial Artery Flap in Reconstruction of Fore–Mid Foot Skin Defect
Authors: Wu Hao , Sheng Jia-Gen , Zhang Chang-Qing
Published: November 2016

Background:

Although there are many surgical treatments for covering the skin defect of the fore–mid foot, how to reconstruct the weight-bearing region remains a challenge. The weight-bearing region of the sole needs to withstand the pressure and shearing stresses of walking, so the plantar skin is anatomically different from other skins in the areas of texture, thickness, subcutaneous tissue, etc. Medial plantar flaps that are harvested from the instep region are regarded as the first choice for weight-bearing region reconstruction because of their excellent functional and aesthetic long-term result. However, when facing an extensive skin defect on a weight-bearing area such as a fore–mid foot avulsion, the application of this flap is limited because if we put the flap in a weight-bearing area of the forefoot, the set of vessels will be exposed to outside.

Methods:

We suggest 2 connected free flaps (posterior tibial artery flap and medial plantar flap) pedicled with 1 set of vessels. The medial plantar flap was used to cover the skin defect of the weight-bearing area in the forefoot. The dorsal skin defect of the injured foot was covered with a posterior tibial artery flap and supplied the medial plantar flap with the posterior tibial vessel. The midfoot skin defect was repaired by a full-skin grafting.

Results:

Long-term follow-up results showed that the shape and function of the injured limbs recovered almost entirely.

Conclusion:

This method of connected flaps is suitable for repairing large skin defects of the fore–mid foot.
Increasing Participation and Improving Engagement in Home Visitation
Authors: Hubel Grace S. , Schreier Alayna , Wilcox Brian L. , Flood Mary Fran , Hansen David J.
Published: November 2016

Home visitation programs are designed to provide comprehensive services that promote parent's abilities to create stable, nurturing care environments for their children. In order for program goals to be met, parents must participate actively and be engaged with the programs' mission. However, promoting engagement and participation are complex processes that have been understudied in research on home visitation. The current qualitative study examined how a national, federally funded home visitation program, Early Head Start (EHS), engaged and retained families so that potentially helpful preventative interventions could be delivered. The study also identified barriers to active engagement. Semistructured interviews were conducted with 10 parents of children enrolled in EHS. Findings suggest that engagement increased when EHS reduced social isolation by forming connections among parents and when the program focused on involving parents in fostering their children's meeting of important developmental milestones. Barriers to engagement identified included logistical and organizational challenges, as well as parental biases and differences in values and attitudes. Practice and policy recommendations for improving EHS and other programs that serve similar populations to increase engagement are discussed.
eCoaching to Enhance Special Educator Practice and Child Outcomes
Authors: Coogle Christan Grygas , Ottley Jennifer R. , Storie Sloan , Rahn Naomi L. , Burt Amy Kurowski
Published: November 2016

Research suggests that there is a gap in what we know is best practice and what is taking place in inclusive early childhood classrooms for children identified with autism spectrum disorder. The purpose of this single-case design study was to examine the effect of eCoaching on (a) a preschool special educator's use of embedded learning opportunities, (b) children's responses to target embedded learning opportunities, and (c) children's expressive communication. Results suggest positive effects on the teacher's use of embedded learning opportunities, increases in child opportunities to practice communication, and variable effects on child communicative outcomes. Implications for practice and future research are discussed.
Long-lasting antinociceptive effects of green light in acute and chronic pain in rats
Authors: Ibrahim Mohab M. , Patwardhan Amol , Gilbraith Kerry B. , Moutal Aubin , Yang Xiaofang , Chew Lindsey A. , Largent-Milnes Tally , Malan T. Philip , Vanderah Todd W. , Porreca Frank , Khanna Rajesh
Published: November 2016

