bluuebunny/crossref_metadata_2025 huggingface dataset:
The Africa-Brazil continuum
Authors: Petter Margarida Maria Taddoni , Negrão Esmeralda Vailati , Viotti Evani
Published: November 2018

This chapter discusses the hypothesis that some impersonal constructions of Brazilian Portuguese and a type of passive of Angolan Portuguese are the outcome of the contact between Classical Portuguese and Bantu languages. This can be taken as possible evidence for the Africa-Brazil linguistic continuum (Petter 2007). Emphasis is given to the Bantu (b)a-passives, and to Classical Portuguese topic constructions. Following Mufwene (2008), the authors argue that a linguistic feature pool with elements of different languages was formed in the ecologies of language practice in the colonies of Brazil and Angola. Linguistic features of the different languages in contact were selected based on what the interactants perceived as congruences among them, thus forming the basis of what later became Brazilian and Angolan Portuguese.
Language contact and variation in Cape Verde and São Tomé and Príncipe
Authors: Alexandre Nélia , Gonçalves Rita
Published: November 2018

Both Cape Verdean Portuguese (CVP) and Santomean Portuguese (STP) are in contact with Portuguese-lexified Creole languages formed during the 15th and 16th centuries: Cape Verdean (CV), in Cape Verde, and Santome, Angolar, and Lung’Ie, in São Tomé and Príncipe. Despite this, Portuguese is the only official language of the two archipelagos. The goal of this chapter is twofold. First, we aim to compare and discuss corpus data from CVP and STP, underlining the impact of socio-historical factors in some morphosyntactic aspects of these Portuguese varieties’ grammars. Second, we will show that the convergence and divergence observed is not only driven by the language contact situation but also by internal mechanisms of change.
Political rhetoric and discursive framing of national identity in Croatia’s commemorative culture
Authors: Banjeglav Tamara
Published: November 2018

The topic of this paper is framing of collective, national identities in commemorative speeches. It identifies abstract conceptions of Croatian national identity articulated by political elites during commemorative practices and examines what patterns are used for their linguistic expression. The questions that are posed are how Croatian nation and national identity are framed in discourse and whether constructs of national identity are formed depending on the context and on the party political affiliation of the speaker. However, the aim is also to track potential changes in elite narratives over time. The analysis is based on a corpus of commemorative speeches delivered by Croatia’s political elites on the occasion of celebration of the Croatian army victory in a military operation. The main focus is on the conceptual and linguistic analysis of the collective identities and sociocultural concepts in the staged communication during commemoration rituals.
Categories of grammar and categories of speech
Authors: Poplack Shana
Published: November 2018

This chapter tracks the response to morphosyntactic variability in a massive corpus of prescriptive grammars of French dating from the 16th century through the present, and relates it to current mainstream approaches. Analysis shows that although variant forms have been recognized since the earliest times, only rarely have they been acknowledged as variant expressions of the same meaning or function. Instead three major strategies are marshaled to factor variability out. Their aim is not to prescribe or even describe, but simply to associate each form with a dedicated context of occurrence, in keeping with the dictates of the traditional grammatical categories from which they derive. This state of affairs is encapsulated in the Doctrine of Form-Function Symmetry. Although it fails to account for the data of spontaneous speech (which reveals asymmetry in the form of robust variability subject to regular conditioning instead), it continues to mold both prescriptive and formal linguistic treatments of variability, contributing to the growing gulf between prescription, description, and actual usage.
LatinUs* and linguistics
Authors: Zentella Ana Celia
Published: November 2018

The languages we study, as well as their speakers and our students, would benefit from a re-imagined approach to linguistics – one that underscores the historical, social, and political contexts surrounding the structures we investigate. Particularly for LatinUs and others whose ways of speaking are stigmatized, a linguistics that focuses on forms while ignoring what people say about their lives alienates the members of those groups who are attracted by the study of language, and its emancipatory possibilities. To combat the reproduction of linguistic and educational inequality, I advocate an anthro-political linguistics, emphasizing the central role that power plays in language and exposing the ways in which language is falsely constructed as the root of educational, cultural, social, and political problems.
Reviving the unicorn
Authors: Varra Rachel
Published: November 2018

This chapter engages the debate on the term Spanglish. Ricardo Otheguy asserts that the term Spanglish has no real-world referent and is “technically flawed.” In response, it is argued that the term Spanglish is neither objectively inaccurate nor technically flawed because the term Spanglish refers to a ‘real’ linguistic phenomenon. Furthermore, the necessary conditions for labeling linguistic varieties as varieties are theoretically untenable or practically unimplementable. The chapter also highlights that linguistic systems are mental objects whose existence is inferred from behavioral epiphenomena and that such a set of behavioral epiphenomena is in evidence for Spanglish. The chapter concludes that sufficient linguistic and sociolinguistic evidence exists to posit the existence of, and thereby justify the use of, the term Spanglish.
Simulated concentration profiling of liquid-phase products in the quaternary solvent system of (carbon dioxide + monoeth-anolamine / diethanolamine + triethanolamine + water)
Authors: Soriano A N , Novhanda M , Cruz J E B D , Adornado A P
Published: November 2018

