bluuebunny/crossref_metadata_2025_split huggingface dataset:
Final report on APMP.T-K7.1 key comparison of water triple point cells, bilateral NMIJ-VMI
Authors: Yamazawa Kazuaki , Nakano Tohru , Binh Pham Thanh 
Published: April 2018

APMP.T-K7.1, was held from July 2014 to May 2015 to compare the national realizations of the water triple point between NMIJ (Japan) and VMI (Vietnam). To reach the objective, VMI sent a transfer cell to NMIJ and stated a value for the temperature difference of the transfer cell, relative to the corresponding national standard, representing 273.16 K.
This report presents the results of the TPW comparison, gives detailed information about the measurements made at the NMIJ and at the VMI, and aims to link the results of APMP.T-K7.1 to APMP.T-K7 and CCT-K7. The results of this key comparison are also represented in the form of degrees of equivalence for the purposes of the MRA.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCT, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
TRUmiCount: correctly counting absolute numbers of molecules using unique molecular identifiers
Authors: Pflug Florian G , von Haeseler Arndt 
Published: April 2018

Abstract

Motivation
Counting molecules using next-generation sequencing (NGS) suffers from PCR amplification bias, which reduces the accuracy of many quantitative NGS-based experimental methods such as RNA-Seq. This is true even if molecules are made distinguishable using unique molecular identifiers (UMIs) before PCR amplification, and distinct UMIs are counted instead of reads: Molecules that are lost entirely during the sequencing process will still cause underestimation of the molecule count, and amplification artifacts like PCR chimeras create phantom UMIs and thus cause over-estimation.

Results
We introduce the TRUmiCount algorithm to correct for both types of errors. The TRUmiCount algorithm is based on a mechanistic model of PCR amplification and sequencing, whose two parameters have an immediate physical interpretation as PCR efficiency and sequencing depth and can be estimated from experimental data without requiring calibration experiments or spike-ins. We show that our model captures the main stochastic properties of amplification and sequencing, and that it allows us to filter out phantom UMIs and to estimate the number of molecules lost during the sequencing process. Finally, we demonstrate that the phantom-filtered and loss-corrected molecule counts computed by TRUmiCount measure the true number of molecules with considerably higher accuracy than the raw number of distinct UMIs, even if most UMIs are sequenced only once as is typical for single-cell RNA-Seq.

Availability and implementation
TRUmiCount is available at http://www.cibiv.at/software/trumicount and through Bioconda (http://bioconda.github.io).

Supplementary information
Supplementary information is available at Bioinformatics online.
Association of Frailty With Recovery From Disability Among Community-Dwelling Older Adults: Results From Two Large U.S. Cohorts
Authors: Wu Chenkai , Kim Dae H , Xue Qian-Li , Lee David S H , Varadhan Ravi , Odden Michelle C 
Published: April 2018

Abstract

Background
Disability in activities of daily living (ADLs) is a dynamic process and transitions among different disability states are common. However, little is known about factors affecting recovery from disability. We examined the association between frailty and recovery from disability among nondisabled community-dwelling elders.

Methods
We studied 1,023 adults from the Cardiovascular Health Study (CHS) and 685 adults from the Health and Retirement Study (HRS), who were ≥65 years and had incident disability, defined as having difficulty in ≥1 ADL (dressing, eating, toileting, bathing, transferring, walking across a room). Disability recovery was defined as having no difficulty in any ADLs. Frailty was assessed by slowness, weakness, exhaustion, inactivity, and shrinking. Persons were classified as “nonfrail” (0 criteria), “prefrail” (1–2 criteria), or “frail” (3–5 criteria).

Results
In total, 539 (52.7%) CHS participants recovered from disability within 1 year. Almost two-thirds of nonfrail persons recovered, while less than two-fifths of the frail recovered. In the HRS, 234 (34.2%) participants recovered from disability within 2 years. Approximately half of the nonfrail recovered, while less than one-fifth of the frail recovered. After adjustment, prefrail and frail CHS participants were 16% and 36% less likely to recover than the nonfrail, respectively. In the HRS, frail persons had a 41% lower likelihood of recovery than the nonfrail.