Treatments for chronic pain are inadequate, and new options are needed. Nonpharmaceutical approaches are especially attractive with many potential advantages including safety. Light therapy has been suggested to be beneficial in certain medical conditions such as depression, but this approach remains to be explored for modulation of pain. We investigated the effects of light-emitting diodes (LEDs), in the visible spectrum, on acute sensory thresholds in naive rats as well as in experimental neuropathic pain. Rats receiving green LED light (wavelength 525 nm, 8 h/d) showed significantly increased paw withdrawal latency to a noxious thermal stimulus; this antinociceptive effect persisted for 4 days after termination of last exposure without development of tolerance. No apparent side effects were noted and motor performance was not impaired. Despite LED exposure, opaque contact lenses prevented antinociception. Rats fitted with green contact lenses exposed to room light exhibited antinociception arguing for a role of the visual system. Antinociception was not due to stress/anxiety but likely due to increased enkephalins expression in the spinal cord. Naloxone reversed the antinociception, suggesting involvement of central opioid circuits. Rostral ventromedial medulla inactivation prevented expression of light-induced antinociception suggesting engagement of descending inhibition. Green LED exposure also reversed thermal and mechanical hyperalgesia in rats with spinal nerve ligation. Pharmacological and proteomic profiling of dorsal root ganglion neurons from green LED-exposed rats identified changes in calcium channel activity, including a decrease in the N-type (CaV2.2) channel, a primary analgesic target. Thus, green LED therapy may represent a novel, nonpharmacological approach for managing pain.
Veterans' Voice Through the Lens of Their Medical Records
Authors: Stevenson Carl W. , Payne Kattie
Published: November 2016

Purpose of Study:

The medical record is a sea of information that can reveal what patients are trying to tell us about their health condition. It can reveal hints and trends as to why veterans with congestive heart failure (CHF) are being readmitted within 30 days after hospital discharge. These hints and trends lead caregivers to key contributing variables to veterans' readmission. Furthermore, these variables can be used to predict patient outcomes such as readmission and even prognosis. This article looks at readmissions for CHF from documentation within the medical record to see what was driving the 30-day readmissions. Second, it examines whether the driving forces can be used to predict a veteran's increased risk for readmission or other poor prognosis.

Primary Practice Setting(s):

The study was conducted at a rural 84-bed Veterans Health Administration hospital in the Western United States.

Methodology and Sample:

A retrospective screen was performed on 1,279 veterans' admissions of which 217 were identified as having CHF as a primary or secondary diagnosis on admission. The descriptive statistics, odds ratio (OR) and multivariate logistic regression were used to examine the data. The multivariate logistic regression equation was p = 1/1 + e−x
, which can be found in the biostatistics textbook by G. Van Belle, L. Fisher, P. Heagerty, & T. Lumley (2004)
.
B. Tabaei and H. William (2002) developed and validated the equation and used it to screen for undiagnosed diabetic patients. The equation was refined by S. Rose, A. Palmer, and A. Valentine (2003). The variables selected for this study were based on a literature review of 30 articles.

Results:

The probability and OR for 30-day readmissions for all ages increased as the age increased. The ORs for 30-day readmissions for the variables selected were as follows: brain natriuretic peptide 6.21 (95% CI [0.36, 108.24]), ejection fraction 1.298 (95% CI [0.68, 2.49]), hypertension 1.795 (95% CI [0.83, 3.85]), comorbid conditions 1.02 (95% CI [0.04, 25.02]), Stage III and below were protective, Stage IV 2.057 (95% CI [0.63, 9.32]), lack of discharge education 0.446 (95% CI [0.19, 6.45]). The impact of these variables on veterans with more than 3 readmissions (N = 66) was examined. In 32% of these admissions, there was insufficient data to compare the values of the variables between readmissions. In almost 26% (N = 17) of the cases as the number of variables increased, the time between admissions decreased. In 23% of the cases (N = 15), the values did not change; of these, 14 died and the one who survived had assistance with his care in the form of home health and telehealth.

