bluuebunny/crossref_metadata_2025_split huggingface dataset:
Short article: Viral dynamics among hepatitis C virus chronic infected patients during direct-acting antiviral agents therapy: impact for monitoring and optimizing treatment duration
Authors: Tabernilla Andres , Grandal Marta , Pernas Berta , Castro-Iglesias Angeles , Rodríguez-Osorio Iria , Mena Alvaro , Delgado Manuel , Cid Purificacion , Pedreira Jose D. , Poveda Eva 
Published: April 2017

Objectives
Direct-acting antiviral agents (DAAs) have provided an ultimate treatment duration of 12 weeks for most hepatitis C virus (HCV)-infected patients. The opportunity to reduce treatment duration to 6 or 8 weeks is being evaluated. Here, the HCV viral dynamics at short times during HCV therapies and its implications for monitoring and optimizing treatment duration have been assessed.

Patients and methods
HCV chronic infected patients who began HCV therapy (March 2014 to June 2015) at a reference hospital of the Northwest of Spain were selected. HCV-RNA was quantified at different short time points during HCV therapy using Abbott RealTime HCV assay. Epidemiological, clinical, and virological data were recorded.

Results
Eleven HCV-infected patients were included; 90.9% had cirrhosis (>12.5 kPa) and 72.7% were treatment-experienced. HCV genotype 1b was the most prevalent (72.7%). All of the combinations were pegylated interferon-free and all included ribavirin. The median HCV-RNA (log IU/ml) at baseline was 5.8 (5.4–6.1); the decline between baseline and day 3, weeks 4, 8, and 12 was 3.2, 4.8, 5.1, and 5.6, respectively. Fewer than 50% of patients achieved undetectable viral load at weeks 4 and 8; however, all patients achieved a sustained virologic response at 12 weeks.

Conclusion
Rapid and high HCV-RNA decline was observed among HCV-infected patients under DAA-based regimens, especially for those without cirrhosis. Despite low rates of patients with undetectable HCV-RNA at weeks 4 and 8, all achieved a sustained virologic response at 12 weeks. These findings suggest that the time points to monitor HCV-RNA during DAA therapies and the treatment duration need to be optimized.
Patterns of Buprenorphine-Naloxone Treatment for Opioid Use Disorder in a Multistate Population
Authors: Saloner Brendan , Daubresse Matthew , Caleb Alexander G. 
Published: April 2017

Background:
Buprenorphine-naloxone treatment for opioid use disorder has rapidly expanded, yet little is known about treatment outcomes among patients in the general population.

Objective:
To examine predictors of treatment duration, dosage, and continuity in a diverse community setting.

Research Design:
We examined QuintilesIMS Real World Data, an all-payer, pharmacy claims database, to conduct an analysis of individuals age 18 years and above initiating buprenorphine-naloxone treatment between January 2010 and July 2012 in 11 states. We used logistic regression to assess treatment duration longer than 6 months. We used accelerated failure time models to assess risk of treatment discontinuation. We used ordinary least squares regression to assess mean daily dosage. For patients with ≥3 fills, we also used logistic regression to assess whether ;an individual had a medication possession ratio of <80% and/or gaps in treatment >14 days. Models adjusted for individual demographics, prescribing physician specialty, state, and county-level variables.

Results:
Overall, 41% of individuals were retained in treatment for at least 6 months and the mean treatment length was 266 days. Compared with individuals who paid primarily for treatment with cash, adjusted odds of 6 month retention were significantly lower for individuals with primary payment from Medicaid fee-for-service, Medicare part D, and third-party commercial. There were substantial differences in 6-month retention across states with the lowest in Arizona and highest in New York. Low-possession ratios occurred for 30% of individuals and 26% experienced treatment episodes with gaps >14 days. Odds of low-possession and treatment gaps were largely similar across demographic groups and geographic areas.

Conclusions:
Current initiatives to improve access and quality of buprenorphine-naloxone treatment should examine geographic barriers as well as the potential role of insurance benefit design in restricting treatment length.
Distinct subtype distribution and somatic mutation spectrum of lymphomas in East Asia
Authors: Ren Weicheng , Li Wei , Ye Xiaofei , Liu Hui , Pan-Hammarström Qiang 
Published: April 2017

Purpose of review
Here, we give an updated overview of the subtype distribution of lymphomas in East Asia and also present the genome sequencing data on two major subtypes of these tumors.