An understanding of the potential environmental impacts of amine solvents used in Carbon Capture and Storage (CCS) is important as more of these technologies are moving to the pilot stage of development and will be more regularly operated. It is clear that solvents with otherwise promising performance may have challenges and considerable inherent problem due to by-product formation, of which often neglected. In this regard, it is also necessary to study the concentration profiles of the by-products formed in aid of treating liquid waste streams. The study also includes the chemistry and reaction mechanisms of amine transformation products. The studied quaternary systems in varying blends were generally written as CO2- amine-TEA-H2O, where amine could be MEA or DEA. TEA corresponds to triethanolamine, MEA to monoethanolamine, and DEA to diethanolamine. The simulation was done using Aspen Plus® v8.6 at different mass flow rates (kg/h): 500, 750, and 1,000; temperatures (oC): 25, 30, 35, 40, 45, and 50; and pressures (atm): 1, 2, and 3. The results shows direct proportionality between the efficiency and solvent’s flow rate, pressure, higher secondary amines ratio along with temperature in majority. At constant temperature, pressure, and mass flow rate, the highest removal efficiency was that of MEA-TEA (10-20 %wt) and the lowest was DEA-TEA (10-20 %wt). In addition, the results yield reasonable predictions on liquid-phase product concentration profiles. The components behave according to their expected trends and the results are very promising.
Study of erosion and sedimentation in urban areas for river with meander pattern
Authors: Murniningsih S
Published: November 2018

Most of the river in Indonesia has a meander pattern particularly located in urban area. Since the river plains and delta consist of alluvial soils, thus, Meander River in urban area usually encourage sediment transport problem for instance river cliff erosion or bank erosion in outer meander bend and sedimentation in the inside of the meander bend that affect migration of the channel. However, to solve problems in the area of meanders is not easy, because the factors that affect the movement of the river flow and channel migration are very complex. Therefore, simulation of channel migration is increasingly required to assess the risk especially from erosion and sedimentation along meander bend. To simulate the process be approached with built a physical modeling of curved channel at hydraulics indoor laboratory with two different soil classification and composition. This model constructed on mobile bed table apparatus, whereas, the table covered by clayey silt material and sandy silt material with 80 mm thickness. Laboratory findings concluded soil composition with high percentage of silt would be change rapidly compare than soil composition with low percentage of silt. The result of the experiment its qualitative approach without quantifying of sedimentation in the inner bend and erodible sand in the outer bank.
Neighborhood Poverty Increases Risk for Cigarette Smoking From Age 30 to 39
Authors: Cambron Christopher , Kosterman Rick , Hawkins J David
Published: November 2018

Background

Lower socioeconomic status (SES) has been associated with higher rates of smoking. Few longitudinal studies have examined indicators of SES at both the neighborhood- and individual-level over time in conjunction with proximal risk factors of cigarette smoking.

Purpose

To examine associations of time-varying measures of SES, demographic factors, and proximal risk factors for smoking net of average trajectories of smoking behavior from ages 30 to 39 in a community sample.

Methods

Data from the Seattle Social Development Project (N = 752), a theory-driven longitudinal study originating in Seattle, WA, were used to estimate trajectories of smoking from age 30 to 39. Time-varying measures of neighborhood poverty, coworker smoking, partner smoking, depression, anxiety, education, income, marital status, and parenthood were associated with smoking over time using latent growth curve modeling.

Results

Results indicated that living in higher poverty neighborhoods was uniquely associated with a greater likelihood of smoking net of average trajectories of smoking from age 30 to 39, gender and race/ethnicity, time-varying measures of SES and demographics, and time-varying measures of proximal risk factors for smoking.

Conclusions

Living in higher poverty neighborhoods presents a unique risk for smoking among adults aged 30 to 39 above and beyond multiple aspects of SES and other potential mechanisms relating SES to smoking.
Therapeutic targeting of tumor hypoxia and necrosis with antibody α-radioconjugates
Authors: Staudacher Alexander H , Liapis Vasilios , Brown Michael P
Published: November 2018

Solid tumors are inherently difficult to treat because of large regions of hypoxia and are often chemotherapy- or radiotherapy-resistant. It seems that cancer stem cells reside in hypoxic and adjacent necrotic tumor areas. Therefore, new treatments that are highly selective for tumors and can eradicate cells in both hypoxic and necrotic tumor regions are desirable. Antibody α-radioconjugates couple an α-emitting radionuclide with the specificity of a tumor-targeting monoclonal antibody. The large mass and energy of α-particles result in radiation dose delivery within a smaller area independent of oxygen concentration, thus matching key criteria for killing hypoxic tumor cells. With advances in radionuclide production and chelation chemistry, α-radioconjugate therapy is regaining interest as a cancer therapy. Here, we will review current literature examining radioconjugate therapy specifically targeting necrotic and hypoxic tumor cells and outline how α-radioconjugate therapy could be used to treat tumor regions harboring more resistant cancer cell types.