Implications for Case Management Practice:

Use of this evidence-based tool will help case managers to strategically plan care and prioritize interventions to impact the major variables and risk factors that are impacting veterans' health.
Whole-Exome Sequencing to Identify Novel Biological Pathways Associated With Infertility After Pelvic Inflammatory Disease
Authors: Taylor Brandie D. , Zheng Xiaojing , Darville Toni , Zhong Wujuan , Konganti Kranti , Abiodun-Ojo Olayinka , Ness Roberta B. , O’Connell Catherine M. , Haggerty Catherine L.
Published: November 2016

Background

Ideal management of sexually transmitted infections (STI) may require risk markers for pathology or vaccine development. Previously, we identified common genetic variants associated with chlamydial pelvic inflammatory disease (PID) and reduced fecundity. As this explains only a proportion of the long-term morbidity risk, we used whole-exome sequencing to identify biological pathways that may be associated with STI-related infertility.

Methods

We obtained stored DNA from 43 non-Hispanic black women with PID from the PID Evaluation and Clinical Health Study. Infertility was assessed at a mean of 84 months. Principal component analysis revealed no population stratification. Potential covariates did not significantly differ between groups. Sequencing kernel association test was used to examine associations between aggregates of variants on a single gene and infertility. The results from the sequencing kernel association test were used to choose “focus genes” (P < 0.01; n = 150) for subsequent Ingenuity Pathway Analysis to identify “gene sets” that are enriched in biologically relevant pathways.

Results

Pathway analysis revealed that focus genes were enriched in canonical pathways including, IL-1 signaling, P2Y purinergic receptor signaling, and bone morphogenic protein signaling.

Conclusions

Focus genes were enriched in pathways that impact innate and adaptive immunity, protein kinase A activity, cellular growth, and DNA repair. These may alter host resistance or immunopathology after infection. Targeted sequencing of biological pathways identified in this study may provide insight into STI-related infertility.
Are Centers for Disease Control and Prevention Guidelines for Preexposure Prophylaxis Specific Enough? Formulation of a Personalized HIV Risk Score for Pre-Exposure Prophylaxis Initiation
Authors: Beymer Matthew R. , Weiss Robert E. , Sugar Catherine A. , Bourque Linda B. , Gee Gilbert C. , Morisky Donald E. , Shu Suzanne B. , Javanbakht Marjan , Bolan Robert K.
Published: November 2016

Background

Preexposure prophylaxis (PrEP) has emerged as a human immunodeficiency virus (HIV) prevention tool for populations at highest risk for HIV infection. Current US Centers for Disease Control and Prevention (CDC) guidelines for identifying PrEP candidates may not be specific enough to identify gay, bisexual, and other men who have sex with men (MSM) at the highest risk for HIV infection. We created an HIV risk score for HIV-negative MSM based on Syndemics Theory to develop a more targeted criterion for assessing PrEP candidacy.

Methods

Behavioral risk assessment and HIV testing data were analyzed for HIV-negative MSM attending the Los Angeles LGBT Center between January 2009 and June 2014 (n = 9481). Syndemics Theory informed the selection of variables for a multivariable Cox proportional hazards model. Estimated coefficients were summed to create an HIV risk score, and model fit was compared between our model and CDC guidelines using the Akaike Information Criterion and Bayesian Information Criterion.

Results

Approximately 51% of MSM were above a cutpoint that we chose as an illustrative risk score to qualify for PrEP, identifying 75% of all seroconverting MSM. Our model demonstrated a better overall fit when compared with the CDC guidelines (Akaike Information Criterion Difference = 68) in addition to identifying a greater proportion of HIV infections.

Conclusions

Current CDC PrEP guidelines should be expanded to incorporate substance use, partner-level, and other Syndemic variables that have been shown to contribute to HIV acquisition. Deployment of such personalized algorithms may better hone PrEP criteria and allow providers and their patients to make a more informed decision prior to PrEP use.
Rate of Decline in Nontreponemal Antibody Titers and Seroreversion After Treatment of Early Syphilis
Authors: Seña Arlene C. , Wolff Mark , Behets Frieda , Martin David H. , Leone Peter , Langley Carol , McNeil Linda , Hook Edward W.
Published: November 2016

Background

Syphilis management is complex and demonstration of treatment response requires monitoring of nontreponemal antibody titers for a ≥ 4-fold decline and/or seroreversion to nonreactive titers.