Recent findings
The distribution of lymphoma types/subtypes among East Asian countries is very similar, with a lower proportion of B-cell malignancies and a higher proportion of T/natural killer (NK)-cell lymphomas as compared to Western populations. Extranodal NK/T-cell lymphoma is more frequently observed in East Asia, whereas follicular lymphoma and chronic lymphocytic leukemia, are proportionally lower. The incidence rate of lymphoma subtypes in Asians living in the US was generally intermediate to the general rate in US and Asia, suggesting that both genetic and environmental factors may underlie the geographical variations observed.
Key cancer driver mutations have been identified in Asian patients with diffuse large B-cell lymphoma or extranodal NK/T-cell lymphoma through genome sequencing. A distinct somatic mutation profile has also been observed in Chinese diffuse large B-cell lymphoma patients.

Summary
The incidence and distribution of lymphoma subtypes differed significantly between patients from East Asia and Western countries, suggesting subtype-specific etiologic mechanisms. Further studies on the mechanism underlying these geographical variations may give new insights into our understanding of lymphomagenesis.
Perceived Stress, Parent-Adolescent/Young Adult Communication, and Family Resilience Among Adolescents/Young Adults Who Have a Parent With Cancer in Taiwan
Authors: Chen Chin-Mi , Du Bao-Feng , Ho Ching-Liang , Ou Wei-Jen , Chang Yue-Cune , Chen Wei-Ching 
Published: April 2017

Background:
Family resilience helps family members successfully overcome adversity, for example, chronic disease or unpleasant situations. However, few studies have identified correlates of family resilience among adolescents/young adults having a parent with cancer.

Objective:
This longitudinal study explored (1) relationships among family resilience, adolescents’ perceived stress, and parent-adolescent/young adult communication; (2) trends in family resilience with data collection time; and (3) differences in parent-adolescent/young adult communication by parent gender (ie, father or mother).

Methods:
Participants were teenagers and young adults (12–25 years) with a parent who had cancer. Data were collected using structured questionnaires at 3 times for 4 to 5 months, with 2 months between each collection.

Results:
Of 96 adolescent/young adult participants enrolled at T1, only 32 completed all measurements at T3. We found that (1) family resilience was negatively associated with adolescents’ perceived stress (B = −0.35) and positively associated with adolescent/young adult communication with both the father (B = 0.58) and the mother (B = 0.36), (2) the degree of family resilience at T3 was significantly lower than at T1 (B = −4.79), and (3) at all 3 data collection times, the degree of adolescent/young adult communication was higher with mothers than with fathers, whether the mother had cancer or did not have cancer.

Conclusions:
Family resilience was positively associated with parent-adolescent/young adult communication and negatively related to perceived stress. Family resilience tended to decline with longer parental survival since cancer diagnosis.

Implications for Practice:
We suggest nursing interventions to reduce adolescent/young adult stress and develop optimal parent-adolescent/young adult communication to enhance family resilience.
Self-Identity After Bereavement
Authors: Boelen Paul A. 
Published: April 2017

Abstract
There is evidence that both the centrality of a loss-event as well as reduced self-concept clarity are involved in emotional problems after the death of a loved one. One issue that is still unexplored is the relative importance of these two concepts in predicting bereavement outcome. The current study examined the degree to which both concepts contribute to emotional distress after loss, both concurrently and longitudinally. Data were available from 124 individuals, all bereaved within the previous half year, who completed measures of prolonged grief, posttraumatic stress, and depression at inclusion into the study and again 6 months later. Loss-centrality and self-unclarity were associated with all three outcome measures, in cross-sectional analyses. Longitudinal analyses indicated that loss-centrality predicted symptom levels of prolonged grief, self-unclarity predicted symptom levels of depression, and both loss-centrality and self-unclarity were associated with posttraumatic stress 6 months after baseline. Implications of these findings are discussed.
Implementation of an ICU Bundle: An Interprofessional Quality Improvement Project to Enhance Delirium Management and Monitor Delirium Prevalence in a Single PICU*
Authors: Simone Shari , Edwards Sarah , Lardieri Allison , Walker L. Kyle , Graciano Ana Lia , Kishk Omayma A. , Custer Jason W. 
Published: April 2017

Objectives:
To examine the impact of an ICU bundle on delirium screening and prevalence and describe characteristics of delirium cases.