Conclusions
Frailty is an independent predictor of poor recovery from disability among nondisabled older adults. These findings validate frailty as a marker of decreased resilience and may offer opportunities for individualized interventions and geriatric care based on frailty assessment.
Variability in adolescent portal privacy features: how the unique privacy needs of the adolescent patient create a complex decision-making process
Authors: Sharko Marianne , Wilcox Lauren , Hong Matthew K , Ancker Jessica S 
Published: April 2018

Abstract

Objective
Medical privacy policies, which are clear-cut for adults and young children, become ambiguous during adolescence. Yet medical organizations must establish unambiguous rules about patient and parental access to electronic patient portals. We conducted a national interview study to characterize the diversity in adolescent portal policies across a range of institutions and determine the factors influencing decisions about these policies.

Methods
Within a sampling framework that ensured diversity of geography and medical organization type, we used purposive and snowball sampling to identify key informants. Semi-structured interviews were conducted and analyzed with inductive thematic analysis, followed by a member check.

Results
We interviewed informants from 25 medical organizations. Policies established different degrees of adolescent access (from none to partial to complete), access ages (from 10 to 18 years), degrees of parental access, and types of information considered sensitive. Federal and state law did not dominate policy decisions. Other factors in the decision process were: technology capabilities; differing patient population needs; resources; community expectations; balance between information access and privacy; balance between promoting autonomy and promoting family shared decision-making; and tension between teen privacy and parental preferences. Some informants believed that clearer standards would simplify policy-making; others worried that standards could restrict high-quality polices.

Conclusions
In the absence of universally accepted standards, medical organizations typically undergo an arduous decision-making process to develop teen portal policies, weighing legal, economic, social, clinical, and technological factors. As a result, portal access policies are highly inconsistent across the United States and within individual states.
Predictors of Unplanned Reoperation After Operative Treatment of Pelvic Ring Injuries
Authors: Ochenjele George , Reid Kristoff R. , Castillo Renan C. , Schoonover Carrie D. , Montalvo Ryan N. , Manson Theodore T. , Sciadini Marcus F. , Nascone Jason W. , Carlini Anthony R. , O'Toole Robert V. 
Published: April 2018

Objectives:
To evaluate the incidence of unplanned reoperations after pelvic ring injuries and to develop a risk prediction model.

Design:
Retrospective review.

Setting:
Level I Trauma Center.

Patients:
The medical records of 913 patients (644 male and 269 female patients; mean age, 39 years; age range, 16–89 years) with unstable pelvic ring fractures operatively treated at our center from 2003 to 2015 were reviewed.

Intervention:
Multiple logistic regression analysis was conducted to evaluate the relative contribution of associated clinical parameters to unplanned reoperations. A risk prediction model was developed to assess the effects of multiple covariates.

Main Outcome Measurements:
Unplanned reoperation for infection, fixation failure, heterotopic ossification, or bleeding complication.

Results:
Unplanned reoperations totaled 137 fractures, with an overall rate of 15% (8% infection, 6% fixation failure, <1% heterotopic ossification, and <1% bleeding complication). Reoperations for infection and fixation failure typically occurred within the first month after the index procedure. Four independent predictors of reoperation were open fractures, combined pelvic ring and acetabular injuries, abdominal visceral injuries, and increasing pelvic fracture grade. No independent association was shown between reoperation and patient, treatment, or other injury factors.

Conclusions:
Unplanned reoperations were relatively common. Infection and fixation failure were the most common indications for unplanned reoperations. Factors associated with reoperation are related to severity of pelvic and abdominal visceral injuries. Our findings suggest that these complications might be inherent and in many cases unavoidable despite appropriate current treatment strategies.