Methods

We evaluated data from a multicenter clinical trial of syphilis treatment conducted from 2000 to 2009 involving human immunodeficiency virus (HIV)–negative patients 18 years or older with early syphilis. To assess the rate of titer decline and seroreversion after effective therapy, rapid plasma reagin (RPR) titers were analyzed at 1, 3, 6, 9, and 12 months among patients with an appropriate treatment response. We plotted the rate of RPR titer decline after treatment, estimated the frequency of seroreversion, and conducted multivariate analyses to assess characteristics associated with seroreversion.

Results

Among 369 (79.4%) of 465 HIV-negative patients with early syphilis who had an appropriate treatment response, 333 participants had complete RPR data over 12 months. Although the decline in RPR titers was ≥ 4-fold among 88.0% (293/333) of participants at 3 months and ≥ 8-fold among 77.8% at 6 months, only 9.6% achieved complete RPR seroreversion at 6 months and 17.1% at 12 months after therapy. Male sex (adjusted odds ratio, 4.3; 95% confidence interval, 1.8–10.5) and baseline RPR titers ≤ 1:32 (adjusted odds ratio, 14.5; 95% confidence interval, 6.8–31.2) were associated with higher odds of seroreversion compared with females and titers > 1:32, respectively.

Conclusions

Despite a ≥ 4-fold RPR titer decline after treatment, the majority of HIV-negative patients with early syphilis failed to have seroreversion at 12 months. Nontreponemal antibody titers often persist despite an appropriate treatment response.
Decline in Herpes Simplex Virus Type 2 Among Non-Injecting Heroin and Cocaine Users in New York City, 2005 to 2014: Prospects for Avoiding a Resurgence of Human Immunodeficiency Virus
Authors: Des Jarlais Don C. , Arasteh Kamyar , Feelemyer Jonathan , McKnight Courtney , Tross Susan , Perlman David C. , Campbell Aimee N.C. , Hagan Holly , Cooper Hannah L.F.
Published: November 2016

Background

Herpes simplex virus type 2 (HSV-2) infection increases both susceptibility to and transmissibility of human immunodeficiency virus (HIV), and HSV-2 and HIV are often strongly associated in HIV epidemics. We assessed trends in HSV-2 prevalence among non-injecting drug users (NIDUs) when HIV prevalence declined from 16% to 8% among NIDUs in New York City.

Methods

Subjects were current non-injecting users of heroin and/or cocaine and who had never injected illicit drugs. Three thousand one hundred fifty-seven NIDU subjects were recruited between 2005 and 2014 among persons entering Mount Sinai Beth Israel substance use treatment programs. Structured interviews, HIV, and HSV-2 testing were administered. Change over time was assessed by comparing 2005 to 2010 with 2011 to 2014 periods. Herpes simplex virus type 2 incidence was estimated among persons who participated in multiple years.

Results

Herpes simplex virus type 2 prevalence was strongly associated with HIV prevalence (odds ratio, 3.9; 95% confidence interval, 2.9–5.1) from 2005 to 2014. Herpes simplex virus type 2 prevalence declined from 60% to 56% (P = 0.01). The percentage of NIDUs with neither HSV-2 nor HIV infection increased from 37% to 43%, (P < 0.001); the percentage with HSV-2/HIV coinfection declined from 13% to 6% (P < 0.001). Estimated HSV-2 incidence was 1 to 2/100 person-years at risk.