Design:
Quality improvement project with prospective observational analysis.

Setting:
Nineteen-bed PICU in an urban academic medical center.

Patients:
All consecutive patients admitted from December 1, 2013, to September 30, 2015.

Interventions:
A multidisciplinary team implemented an ICU bundle consisting of three clinical protocols: delirium, sedation, and early mobilization using the Plan-Do-Study-Act cycles as part of a quality improvement project. The delirium protocol implemented in December 2013 consisted of universal screening with the Cornell Assessment of Pediatric Delirium revised instrument, prevention and treatment strategies, and case conferences. The sedation protocol and early mobilization protocol were implemented in October 2014 and June 2015, respectively.

Measurements and Main Results:
One thousand eight hundred seventy-five patients were screened using the Cornell Assessment of Pediatric Delirium revised tool. One hundred forty patients (17%) had delirium (having Cornell Assessment of Pediatric Delirium revised scores ≥ 9 for 48 hr or longer). Seventy-four percent of delirium positive patients were mechanically ventilated of which 46% were younger than 12 months and 59% had baseline developmental delays. Forty-one patients had emerging delirium (having one Cornell Assessment of Pediatric Delirium revised score ≥ 9). Statistical process control was used to evaluate the impact of three ICU bundle process changes on monthly delirium rates over a 22-month period. The delirium rate decreased with the implementation of each phase of the ICU bundle. Ten months after the delirium protocol was implemented, the mean delirium rate was 19.3%; after the sedation protocol and early mobilization protocols were implemented, the mean delirium rate was 11.84%.

Conclusions:
Implementation of an ICU bundle along with staff education and case conferences is effective for improving delirium screening, detection, and treatment and is associated with decreased delirium prevalence.
Ultrasound-Guided S1 Transforaminal Epidural Injection Using the In-Plane Approach and Color Doppler Imaging
Authors: Park Donghwi 
Published: April 2017

Abstract
Recently, several studies have investigated the effectiveness of the ultrasound-guided lumbosacral transforaminal epidural injection. However, the ultrasound-guided S1 transforaminal epidural injection using an out-of-plane approach, which was previously reported, may cause an intestinal injury or intravascular injection because the needle tip tends to be invisible in the out-of-plane approach. In this study, therefore, we report a new method of ultrasound-guided S1 transforaminal epidural injection using the in-plane approach and color Doppler. In addition, we also report the usefulness of color Doppler imaging for finding the S1 foramen and confirming the accuracy of the injection.
Association of Need for Tracheotomy With Decreasing Mechanical In-Exsufflation Flows in Amyotrophic Lateral Sclerosis
Authors: Bach John R. , Upadhyaya Neelam 
Published: April 2017

Abstract
Although patients with lower motor neuron and myopathic disorders can prolong their lives by depending on continuous noninvasive ventilatory support, most patients with amyotrophic lateral sclerosis (ALS) cannot and must use tracheostomy mechanical ventilation to prolong survival. This case demonstrates that this occurs because amyotrophic lateral sclerosis patients' upper motor neuron reflex laryngeal closure and stridor cause upper airway collapse that renders mechanical insufflation-exsufflation (MIE) ineffective in expulsing airway secretions as well as for permitting continuous noninvasive ventilatory support. A decrease in MIE-exsufflation flows is a marker for a decrease in upper airway patency that renders MIE ineffective. As airway secretions accumulate and baseline oxyhemoglobin saturation decreases, tracheotomy becomes necessary for further survival. This case demonstrates an association between diminishing MIE-exsufflation flow and need to resort to tracheotomy.
Subjective General Health and the Social Regulation of Hypothalamic Activity
Authors: Brown Casey L. , Beckes Lane , Allen Joseph P. , Coan James A. 
Published: April 2017

ABSTRACT

Objective
Social support is associated with better health. This association may be partly mediated through the social regulation of adrenomedullary activity related to poor cardiovascular health and glucocorticoid activity known to inhibit immune functioning. These physiological cascades originate in the hypothalamic areas that are involved in the neural response to threat. The aim of the study investigated whether the down regulation, by social support, of hypothalamic responses to threat is associated with better subjective health.