Statement of Significance Tumor-targeting antibodies are excellent vehicles for the delivery of toxic payloads directly to the tumor site. Tumor hypoxia and necrosis promote treatment recurrence, resistance, and metastasis. Targeting these areas with antibody α-radioconjugates would aid in overcoming treatment resistance.
wgd—simple command line tools for the analysis of ancient whole-genome duplications
Authors: Zwaenepoel Arthur , Van de Peer Yves
Published: November 2018

Ancient whole-genome duplications (WGDs) have been uncovered in almost all major lineages of life on Earth and the search for traces or remnants of such events has become standard practice in most genome analyses. This is especially true for plants, where ancient WGDs are abundant. Common approaches to find evidence for ancient WGDs include the construction of KS distributions and the analysis of intragenomic colinearity. Despite the increased interest in WGDs and the acknowledgment of their evolutionary importance, user-friendly and comprehensive tools for their analysis are lacking. Here, we present an easy to use command-line tool for KS distribution construction named wgd. The wgd suite provides commonly used KS and colinearity analysis workflows together with tools for modeling and visualization, rendering these analyses accessible to genomics researchers in a convenient manner.

Availability and implementation

wgd is free and open source software implemented in Python and is available at https://github.com/arzwa/wgd.

Supplementary information

Supplementary data are available at Bioinformatics online.
Obese Patients Benefit, but do not Fare as Well as Nonobese Patients, Following Lumbar Spondylolisthesis Surgery: An Analysis of the Quality Outcomes Database
Authors: Chan Andrew K , Bisson Erica F , Bydon Mohamad , Glassman Steven D , Foley Kevin T , Potts Eric A , Shaffrey Christopher I , Shaffrey Mark E , Coric Domagoj , Knightly John J , Park Paul , Wang Michael Y , Fu Kai-Ming , Slotkin Jonathan R , Asher Anthony L , Virk Michael S , Kerezoudis Panagiotis , DiGiorgio Anthony M , Haid Regis W , Mummaneni Praveen V
Published: November 2018

BACKGROUND

Given recent differing findings following 2 randomized clinical trials on degenerative lumbar spondylolisthesis (DLS) surgery, there is a need to better define how subsets of patients fare following surgery.

OBJECTIVE

To investigate the impact of obesity on patient-reported outcomes (PROs) following DLS surgery.

METHODS

A total of 12 high-enrolling sites were queried, and we found 797 patients undergoing surgery for grade 1 DLS. For univariate comparisons, patients were stratified by BMI ≥ 30 kg/m2 (obese) and < 30 kg/m2 (nonobese). Baseline, 3-mo, and 12-mo follow-up parameters were collected. PROs included the North American Spine Society satisfaction questionnaire, numeric rating scale (NRS) back pain, NRS leg pain, Oswestry Disability Index (ODI), and EuroQoL-5D (EQ-5D) Questionnaire.

RESULTS

We identified 382 obese (47.9%) and 415 nonobese patients (52.1%). At baseline, obese patients had worse NRS back pain, NRS leg pain, ODI, and EQ-5D scores (P < .001, P = .01, P < .001, and P = .02, respectively). Both cohorts improved significantly for back and leg pain, ODI, and EQ-5D at 12 mo (P < .001). At 12 mo, similar proportions of obese and nonobese patients responded that surgery met their expectations (62.6% vs 67.4%, P = .24). In multivariate analyses, BMI was independently associated with worse NRS leg pain and EQ-5D at 12 mo (P = .01 and P < .01, respectively) despite adjusting for baseline differences.

CONCLUSION

Obesity is associated with inferior leg pain and quality of life—but similar back pain, disability, and satisfaction—12 mo postoperatively. However, obese patients achieve significant improvements in all PRO metrics at 12 mo.
A Two-Year Prospective Multicenter Study of Opioid Therapy for Chronic Noncancer Pain: Prescription Trends and Predictors
Authors: Veiga Dalila R , Mendonça Liliane , Sampaio Rute , Castro-Lopes José M , Azevedo Luís F
Published: November 2018

Objectives

Opioid use in chronic pain has increased worldwide in recent years. The aims of this study were to describe the trends and patterns of opioid therapy over two years of follow-up in a cohort of chronic noncancer pain (CNCP) patients and to assess predictors of long-term opioid use and clinical outcomes.

Methods

A prospective cohort study with two years of follow-up was undertaken in four multidisciplinary chronic pain clinics. Demographic data, pain characteristics, and opioid prescriptions were recorded at baseline, three, six, 12, and 24 months.

Results

Six hundred seventy-four CNCP patients were recruited. The prevalence of opioid prescriptions at baseline was 59.6% (N = 402), and 13% (N = 86) were strong opioid prescriptions. At 24 months, opioid prescription prevalence was as high as 74.3% (N = 501), and strong opioid prescription was 31% (N = 207). Most opioid users (71%, N = 479) maintained their prescription during the two years of follow-up. Our opioid discontinuation was very low (1%, N = 5). Opioid users reported higher severity and interference pain scores, both at baseline and after two years of follow-up. Opioid use was independently associated with continuous pain, pain location in the lower limbs, and higher pain interference scores.