Conclusions

There were parallel declines in HIV and HSV-2 among NIDUs in New York City from 2005 to 2014. The increase in the percentage of NIDUs with neither HSV-2 nor HIV infection, the decrease in the percentage with HSV-2/HIV coinfection, and the low to moderate HSV-2 incidence suggest some population-level protection against resurgence of HIV. Prevention efforts should be strengthened to end the combined HIV/HSV-2 epidemic among NIDUs in New York City.
Fracture and Nonaccidental Injury
Authors: Levin Helen , Sangha Gurinder , Carey Timothy P. , Lim Rodrick
Published: November 2016

Pediatric nonaccidental injury (NAI) is an important entity that is commonly seen in a variety of medical settings. These children often present to the emergency department or primary care physicians as the first point of contact after an NAI. There is a major risk associated with nonrecognition of an NAI, including a 35% chance of subsequent injury and a 5% to 10% risk of mortality.
1,2
Therefore, it is essential for physicians to be vigilant when assessing injuries compatible with NAI, especially in infants and young children who are not able to independently express themselves. As fracture is the second most common manifestation of NAI, practitioners should be vigilant to recognize unusual fractures in atypical age ranges to aid in its diagnosis. Here, we present a novel case of a lateral condylar fracture in an almost 13-month-old-child that has not been previously associated with NAI.
Traumatic Femoral Artery Thrombosis Diagnosed by Point-of-Care Ultrasonography in the Pediatric Emergency Department
Authors: Jones Sarah D. , Fischer Jason , Kwan Charisse , Tessaro Mark
Published: November 2016

Femoral artery injuries are a rare complication of blunt trauma in children that require expeditious diagnosis and treatment to prevent permanent limb dysfunction. Point-of-care ultrasonography of femoral vessels is a well-established emergency physician technique for ruling out deep vein thrombosis and guiding femoral vessel catheterization. We present the first report of a pediatric emergency physician diagnosing a traumatic femoral artery thrombus using point-of-care ultrasonography.
Influenza-Like Illness Diagnosis and Management in the Acute Care Setting
Authors: Humiston Sharon G. , Pham Thuylinh N.
Published: November 2016

During influenza season, acute respiratory illness due to influenza is difficult to distinguish from other influenza-like illnesses, but testing should be reserved for situations when timely results will influence management or infection control measures. Immunization status and timing of disease onset notwithstanding, a neuraminidase inhibitor should be offered immediately for certain high-risk children; neuraminidase inhibitor treatment should be considered if shorter illness is warranted or an at-risk sibling may be protected. Antipyretics and cough control may be useful. Immunization with an age-appropriate dose of an inactivated influenza vaccine is the cornerstone of prevention for health care personnel and our patients.
Enhancing Themes and Strengths Assessment: Leveraging Academic-Led Qualitative Inquiry in Community Health Assessment to Uncover Roots of Community Health Inequities
Authors: Hebert-Beirne Jennifer , Felner Jennifer K. , Castañeda Yvette , Cohen Sheri
Published: November 2016

Context:

Rigorous qualitative research can enhance local health departments' efforts to gain a deeper insight into residents' perceived community health inequities necessary for productive community health assessments (CHAs) and community health improvement plans (CHIPs).

Objective:

The Chicago Department of Public Health and the Partnership for Healthy Chicago used the National Association of County & City Health Officials' Mobilizing for Action through Planning and Partnerships (MAPP) model to conduct its CHA/CHIP, Healthy Chicago 2.0 (HC 2.0). Public health graduate students conducted qualitative research for part of the Community Themes and Strengths Assessment (CTSA), one of the 4 MAPP assessments.

Design:

Using a health equity lens, this qualitative component included focus groups and oral histories with residents in Chicago Community Areas with the highest social and economic hardship to better understand how residents perceive health inequities in their respective neighborhoods.

Settings:

Community-based organizations in 6 Chicago neighborhoods with the highest quartile of social and economic hardship.

Participants:

Forty-eight Chicago residents from 5 community areas participated in focus groups, and 6 residents of a Mexican ethnic enclave shared oral histories.

Main Outcome Measure:

Residents' perceptions of community needs and assets.

Results:

Needs identified include inaccessible resources and opportunities, economic instability, and safety. Assets include the efficacy and agency of resilient residents, as well as faith and spirituality. Systemic and institutional discrimination was identified at the roots of community health inequities.