Level of Evidence:
Prognostic Level III. See Instructions for Authors for a complete description of levels of evidence.
Tumoral Calcinosis: A Giant Tumoral Mass in the Shoulder Joint of a Dialysis Patient
Authors: Chi Daekwan , Kamochi Hideaki , Sunaga Ataru , Sarukawa Shunji , Uda Hirokazu , Nakagawa Shiho , Asahi Rintaro , Mori Masanori , Yoshimura Kotaro 
Published: April 2018

Summary:
Tumoral calcinosis is a rare condition in which a calcified mass grows around a large joint, and can occur in patients undergoing renal dialysis. Here, we report the case of a 64-year-old man with a long history of dialysis who presented with a giant, painless mass in his right shoulder joint. A near-complete surgical resection is performed without muscle function loss and with no sign of recurrence after 1 year.
Technique Refinement in Prepectoral Implant Breast Reconstruction with Vicryl Mesh Pocket and Acellular Dermal Matrix Support
Authors: Gfrerer Lisa , Liao Eric C. 
Published: April 2018

Summary:
Direct-to-implant reconstruction after mastectomy is routinely performed with excellent oncologic and aesthetic outcomes. Several different techniques for placement of the prosthesis including total and partial subpectoral coverage have been described. Prepectoral implant placement is increasingly reported as a safe method, while patient selection and techniques are areas of further work. Most prepectoral prosthesis placement techniques describe complete acellular dermal matrix (ADM) coverage of the implant, often requiring multiple or larger ADM sheets than a comparable subpectoral implant procedure, resulting in high cost per reconstructed breast. This article describes the use of a vicryl mesh pocket and ADM support in prepectoral breast reconstruction achieving predicable and safe results at a lower cost.
Optimum Detection of Ureaplasma in Premature Infants
Authors: Brand M. Colleen , Mandy George T. , Arora Sushrut , Castro Eumenia C. , Gordon Pamela S. , Hagan Joseph L. , Zodin Amy L. , Weisman Leonard E. 
Published: April 2018

Background:

Ureaplasma spp. is a known risk factor for bronchopulmonary dysplasia in premature infants. Emerging research suggests treatment with azithromycin or clarithromycin in the first days of life (DOLs) reduces bronchopulmonary dysplasia in Ureaplasma spp. positive infants. Side effects of these antibiotics make it imperative to optimize reliable noninvasive screening procedures to identify infants who would benefit from treatment.

Methods:
The aim of this study was to determine the best site and time to screen for Ureaplasma spp. in 24- to 34-week premature infants. Oral, nasal, gastric and tracheal cultures were collected and placed immediately in 10B broth media. Polymerase chain reaction verified culture results and identified the Ureaplasma spp.

Results:
Cultures yielded a Ureaplasma spp. incidence of 80/168 = 47.6% [95% confidence interval (CI): 40–56]. Nasal cultures had greater sensitivity to detect Ureaplasma spp. than oral cultures (P = 0.008): however, a significant proportion of infants with Ureaplasma spp. would have been missed (12/79 = 15.2%, 95% CI: 8%–25%, P < 0.001) if oral cultures were not obtained. For all sites, the collection at DOL 7–10 were more likely to be positive than the collection at DOL 1–2: however, a significant proportion (5/77 = 6.5%, 95% CI: 2–15, P < 0.001) of infants with Ureaplasma spp. would have been missed if the DOL 1–2 cultures were not obtained.

Conclusions:
For optimal Ureaplasma spp. detection in 24- to 34-week premature infants, cultures need to be taken both early and late in the first 10 DOLs both from nasal and oral secretions.
An Individualized 3-Dimensional Designed and Printed Conformer After Dermis Fat Grafting for Complex Sockets
Authors: Mourits Daphne L. , Remmers Jelmer S. , Tan Stevie H. , Moll Annette C. , Hartong Dyonne T. 
Published: April 2018

Purpose:
To introduce a novel technique to design individually customized conformers for postenucleation sockets with dermis fat implants.

Methods:
We use a 3-dimensional scan of the frontal face/orbit and eyelid contour to design an individualized conformer. This polymethylmetacrylate printed conformer is adapted to patients’ socket, palpebral fissures, horizontal eyelid aperture, curvature of the eyelids, and mean diameter of patients’ contralateral eye. Sutures through holes in the inferior part of the conformer and in the extension can be placed to fixate the conformer and anchor fornix deepening sutures.

Results:
A correct fitting conformer can be printed and attached to the socket and eyelids. The shape of this conformer can be used subsequently postsurgically to design the ocular prosthesis.