Conclusions

This study describes a pattern of increasing opioid prescription in chronic pain patients. Despite the limited improvement of clinical outcomes, most patients keep their long-term opioid prescriptions. Our results underscore the need for changes in clinical practice and further research into the effectiveness and safety of chronic opioid therapy for CNPC.
Estimating digestible energy values of feeds and diets and integrating those values into net energy systems
Authors: Weiss William P , Tebbe Alexander W
Published: November 2018

The California Net Energy System (CNES) used a combination of measured and tabular metabolizable energy (ME) values and changes in body composition gain to determine net energy requirements for maintenance and gain and their corresponding dietary concentrations. The accuracy of the CNES depends on the accuracy of the feed ME values. Feed or diet ME values can be measured directly but are expensive and require specialized facilities; therefore, most ME values are estimated from digestible energy (DE) values, which are often estimated from the concentration of total digestible nutrients (TDN). Both DE and TDN values are often from tables and not based on actual nutrient analysis. The use of tabular values eliminates important within-feed variation in composition and digestibility. Furthermore, the use of TDN to estimate DE does not account for important variation in the gross energy value of feeds. A better approach would be to estimate DE concentration directly from nutrient composition or in vitro (or in situ) digestibility measurements. This approach incorporates within-feed variation into the energy system and eliminates the issues of using TDN. A widely used summative equation based on the commonly measured feed fractions (ash, crude protein, neutral detergent fiber, and fat) has been shown to accurately estimate DE concentrations of many diets for cattle; however, deficiencies in that equation have been identified and include an overestimation of DE provided by fat and an exaggerated negative effect of intake on digestibility. Replacing the nonfiber carbohydrate term (which included everything that was not measured) in the equation with measured starch concentration and residual organic matter (i.e., nonfiber carbohydrate minus starch) should improve accuracy by accounting for more variation in starch digestibility. More accurate estimates of DE will improve the accuracy of ME values, which will ultimately lead to more accurate NE values.
Developing a smartphone-based ecological momentary assessment protocol to collect biopsychosocial data with community-dwelling late-middle-aged and older adults
Authors: Liu Huiying , Lou Vivian W Q
Published: November 2018

Although ecological momentary assessment (EMA) has been used in youth and adult populations, very few of the studies provided evidence of the feasibility and utility of smartphone-based EMA protocols to collect biopsychosocial data from aging populations. This study aimed to describe the design and implementation of a smartphone-based EMA protocol, and to evaluate the feasibility and utility of this EMA protocol among community-dwelling late-middle-aged and older Chinese. A sample of 78 community-dwelling Chinese aged between 50 and 70 years was trained to participate in a 1-week EMA data collection, during which each participant carried an Android smartphone loaded with a researcher-developed EMA application and a smartphone-based electrocardiogram (ECG) monitor to provide psychosocial (e.g., daily activities, social interaction, affect) data and ECG recordings six times daily. Adherence was demonstrated with a total response rate of 91.5% of all scheduled assessments (n = 3,822) and a moderately high level of perceived feasibility. Female participants reported higher compliance to the study and rated the overall experience as more pleasant and interesting than male participants. Our study provided the first evidence of the feasibility and utility of smartphone-based EMA protocols among late-middle-aged and older Chinese. Key areas for improvement in future design and implementation of mobile-based EMA include the incorporation of usable technology, adequate and training, and timely assistance.
Evidence for increased surveillance of executive functioning in adolescent and young adult survivors of childhood cancer
Authors: Lee Jennifer L , Gutierrez-Colina Ana , Meacham Lillian R , Mertens Ann C , Gilleland Marchak Jordan
Published: November 2018

Comprehensive long-term follow-up (LTFU) for survivors of childhood cancer is critical for reducing morbidity and mortality. Current standards recommend screening all survivors for psychological and academic problems and certain survivors for neurocognitive problems based upon treatment exposures. This study aimed to determine if differences exist in executive functioning (EF) based on treatment exposures and characterize relationships between EF, treatment exposure, and internalizing problems. Participants included adolescent and young adult (AYA) survivors (N = 70) of non-central nervous system cancer, aged 14–21 presenting for LTFU. Patient-reported data were obtained on survivors’ EF, internalizing symptoms, academic performance, and educational supports. Children’s Oncology Group’s LTFU Guidelines classified survivors as at risk or not at risk for neurocognitive deficits based on treatment exposures. Group differences, relationships, and moderation by risk group were examined. No differences were found in EF, internalizing symptoms, academic performance, or educational supports between survivors who were at risk versus those not at risk for neurocognitive deficits. Problems with EF predicted internalizing symptoms, an effect that was moderated by risk group (R2= .64 for AYA self-report; R2 = .38 for parent-proxy report). Survivors with poorer EF experienced higher levels of internalizing symptoms. These data indicate that current screening practices may not identify survivors who are not at risk for neurocognitive deficits, yet struggle with EF. Survivor care providers should consider universal screening for EF problems in AYAs, regardless of treatment exposure history. Clinical assessment of internalizing problems in survivors with EF problems is also recommended.
PA practice analysis
Authors: Barnhill Grady C. , Dallas Andrew D. , Mauldin Sheila G. , Hooker Roderick S.
Published: November 2018