Conclusion:

Through qualitative inquiry, the more nuanced understanding of how residents perceive health inequities better positioned HC 2.0 to develop upstream strategies in line with advanced health equity practice. Engaging qualitative academic researchers in CTSA brings academic expertise to enrich the CHA while providing real-time learning experiences to prepare future public health practitioners to work on upstream structural determinants of health.
Characterization of HCV NS3 Protease Variants in HCV/HIV-Coinfected Patients by Ultra-Deep Sequence Analysis: Relationship with Hepatic Fibrosis
Authors: Abdel-hameed Enass A. , Rouster Susan D. , Zhang Xiang , Chen Jing , Medvedovic Mario , Goodman Zachary D. , Sherman Kenneth E.
Published: November 2016

Background:

Treatment of HCV/HIV coinfection is now largely based on utilization of direct acting agents. Pretreatment viral resistant-associated variants (RAVs) and host liver condition may affect the sustained virological response. In this study, we explored relative prevalence of protease resistance-associated mutations, the evolution of those RAVs after 12 weeks of pegylated interferon alfa exposure, and the role hepatic fibrosis might have on RAV display.

Methods:

Thirty nonresponder HCV/HIV-coinfected subjects were evaluated before and after 12 weeks of PegIFN treatment. Ultra-deep sequence analysis of NS3 RAVs was performed. Hepatic fibrosis was determined by sensitive computer-assisted histomorphometry determination.

Results:

At baseline, protease inhibitor RAVs were present in 73.3% of patients and expanded to 83.3% of patients after 12 weeks of PegIFN exposure. Q80K showed the highest prevalence before and after treatment at 46.7% and 56.7%, respectively. The presence of Q80K is positively correlated with percent collagen content of the liver tissue.

Conclusions:

Key RAVs for HCV protease inhibitors are present in a major portion of the HCV/HIV-coinfected population before therapy. Some variants get selected after exposure. Correlation of Q80K with collagen content of the liver suggests that compartmentalization within the liver may contribute to persistence of mutations less fit than wildtype.
Soft sweeps are the dominant mode of adaptation in the human genome
Authors: Schrider Daniel R. , Kern Andrew D.
Published: November 2016

The degree to which adaptation in recent human evolution shapes genetic variation remains controversial. This is in part due to the limited evidence in humans for classic “hard selective sweeps,” wherein a novel beneficial mutation rapidly sweeps through a population to fixation. However, positive selection may often proceed via “soft sweeps” acting on mutations already present within a population. Here we examine recent positive selection across six human populations using a powerful machine learning approach that is sensitive to both hard and soft sweeps. We found evidence that soft sweeps are widespread and account for the vast majority of recent human adaptation. Surprisingly, our results also suggest that linked positive selection affects patterns of variation across much of the genome, and may increase the frequencies of deleterious mutations. Our results also reveal insights into the role of sexual selection, cancer risk, and central nervous system development in recent human evolution.
Hydrogen Bond Networks and Hydrophobic Effects in the Amyloidβ30–35Chain in Water: A Molecular Dynamics Study
Authors: Jong KwangHyok , Grisanti Luca , Hassanali Ali
Published: November 2016

We study the conformational landscape of the C-terminal fragment of the Amyloid protein Aβ30–35in water using well-tempered metadynamics simulations and find that it resembles an intrinsically disordered protein. The conformational fluctuations of the protein are facilitated by a collective reorganization of both protein and water hydrogen bond networks, combined with electrostatic interactions between termini as well as hydrophobic interactions of the side chains. The stabilization of hydrophobic interactions in one of the conformers involves a collective collapse of the sidechains along with a squeeze out of water sandwiched in between. The charged N and C termini play a critical role in stabilizing different types of protein conformations including those involving contact ion salt-bridges as well as solvent mediated interactions of the termini and amide backbone. We examine this by probing the distribution of directed water wires forming the hydrogen bond network enveloping the polypeptide. Water wires and their fluctuations form an integral part of structural signature of the protein conformation.
Linking the development and functioning of a carnivorous pitcher plant’s microbial digestive community
Authors: Armitage David W.
Published: November 2016