Conclusion:
Presurgical planning is important to anticipate for a functional socket to adequately fit an artificial eye. The presented technique using 3-dimensional imaging, designing, and printing promises to prevent conformer extrusion and forniceal shortening.
Achieving Outcomes With Innovative Smart Pump Technology
Authors: Lehr Jennifer , Vitoux Rachel R. , Evanovich Zavotsky Kathleen , Pontieri-Lewis Vicky , Colineri Lori 
Published: April 2018

Background:
A 5-time designated Magnet academic medical center partnered with its infusion systems supplier to successfully integrate 1327 smart pumps across 45 departments with an aggressive 3-month timeline. The team also achieved quality improvement (QI) outcomes through increased drug library compliance and decreased alerts with their new technology.

Problem:
This large academic medical center needed to implement innovative wireless infusion pump technology in a short time frame.

Approach:
The approach involved a strong partnership from the medical center and the supplier, with extensive planning and collaboration among the clinical nurse specialists and consultants from both organizations to accomplish QI goals. Lean principles were also followed to enhance efficiency and accountability.

Outcomes:
Quality improvement outcomes included 100% drug library compliance across all 6 intensive care units, a decrease in pump alert rates from 4.18% to 0.79%, and a decrease in pump programming correction rate from 0.36% to 0.06%.

Conclusions:
A partnership led to a large implementation being completed efficiently across an academic medical center. Through these joint efforts, quality of care was improved within a short period of time.
Effects of an Interdisciplinary Practice Bundle for Second-Stage Labor on Clinical Outcomes
Authors: Garpiel Susan J. 
Published: April 2018

Abstract

Background:
There is renewed interest in second-stage labor practices as recent evidence has challenged historical perspectives on safe duration of second-stage labor. Traditional practices and routine interventions during second-stage have uncertain benefit for low-risk women and may result in cesarean birth.

Purpose:
The purpose of this quality improvement project was to implement an interdisciplinary second-stage practice bundle to promote safe outcomes including method of birth and women's birth experience.

Methods:
Standardized second-stage labor evidence-based practice recommendations structured into a 5 Ps practice bundle (patience, positioning, physiologic resuscitation, progress, preventing urinary harm) were implemented across 34 birthing hospitals in the Trinity Health system.

Results:
Significant improvements were observed in second-stage practices. Association of Women's Health, Obstetric and Neonatal Nurses' perinatal nursing care quality measure Second-Stage of Labor: Mother-Initiated Spontaneous Pushing significantly improved [pre-implementation 43% (510/1,195), post-implementation 76% (1,541/2,028), p < .0001]. Joint Commission Perinatal Care-02: nulliparous, term, singleton, vertex cesarean rate significantly decreased (p = 0.02) with no differences in maternal morbidity, or negative newborn birth outcomes. Unexpected complications in term births significantly decreased in all newborns (p < 0.001), and for newborns from vaginal births (p = 0.03). Birth experience satisfaction rose from the 69th to the 81st percentile.

Clinical Implications:
Implementing 13 evidence-based second-stage labor practices derived from the Association of Women's Health, Obstetric and Neonatal Nurses and the American College of Nurse-Midwives professional guidelines achieved our goals of safely reducing primary cesarean birth among low-risk nulliparous women, and optimizing maternal and fetal outcomes associated with labor and birth. By minimizing routine interventions, nurses support physiologic birth and improve women's birth satisfaction.
Disease-modifying treatments for early and advanced multiple sclerosis: a new treatment paradigm
Authors: Giovannoni Gavin 
Published: April 2018

Purpose of review
The treatment of multiple sclerosis is evolving rapidly with 11 classes of disease-modifying therapies (DMTs). This article provides an overview of a new classification system for DMTs and treatment paradigm for using these DMTs effectively and safely.

Recent findings
A summary of research into the use of more active approaches to early and effective treatment of multiple sclerosis with defined treatment targets of no evident disease activity (NEDA). New insights are discussed that is allowing the field to begin to tackle more advanced multiple sclerosis, including people with multiple sclerosis using wheelchairs. However, the need to modify expectations of what can be achieved in more advanced multiple sclerosis are discussed; in particular, the focus on neuronal systems with reserve capacity, for example, upper limb, bulbar and visual function.