In conducting its practice analysis, the National Commission on Certification of Physician Assistants incorporated new approaches in 2015. Twelve groups of PAs identified knowledge, tasks, and skills required for practice not only in primary care, but also in 11 practice focus areas (specialties). In addition, a list of diseases and disorders likely to be encountered was identified for each specialty. A representative sample of 15,771 certified PAs completed an online algorithm-driven survey and data were analyzed to determine how practice is the same for all PAs and how it differs depending on the practice focus. Larger differences between PAs in different specialties were seen in the frequency ratings of diseases and disorders encountered than for ratings of task, knowledge, and skill statements. Distinctions between PAs in primary care and those in other specialties were more pronounced, as the specialty was more divergent from primary care.
Leading Practices and Future Directions for Technical Standards in Medical Education
Authors: Kezar Laura B. , Kirschner Kristi L. , Clinchot Daniel M. , Laird-Metke Elisa , Zazove Philip , Curry Raymond H.
Published: November 2018

The medical profession first addressed the need for technical standards (TS), defining the nonacademic requirements deemed essential for participation in an educational program, in guidelines published by the Association of American Medical Colleges in 1979. Despite many changes in the practice of medicine and legal, cultural, and technological advances that afford greater opportunities for people with disabilities, the profession’s approach to TS largely has not changed over the ensuing four decades. Although physicians with disabilities bring unique perspectives to medicine and contribute to a diverse physician workforce of culturally competent practitioners, they remain underrepresented in the profession.

As part of an initiative sponsored by the Association of Academic Physiatrists, the authors describe the need for an updated TS framework, outlining interval changes in the legal and regulatory climate, medical practice, and medical education since the initial TS guidelines were put forth. They conclude by offering eight recommendations and two functional approaches to TS that are consistent with now-prevalent competency-based medical education constructs.

The profession’s commitment to diversity and inclusion should extend explicitly to people with disabilities, and this stance should be clearly communicated through medical schools’ TS and procedures for requesting accommodations. To this end, schools should consider the principles of universal design to create policies and assessments that work for all learners, to the greatest extent possible, without the need for after-the-fact accommodations. A thoughtful and concerted effort along these lines is long overdue in medical education.
Simulation-based Assessment to Reliably Identify Key Resident Performance Attributes
Authors: Blum Richard H. , Muret-Wagstaff Sharon L. , Boulet John R. , Cooper Jeffrey B. , Petrusa Emil R.
Published: November 2018

Background

Obtaining reliable and valid information on resident performance is critical to patient safety and training program improvement. The goals were to characterize important anesthesia resident performance gaps that are not typically evaluated, and to further validate scores from a multiscenario simulation-based assessment.

Methods

Seven high-fidelity scenarios reflecting core anesthesiology skills were administered to 51 first-year residents (CA-1s) and 16 third-year residents (CA-3s) from three residency programs. Twenty trained attending anesthesiologists rated resident performances using a seven-point behaviorally anchored rating scale for five domains: (1) formulate a clear plan, (2) modify the plan under changing conditions, (3) communicate effectively, (4) identify performance improvement opportunities, and (5) recognize limits. A second rater assessed 10% of encounters. Scores and variances for each domain, each scenario, and the total were compared. Low domain ratings (1, 2) were examined in detail.

Results

Interrater agreement was 0.76; reliability of the seven-scenario assessment was r = 0.70. CA-3s had a significantly higher average total score (4.9 ± 1.1 vs. 4.6 ± 1.1, P = 0.01, effect size = 0.33). CA-3s significantly outscored CA-1s for five of seven scenarios and domains 1, 2, and 3. CA-1s had a significantly higher proportion of worrisome ratings than CA-3s (chi-square = 24.1, P < 0.01, effect size = 1.50). Ninety-eight percent of residents rated the simulations more educational than an average day in the operating room.

Conclusions

Sensitivity of the assessment to CA-1 versus CA-3 performance differences for most scenarios and domains supports validity. No differences, by experience level, were detected for two domains associated with reflective practice. Smaller score variances for CA-3s likely reflect a training effect; however, worrisome performance scores for both CA-1s and CA-3s suggest room for improvement.
Standard Short Peripheral Catheters (SPCs) Versus Power Injectable SPCs During Contrast Computed Tomography and Magnetic Resonance Imaging Angiography
Authors: Pohlod Virginia
Published: November 2018

To perform high-resolution computed tomography and magnetic resonance imaging angiographies, contrast typically is rapidly injected through a 20-gauge or larger short peripheral catheter (SPC). Intravenous access in infants and children can be challenging, and the use of large-gauge catheters is not always feasible. An institutional review board-approved quality improvement study was undertaken at a 250-bed pediatric hospital on Florida's Gulf Coast that compared the use and outcomes of standard SPCs (nonfenestrated) versus a power injectable SPC (fenestrated with 3 side holes distal to the catheter tip).
Implementation of Smart Pump Technology With Home Infusion Providers
Authors: Brown Thomas D. , Michael Martha , Grady David S.
Published: November 2018