Ecosystem development theory predicts that successional turnover in community composition can influence ecosystem functioning. However, tests of this theory in natural systems are made difficult by a lack of replicable and tractable model systems. Using the microbial digestive associates of a carnivorous pitcher plant, I tested hypotheses linking host age-driven microbial community development to host functioning. Monitoring the yearlong development of independent microbial digestive communities in two pitcher plant populations revealed a number of trends in community succession matching theoretical predictions. These included mid-successional peaks in bacterial diversity and metabolic substrate use, predictable and parallel successional trajectories among microbial communities, and convergence giving way to divergence in community composition and carbon substrate use. Bacterial composition, biomass, and diversity positively influenced the rate of prey decomposition, which was in turn positively associated with a host leaf’s nitrogen uptake efficiency. Overall digestive performance was greatest during late summer. These results highlight links between community succession and ecosystem functioning and extend succession theory to host-associated microbial communities.

Statement of authorship

DWA conceived this work, performed data collection and analysis, and wrote the manuscript
The accuracy and bias of single-step genomic prediction for populations under selection
Authors: Hsu Wan-Ling , Garrick Dorian J. , Fernando Rohan L.
Published: November 2016

In single-step analyses, missing genotypes are explicitly or implicitly imputed, and this requires centering the observed genotypes, ideally using the mean of the unselected founders. If genotypes are only available on selected individuals, centering on the unselected founder mean is impossible. Here, computer simulation is used to study an alternative analysis that does not require centering genotypes but fits the meanµgof unselected individuals as a fixed effect. To improve numerical properties of the analysis, centering the entire matrix of observed and imputed genotypes, using their sample means can be done in addition to fittingµg. Starting with observed diplotypes from 721 cattle, a 5 generation population was simulated with sire selection to produce 40,000 individuals with phenotypes of which the 1,000 sires had genotypes. The next generation of 8,000 genotyped individuals was used for validation. Evaluations were undertaken: with (J) or without (N)µgwhen marker covariates were not centered; and with (JC) or without (C)µgwhen all marker covariates were centered. A pedigree based evaluation was less accurate than genomic analyses. Centering did not influence accuracy of genomic prediction, but fittingµgdid. Accuracies were improved when the panel comprised only QTL, models JC and J had accuracies of 99.2%; and models C and N had accuracies of 85.6%. When only markers were in the panel, the 4 models had accuracies of 63.9%. In panels that included causal variants, fittingµgin the model improved accuracy, but had little impact when the panel contained only markers.
Nucleosome occupancy as a novel chromatin parameter for replication origin functions
Authors: Rodriguez Jairo , Lee Laura , Lynch Bryony , Tsukiyama Toshio
Published: November 2016

Eukaryotic DNA replication initiates from multiple discrete sites in the genome, termed origins of replication (origins). Prior to S phase, multiple origins are poised to initiate replication by recruitment of the pre-replicative complex (pre-RC). For proper replication to occur, origin activation must be tightly regulated. At the population level, each origin has a distinct firing time and frequency of activation within S phase. Many studies have shown that chromatin can strongly influence initiation of DNA replication. However, the chromatin parameters that affect properties of origins have not been thoroughly established. We found that nucleosome occupancy in G1 varies greatly around origins across the S. cerevisiae genome, and nucleosome occupancy around origins significantly correlates with the activation time and efficiency of origins, as well as pre-RC formation. We further demonstrate that nucleosome occupancy around origins in G1 is established during transition from G2/M to G1 in a pre-RC-dependent manner. Importantly, the diminished cell-cycle changes in nucleosome occupancy around origins in the orc1-161 mutant are associated with an abnormal global origin usage profile, suggesting that proper establishment of nucleosome occupancy around origins is a critical step for regulation of global origin activities. Our work thus establishes nucleosome occupancy as a novel and key chromatin parameter for proper origin regulation.
A general algorithm for generating isotropy subgroups in superspace
Authors: Stokes Harold T. , Campbell Branton J.
Published: November 2016