Methods
A diverse community sample of seventy-five individuals, aged 23 to 26 years, were recruited from an ongoing longitudinal study. Participants completed the Short Form Health Survey, a well-validated self-report measure used to assess subjective general health. They were scanned, using functional magnetic resonance imaging, during a threat of shock paradigm involving various levels of social support, which was manipulated using handholding from a close relational partner, a stranger, and an alone condition. We focused on a hypothalamic region of interest derived from an independent sample to examine the association between hypothalamic activity and subjective general health.

Results
Results revealed a significant interaction between handholding condition and self-reported general health (F(2,72) = 3.53, p = .032, partial η2 = 0.05). Down regulation of the hypothalamic region of interest during partner handholding corresponded with higher self-ratings of general health (ß = −0.31, p = .007).

Conclusions
Higher self-ratings of general health correspond with decreased hypothalamic activity during a task that blends threat with supportive handholding. These results suggest that associations between social support and health are partly mediated through the social regulation of hypothalamic sensitivity to threat.
Improved HIV and TB Knowledge and Competence Among Mid-level Providers in a Cluster-Randomized Trial of One-on-One Mentorship for Task Shifting
Authors: Naikoba Sarah , Senjovu Kaggwa D. , Mugabe Pallen , McCarthy Carey F. , Riley Patricia L. , Kadengye Damazo T. , Dalal Shona 
Published: April 2017

Introduction:
Health worker shortages pose a challenge to the scale up of HIV care and treatment in Uganda. Training mid-level providers (MLPs) in the provision of HIV and tuberculosis (TB) treatment can expand existing health workforce capacity and access to HIV services.

Methods:
We conducted a cluster-randomized trial of on-site clinical mentorship for HIV and TB care at 10 health facilities in rural Uganda. Twenty MLPs at 5 randomly assigned to an intervention facilities received 8 hours a week of one-on-one mentorship, every 6 weeks over a 9-month period; and another 20 at 5 control facilities received no clinical mentorship. Enrolled MLPs' clinical knowledge and competence in management of HIV and TB was assessed using case scenarios and clinical observation at baseline and immediately after the 9-month intervention. The performance of the study health facilities on 8 TB and HIV care indicators was tracked over the 9-month period using facility patient records.

Results:
Thirty-nine out 40 enrolled MLPs had case scenario and clinical observation scores for both the baseline and end of intervention assessments. Mentorship was associated with a mean score increase of 16.7% (95% confidence interval: 9.8 to 23.6, P < 0.001) for the case scenario assessments and 25.9% (95% confidence interval: 14.4 to 37.5, P < 0.001) for the clinical observations. On-site clinical mentorship was significantly associated with an overall improvement for 5 of the 8 health facility TB and HIV indicators tracked.

Conclusions:
One-on-one on-site mentorship improves individual knowledge and competence, has a downstream effect on facility performance, and is a simple approach to training MLPs for task shifting.
Evaluation of the Angus ICD9-CM Sepsis Abstraction Criteria
Authors: Horng Steven , Nathanson Larry A. , Sontag David A. , Shapiro Nathan I. 
Published: April 2017