While hospitals have adopted smart pump technology (SPT) featuring drug libraries and medication safety software, most home infusion providers (HIPs) continue to use traditional infusion pumps that don't offer drug libraries or medication safety software. As infusion delivery is moving from the hospital to the home, the purpose of this study was to determine whether SPT was a feasible alternative at both a hospital-based and a rural HIP. HIP personnel were trained on an ambulatory infusion pump. Patients requiring home infusion used the pump and recorded daily pump interactions for 5 to 7 days. After the creation of a drug library, clinicians felt comfortable programming pumps after 7 uses. Patients reported 100% overall satisfaction, and the majority of alarms were resolved without contacting the HIP. Ambulatory SPT can be implemented successfully by HIPs and can be used effectively by patients.
Improving Vascular Access Outcomes and Enhancing Practice
Authors: Platt Valerie , Osenkarski Seth
Published: November 2018

With most hospitalized patients requiring peripheral intravenous catheters (PIVCs), PIVC-related process improvement may substantially affect the health, safety, and satisfaction of patients and health care workers, in addition to reducing costs. This study examined PIVC practice-related metrics before and after a comprehensive process improvement program, which included a change to closed catheter technology. Data were obtained from observations, clinician interviews, and patient records. Metrics included assessment of risk, especially blood exposure and contamination; measurement of insertion efficiency; and quantification of PIVC failure. A significant improvement in most metrics was achieved after the process improvement program.
Brief Report: Rate of Nicotine Metabolism and Tobacco Use Among Persons With HIV: Implications for Treatment and Research
Authors: Schnoll Robert A. , Thompson Morgan , Serrano Katrina , Leone Frank , Metzger David , Frank Ian , Gross Robert , Mounzer Karam , Tyndale Rachel F. , Weisbrot Jessica , Meline Miles , Collman Ronald G. , Ashare Rebecca L.
Published: November 2018

Background:

The nicotine metabolite ratio (NMR) is a biomarker that represents individual variation in the speed that nicotine is metabolized. The rate of nicotine metabolism alters smoking behavior (eg, amount) and has been validated for personalizing tobacco dependence medication selection to increase treatment efficacy and reduce treatment side effects in the general population of smokers. Although smoking rates are extremely high among those with HIV, the NMR has not been evaluated in this underserved population.

Methods:

We used baseline data from a smoking cessation clinical trial for smokers with HIV (N = 131) to examine associations between NMR and demographic, smoking, disease-related, and psychological characteristics. Pearson r and analysis of variance were used to identify univariate correlates of NMR, which were then entered into a multiple linear regression model.

Results:

In univariate analyses, a higher NMR (faster nicotine metabolism) was associated with being white, and more cigarettes per day, nicotine dependence, exhaled carbon monoxide, and symptoms of depression and anxiety, and using efavirenz. In a multiple regression model, a higher NMR was associated with more cigarettes per day, higher anxiety symptoms, and efavirenz use.

Conclusions:

As in other populations, faster nicotine metabolism was associated with the use of more cigarettes and higher anxiety symptoms. Notably, efavirenz use was associated with faster metabolism, which might make it harder to quit smoking for people with HIV treated with that medication. These findings could help guide further study and the clinical use of the NMR to personalize nicotine dependence treatment in this underserved population.
Brief Report: Role of Sociobehavioral Factors in Subprotective TFV-DP Levels Among YMSM Enrolled in 2 PrEP Trials
Authors: Arrington-Sanders Renata , Wilson Craig M. , Perumean-Chaney Suzanne E. , Patki Amit , Hosek Sybil
Published: November 2018

Background:

Young men who have sex with men (YMSM) experience disparities in HIV acquisition more than any other group. Daily oral pre-exposure prophylaxis (PrEP) with tenofovir/emtricitabine has been shown to effectively prevent HIV transmission in YMSM; however, recent studies suggest that young Black men who have sex with men experience subprotective levels of tenofovir diphosphate more frequently than other groups.

Setting:

Combined data from Adolescent Medicine Trials Network for HIV/AIDS Interventions (ATN) 110/113, 2 open-label PrEP studies that provided PrEP and evidence-based behavioral interventions to YMSM aged 15–22 years.

Methods:

Bivariate and logistic regression analyses were used to examine sociodemographic and behavioral factors associated with protective tenofovir diphosphate levels (defined as ≥700 fmol/punch) in ATN 110/113 data.

Results:

In bivariate analysis, self-identified Black participants, residential displacement due to sexual orientation, low perceived risk, and stigma with the medication were associated with subprotective levels. Hispanic ethnicity was associated with protective levels. In the final models, Black males were less likely to have subprotective levels than non-Black males at 4, 8, and 12 weeks. Self-reported displacement due to sexual orientation was associated with subprotective levels, whereas older age was as associated with protective levels.