This paper presents a general algorithm for generating the isotropy subgroups of superspace extensions of crystallographic space groups involving arbitrary superpositions of multi-korder parameters from incommensurate and commensuratekvectors. Several examples are presented in detail in order to illuminate each step of the algorithm. The practical outcome is that one can now start with any commensurate parent crystal structure and generate a structure model for any conceivable incommensurate modulation of that parent, fully parameterized in terms of order parameters of irreducible representations at the relevant wavevectors. The resulting modulated structures have (3 +d)-dimensional superspace-group symmetry. Because incommensurate structures are now commonly encountered in the context of many scientifically and technologically important functional materials, the opportunity to apply the powerful methods of group representation theory to this broader class of structural distortions is very timely.
Crystal structure and computational studies of (3Z)-4-benzoyl-3-[(2,4-dinitrophenyl)hydrazinylidene]-5-phenylfuran-2(3H)-one
Authors: Köysal Yavuz , Bülbül Hakan , İlhan İlhan Özer , Akın Nazenin , Dege Necmi
Published: November 2016

In the molecular structure of the title compound, C23H14N4O7, the furan, dinitrophenyl and phenyl rings are almost in the same plane (r.m.s. deviation = 0.127 Å), with the benzoyl ring inclined by a dihedral angle of 56.4 (1)° to the three-ring system. A bifurcated intramolecular N—H...(O,O) hydrogen bond is present. In the crystal, adjacent molecules are linked by C—H...O hydrogen bonds into chains parallel to [001]. A π–π stacking interaction between the benzoyl and dinitrophenyl moieties contributes to the crystal packing. Theoretical calculations using DFT(B3YLP) methods were used to confirm the molecular structure.
Crystal structure of (acetonitrile-κN)iodido(2-(naphthalen-1-yl)-6-{1-[(2,4,6-trimethylphenyl)imino]ethyl}pyridine-κ2N,N′)copper(I)
Authors: Al-Najjar Nada , Solan Gregory A. , Singh Kuldip
Published: November 2016

In the mononuclear title complex, [CuI(C2H3N)(C26H24N2)], the CuIion has a distorted tetrahedral coordination environment, defined by two N atoms of the chelating 2-(naphthalen-1-yl)-6-[(2,4,6-trimethylphenyl)imino]pyridine ligand, one N atom of an acetonitrile ligand and one iodide ligand. Within the complex, there are weak intramolecular C—H...N hydrogen bonds, while weak intermolecular C—H...I interactions between complex molecules, help to facilitate a three-dimensional network.
The N14 anti-afamin antibody Fab: a rare VL1 CDR glycosylation, crystallographic re-sequencing, molecular plasticity and conservativeversusenthusiastic modelling
Authors: Naschberger Andreas , Fürnrohr Barbara G. , Lenac Rovis Tihana , Malic Suzana , Scheffzek Klaus , Dieplinger Hans , Rupp Bernhard
Published: November 2016

The monoclonal antibody N14 is used as a detection antibody in ELISA kits for the human glycoprotein afamin, a member of the albumin family, which has recently gained interest in the capture and stabilization of Wnt signalling proteins, and for its role in metabolic syndrome and papillary thyroid carcinoma. As a rare occurrence, the N14 Fab is N-glycosylated at Asn26L at the onset of the VL1 antigen-binding loop, with the α-1–6 core fucosylated complex glycan facing out of the L1 complementarity-determining region. The crystal structures of two non-apparent (pseudo) isomorphous crystals of the N14 Fab were analyzed, which differ significantly in the elbow angles, thereby cautioning against the overinterpretation of domain movements upon antigen binding. In addition, the map quality at 1.9 Å resolution was sufficient to crystallographically re-sequence the variable VLand VHdomains and to detect discrepancies in the hybridoma-derived sequence. Finally, a conservatively refined parsimonious model is presented and its statistics are compared with those from a less conservatively built model that has been modelled more enthusiastically. Improvements to the PDB validation reports affecting ligands, clashscore and buried surface calculations are suggested.