AbstractObjectiveValidate the infection component of the Angus International Classification of Diseases, Ninth Revision, Clinical Modification (ICD9-CM) sepsis abstraction criteriaDesignObservational cohort studySetting55,000 visits/year Adult Emergency Department (ED)PatientsAll consecutive ED patient visits between 12/16/2011 and 08/13/2012 were included in the study. Patients were excluded if there was a missing outcome measure.InterventionsNone.Measurements and Main ResultsThe primary outcome measure was suspected infection at conclusion of the ED work-up as judged by the physician. There were 34,796 patients who presented to the ED between 12/16/11 and 8/13/12, of which 31,755 (91%) patients were included and analyzed. The original Angus sepsis abstraction criteria had a sensitivity of 55%, specificity of 97%, PPV of 82%, NPV of 88%, accuracy of 87%, and a F1score of 0.66. The modified Angus sepsis abstraction criteria which includes codes added after the original publication had a sensitivity of 65%, specificity of 96%, PPV of 81%, NPV of 91%, accuracy of 89%, and F1score of 0.72.ConclusionsIn our study, the Angus abstraction criteria have high specificity (97%), but moderate sensitivity (55%) in identifying patients with suspected infection as defined by physician at the time of disposition from the emergency department. Given these findings, it is likely that we are underestimating the true incidence of sepsis in the United States and worldwide.
Why do scientists fabricate and falsify data? A matched-control analysis of papers containing problematic image duplications
Authors: Fanelli Daniele , Costas Rodrigo , Fang Ferric C. , Casadevall Arturo , Bik Elisabeth M. 
Published: April 2017

ABSTRACTIt is commonly hypothesized that scientists are more likely to engage in data falsification and fabrication when they are subject to pressures to publish, when they are not restrained by forms of social control, when they work in countries lacking policies to tackle scientific misconduct, and when they are male. Evidence to test these hypotheses, however, is inconclusive due to the difficulties of obtaining unbiased data.Here we report a pre-registered test of these four hypotheses, conducted on papers that were identified in a previous study as containing problematic image duplications through a systematic screening of the journal PLoS ONE. Image duplications were classified into three categories based on their complexity, with category 1 being most likely to reflect unintentional error and category 3 being most likely to reflect intentional fabrication. Multiple parameters connected to the hypotheses above were tested with a matched-control paradigm, by collecting two controls for each paper containing duplications.Category 1 duplications were mostly not associated with any of the parameters tested, in accordance with the assumption that these duplications were mostly not due to misconduct. Category 2 and 3, however, exhibited numerous statistically significant associations. Results of univariable and multivariable analyses support the hypotheses that academic culture, peer control, cash-based publication incentives and national misconduct policies might affect scientific integrity. Significant correlations between the risk of image duplication and individual publication rates or gender, however, were only observed in secondary and exploratory analyses.Country-level parameters generally exhibited effects of larger magnitude than individual-level parameters, because a subset of countries was significantly more likely to produce problematic image duplications. Promoting good research practices in all countries should be a priority for the international research integrity agenda.
Interactome INSIDER: a multi-scale structural interactome browser for genomic studies
Authors: Meyer Michael J. , Beltrán Juan Felipe , Liang Siqi , Fragoza Robert , Rumack Aaron , Liang Jin , Wei Xiaomu , Yu Haiyuan 
Published: April 2017

ABSTRACTProtein interactions underlie nearly all known cellular function, making knowledge of their binding conformations paramount to understanding the physical workings of the cell. Studying binding conformations has allowed scientists to explore some of the mechanistic underpinnings of disease caused by disruption of protein interactions. However, since experimentally determined interaction structures are only available for a small fraction of the known interactome such inquiry has largely excluded functional genomic studies of the human interactome and broad observations of the inner workings of disease. Here we present Interactome INSIDER, an information center for genomic studies using the first full-interactome map of human interaction interfaces. We applied a new, unified framework to predict protein interaction interfaces for 184,605 protein interactions with previously unresolved interfaces in human and 7 model organisms, including the entire experimentally determined human binary interactome. We find that predicted interfaces share several known functional properties of interfaces, including an enrichment for disease mutations and recurrent cancer mutations, suggesting their applicability to functional genomic studies. We also performed 2,164de novomutagenesis experiments and show that mutations of predicted interface residues disrupt interactions at a similar rate to known interface residues and at a much higher rate than mutations outside of predicted interfaces. To spur functional genomic studies in the human interactome, Interactome INSIDER (http://interactomeinsider.yulab.org) allows users to explore known population variants, disease mutations, and somatic cancer mutations, or upload their own set of mutations to find enrichment at the level of protein domains, residues, and 3D atomic clustering in known and predicted interaction interfaces.