Conclusions:

These findings highlight how future behavioral research and biomedical prevention efforts in YMSM will need to address PrEP disparities that may occur in young Black men who have sex with men, perception of risk, and lack of key supportive housing during this period that may be critical factors that contribute to HIV acquisition.
Possible Sertraline-Induced Hiccups in a Boy With Obsessive-Compulsive Disorder and Attention-Deficit/Hyperactivity Disorder
Authors: Bilgiç Ayhan
Published: November 2018

Hiccup is a sudden-onset repeated involuntary and spasmodic contraction of the diaphragm and intercostal muscle accompanied by laryngeal closure, generating the characteristic inspiratory sound and discomfort. Various factors including drugs may trigger the hiccups. There are some reports regarding the possible links between psychotropic agents that can affect the dopaminergic system and the triggering of hiccup; however, to our knowledge, there are no data regarding sertraline-induced hiccup. We present the case of a boy with obsessive-compulsive disorder and attention-deficit/hyperactivity disorder who displayed hiccup after sertraline therapy.
5′ and 3′ modifications controlling RNA degradation: from safeguards to executioners
Authors: Gagliardi Dominique , Dziembowski Andrzej
Published: November 2018

RNA degradation is a key process in the regulation of gene expression. In all organisms, RNA degradation participates in controlling coding and non-coding RNA levels in response to developmental and environmental cues. RNA degradation is also crucial for the elimination of defective RNAs. Those defective RNAs are mostly produced by ‘mistakes’ made by the RNA processing machinery during the maturation of functional transcripts from their precursors. The constant control of RNA quality prevents potential deleterious effects caused by the accumulation of aberrant non-coding transcripts or by the translation of defective messenger RNAs (mRNAs). Prokaryotic and eukaryotic organisms are also under the constant threat of attacks from pathogens, mostly viruses, and one common line of defence involves the ribonucleolytic digestion of the invader's RNA. Finally, mutations in components involved in RNA degradation are associated with numerous diseases in humans, and this together with the multiplicity of its roles illustrates the biological importance of RNA degradation. RNA degradation is mostly viewed as a default pathway: any functional RNA (including a successful pathogenic RNA) must be protected from the scavenging RNA degradation machinery. Yet, this protection must be temporary, and it will be overcome at one point because the ultimate fate of any cellular RNA is to be eliminated. This special issue focuses on modifications deposited at the 5′ or the 3′ extremities of RNA, and how these modifications control RNA stability or degradation.

This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.
mRNA decapping: finding the right structures
Authors: Charenton Clément , Graille Marc
Published: November 2018

In eukaryotes, the elimination of the m7GpppN mRNA cap, a process known as decapping, is a critical, largely irreversible and highly regulated step of mRNA decay that withdraws the targeted mRNAs from the pool of translatable templates. The decapping reaction is catalysed by a multi-protein complex formed by the Dcp2 catalytic subunit and its Dcp1 cofactor, a holoenzyme that is poorly active on its own and needs several accessory proteins (Lsm1–7 complex, Pat1, Edc1–2, Edc3 and/or EDC4) to be fully efficient. Here, we discuss the several crystal structures of Dcp2 domains bound to various partners (proteins or small molecules) determined in the last couple of years that have considerably improved our current understanding of how Dcp2, assisted by its various activators, is recruited to its mRNA targets and adopts its active conformation upon substrate recognition. We also describe how, over the years, elegant integrative structural biology approaches combined to biochemistry and genetics led to the identification of the correct structure of the active Dcp1–Dcp2 holoenzyme among the many available conformations trapped by X-ray crystallography.

This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.
Fidelity in RNA-based recognition of transposable elements
Authors: Ugolini Ilaria , Halic Mario
Published: November 2018

Genomes are under constant threat of invasion by transposable elements and other genomic parasites. How can host genomes recognize these elements and target them for degradation? This requires a system that is highly adaptable, and at the same time highly specific. Current data suggest that perturbation of transcription patterns by transposon insertions could be detected by the RNAi surveillance pathway. Multiple transposon insertions might generate sufficient amounts of primal small RNAs to initiate generation of secondary small RNAs and silencing. At the same time primal small RNAs need to be constantly degraded to reduce the level of noise small RNAs below the threshold required for initiation of silencing. Failure in RNA degradation results in loss of fidelity of small RNA pathways and silencing of ectopic targets.

This article is part of the theme issue ‘5′ and 3′ modifications controlling RNA degradation’.
Recombinant production of rabbit β-Nerve Growth Factor and its biological effect on rabbit sperm
Authors: Sanchez-Rodriguez Ana , Abad Paloma , Arias-Alvarez Maria , Rebollar Pilar G. , Bautista José M. , Lorenzo Pedro L. , Garcia-Garcia Rosa M.
Published: November 2018