Summary
The review describes a new more active way of managing multiple sclerosis and concludes with a call to action in solving the problem of slow adoption of innovations and the global problem of untreated, or undertreated, multiple sclerosis.
The Queen Gut Refines with Age: Longevity Phenotypes in a Social Insect Model
Authors: Anderson Kirk E. , Ricigliano Vincent A. , Mott Brendon M. , Copeland Duan C. , Floyd Amy S. , Maes Patrick 
Published: April 2018

AbstractBackgroundIn social insects, identical genotypes can show extreme lifespan variation providing a unique perspective on age-associated microbial succession. In honey bees, short and long-lived host phenotypes are polarized by a suite of age-associated factors including hormones, nutrition, immune senescence and oxidative stress. Similar to other model organisms, the aging gut microbiota of short-lived (worker) honey bees accrue Proteobacteria and are depleted of Lactobacillus and Bifidobacterium, consistent with a suite of host senescence markers. In contrast, long-lived (queen) honey bees maintain youthful cellular function without expressing oxidative stress genes, suggesting a very different host environment for age-associated microbial succession.ResultsWe sequenced the microbiota of 63 honey bee queens exploring two chronological ages and four alimentary tract niches. To control for individual variation we quantified carbonyl accumulation in queen fat body tissue as a proxy for biological aging. We compared our results to the age-specific microbial succession of worker guts. Accounting for queen source variation, two or more bacterial species per niche differed significantly by queen age. Biological aging in queens was correlated with microbiota composition highlighting the relationship of microbiota with oxidative stress. Queens and workers shared many major gut bacterial species, but differ markedly in community structure and age succession. In stark contrast to aging workers, carbonyl accumulation in queens was significantly associated with increased Lactobacillus and Bifidobacterium and depletion of various Proteobacteria.ConclusionsWe present a model system linking changes in gut microbiota to diet and longevity, two of the most confounding variables in human microbiota research. As described for other model systems, metabolic changes associated with diet and host longevity correspond to the changing microbiota. The pattern of age-associated succession in the queen microbiota is largely the reverse of that demonstrated for workers. The guts of short-lived worker phenotypes are progressively dominated by three major Proteobacteria, but these same species were sparse or significantly depleted in long-lived queen phenotypes. More broadly, our results suggest that lifespan evolution formed the context for host-microbial interactions and age-related succession of honey bee microbiota.
Low-frequency variant functional architectures reveal strength of negative selection across coding and non-coding annotations
Authors: Gazal Steven , Loh Po-Ru , Finucane Hilary K. , Ganna Andrea , Schoech Armin , Sunyaev Shamil , Price Alkes L. 
Published: April 2018

AbstractCommon variant heritability is known to be concentrated in variants within cell-type-specific non-coding functional annotations, with a limited role for common coding variants. However, little is known about the functional distribution of low-frequency variant heritability. Here, we partitioned the heritability of both low-frequency (0.5% ≤ MAF < 5%) and common (MAF ≥ 5%) variants in 40 UK Biobank traits (average N = 363K) across a broad set of coding and non-coding functional annotations, employing an extension of stratified LD score regression to low-frequency variants that produces robust results in simulations. We determined that non-synonymous coding variants explain 17±1% of low-frequency variant heritabilityversus only 2.1±0.2% of common variant heritability, and that regions conserved in primates explain nearly half of(43±2%). Other annotations previously linked to negative selection, including non-synonymous variants with high PolyPhen-2 scores, non-synonymous variants in genes under strong selection, and low-LD variants, were also significantly more enriched foras compared to. Cell-type-specific non-coding annotations that were significantly enriched forof corresponding traits tended to be similarly enriched forfor most traits, but more enriched for brain-related annotations and traits. For example, H3K4me3 marks in brain DPFC explain 57±12% ofvs. 12±2% offor neuroticism, implicating the action of negative selection on low-frequency variants affecting gene regulation in the brain. Forward simulations confirmed that the ratio of low-frequency variant enrichment vs. common variant enrichment primarily depends on the mean selection coefficient of causal variants in the annotation, and can be used to predict the effect size variance of causal rare variants (MAF < 0.5%) in the annotation, informing their prioritization in whole-genome sequencing studies. Our results provide a deeper understanding of low-frequency variant functional architectures and guidelines for the design of association studies targeting functional classes of low-frequency and rare variants.