The neurotrophin β-Nerve Growth Factor (β-NGF) is flourishing as a protein with important roles in the ovulation induction process in induced-ovulation species but data in rabbits are still inconclusive, probably due to the species-specificity effect of the neurotrophin to trigger the ovulation. Moreover, β-NGF seems to have a role in sperm function. To clarify these functionalities we aimed, in the present research: 1) to newly synthesize a functional recombinant β-NGF from rabbit (rrβ-NGF), 2) to reveal differences in the amino acid sequence of rabbit β-NGF compared to other sequences of induced and spontaneous ovulator species, and 3) to assess the effects of rrβ-NGF on sperm viability and motility. The nucleotide sequence of NGF from rabbit prostate was sequenced by Rapid Amplification of cDNA Ends (RACE) and annotated in GenBank (KX528686). Then, rrβ-NGF was produced in CHO cells and purified by affinity chromatography. Western blot and MALDI-TOF analyses confirmed the correct identity of the recombinant protein. rrβ-NGF functionality was validated in PC12 cells through a successful dose-response effect along 8 days. The comparison of the amino acid sequences of NGF between rabbit and other species suggested some relevant substitutions at its binding site to both the high-(TrkA) and the low-(p75) affinity receptors. The addition of rrβ-NGF in rabbit sperm, in a time- and dose-response study, did not affect its viability but slightly changed some of its motility parameters at the highest concentration used (100 ng/ml). Thus, it can be considered that this new recombinant protein may be used for biotechnological and reproduction assisted techniques in ovulation-induced species.
Universal nature of collapsibility in the context of protein folding and evolution
Authors: Thirumalai D. , Samanta Himadri S. , Maity Hiranmay , Reddy Govardhan
Published: November 2018

Theory and simulations predicted sometime ago that the sizes of unfolded states of globular proteins should decrease continuously as the denaturant concentration is shifted from a high to a low value. However, small angle X-ray scattering (SAXS) data were used to assert the opposite, while interpretation of single molecule Forster resonance energy transfer experiments (FRET) supported the theoretical predictions. The disagreement between the two experiments is the SAXS-FRET controversy. By harnessing recent advances in SAXS and FRET experiments and setting these findings in the context of a general theory and simulations, we establish that compaction of unfolded states is universal. The theory also predicts that proteins rich inβ-sheets are more collapsible thanα-helical proteins. Because the extent of compaction is small, experiments have to be accurate and their interpretations should be as model free as possible. Theory also suggests that collapsibility itself could be a physical restriction on the evolution of foldable sequences, and provides a physical basis for the origin of multi-domain proteins.
Characterization of oral microbiota in marmosets: feasibility of using the marmoset as a human oral disease model
Authors: Takehara Sachiko , Zeredo Jorge L , Kumei Yasuhiro , Kagiyama Kensuke , Fukasawa Kazumasa , Oshiro Akiko , Ueno Masayuki , Minakuchi Shunsuke , Kawaguchi Yoko
Published: November 2018

As the world’s population is aging, there is an increasing demand for research regarding aging and aging-related disorders, to achieve better understanding of aging. Ideally, such research would be performed with human subjects. However, due to ethical considerations, animals such as rodents and monkeys are used as alternatives. Among these alternative models, non-human primates are preferred because they share common traits with humans. The small South American common marmoset (Callithrix jacchus) may offer a number of advantages over other non-human primates in terms of its relatively small size, short life span, and identical dental anatomy, compared with humans. The purpose of this study was to clarify the viability of using the marmoset as a human oral disease model.

We collected saliva samples from eight common marmosets and eight human subjects. Prokaryotic DNA was extracted from the saliva samples, and 16S bacterial rRNA gene sequencing was performed on each of the samples. Our results indicated that the types of oral microbiomes detected among human and marmoset samples were nearly identical. In contrast, the oral microbiomes of our human and marmoset subjects were distinctly different from those of rat and dogs, which are popular animal models. The oral microbiomes of marmosets showed greater diversity than those of humans. With respect to individual variation, marmosets exhibited less variation in their oral flora, compared with humans. This difference in variation might be attributed to the fact that marmoset subjects were kept in a controlled environment with identical lifestyles.

The characteristics of its oral microbiota, combined with other technical advantages, suggest that the marmoset may provide the best animal model thus far for the study of oral health. This study characterized the oral microbes of the marmoset, thereby providing information to support future application of the marmoset as a model for age-related oral disease.
PREMONition: An algorithm for predicting the circadian clock-regulated molecular network
Authors: Bosman Jasper , Eelderink-Chen Zheng , Laing Emma , Merrow Martha
Published: November 2018

A transcriptional feedback loop is central to clock function in animals, plants and fungi. The clock genes involved in its regulation are specific to - and highly conserved within - the kingdoms of life. However, other shared clock mechanisms, such as phosphorylation, are mediated by proteins found broadly among living organisms, performing functions in many cellular sub-systems. Use of homology to directly infer involvement/association with the clock mechanism in new, developing model systems, is therefore of limited use. Here we describe the approach PREMONition,PREdictingMolecularNetworks, that uses functional relationships to predict molecular circadian clock associations. PREMONition is based on the incorporation of proteins encoded by known clock genes (when available), rhythmically expressed clock-controlled genes and non-rhythmically expressed but interacting genes into a cohesive network. After tuning PREMONition on the networks derived for human, fly and fungal circadian clocks, we deployed the approach to predict a molecular clock network forSaccharomyces cerevisiae, for which there are no readily-identifiable clock gene homologs. The predicted network was validated using gene expression data and a growth assay for sensitivity to light, a zeitgeber of circadian clocks of most organisms. PREMONition may be used to identify candidate clock-regulated processes and thus candidate clock genes in other organisms.