bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-Quality Whole-Genome Sequences for 59 Historical Shigella Strains Generated with PacBio Sequencing
Authors: Kim Justin , Lindsey Rebecca L. , Garcia-Toledo Lisley , Loparev Vladimir N. , Rowe Lori A. , Batra Dhwani , Juieng Phalasy , Stoneburg Devon , Martin Haley , Knipe Kristen , Smith Peyton , Strockbine Nancy 
Published: April 2018

ABSTRACT

Shigella
spp. are enteric pathogens that cause shigellosis. We report here the high-quality whole-genome sequences of 59 historical
Shigella
strains that represent the four species and a variety of serotypes.
Draft Genome Sequence of Strain B 225, an Iron-Depositing Isolate of the Genus Novosphingobium
Authors: Braun Burga , Künzel Sven , Szewzyk Ulrich 
Published: April 2018

ABSTRACT

Here, we report the draft genome sequence of
Novosphingobium
sp. strain B 225, an iron-depositing bacterium isolated from a phenazone-amended naturally grown biofilm. This biofilm was grown in the Unteres Odertal National Park, Germany. Illumina NextSeq sequencing was used to determine the genome of the strain.
Draft Genomic Sequences of Chromobacterium sp. nov. Strains MWU13-2610 and MWU14-2602, Isolated from Wild Cranberry Bogs in Massachusetts
Authors: O’Hara-Hanley Kory , Harrison Alisha , Soby Scott D. 
Published: April 2018

ABSTRACT

Chromobacterium
sp. nov. strains MWU13-2610 and MWU14-2602 were isolated from cranberry bogs in the Cape Cod National Seashore. These nonpigmented bacteria represent two new presumptive species of the rapidly growing genus
Chromobacterium
. Gene homologs are present for multiple antibiotic resistance, virulence functions, and prophages.
T Cell-Independent Gamma Interferon and B Cells Cooperate To Prevent Mortality Associated with Disseminated Chlamydia muridarum Genital Tract Infection
Authors: Poston Taylor B. , O'Connell Catherine M. , Girardi Jenna , Sullivan Jeanne E. , Nagarajan Uma M. , Marinov Anthony , Scurlock Amy M. , Darville Toni 
Published: April 2018

ABSTRACTCD4 T cells and antibody are required for optimal acquired immunity toChlamydia muridarumgenital tract infection, and T cell-mediated gamma interferon (IFN-γ) production is necessary to clear infection in the absence of humoral immunity. However, the role of T cell-independent immune responses during primary infection remains unclear. We investigated this question by inoculating wild-type and immune-deficient mice withC. muridarumCM001, a clonal isolate capable of enhanced extragenital replication. Genital inoculation of wild-type mice resulted in transient dissemination to the lungs and spleen that then was rapidly cleared from these organs. However, CM001 genital infection proved lethal forSTAT1−/−andIFNG−/−mice, in which IFN-γ signaling was absent, and forRag1−/−mice, which lacked T and B cells and in which innate IFN-γ signaling was retained. In contrast, B cell-deficient muMT mice, which can generate a Th1 response, and T cell-deficient mice with intact B cell and innate IFN-γ signaling survived. These data collectively indicate that IFN-γ prevents lethal CM001 dissemination in the absence of T cells and suggests a B cell corequirement. Adoptive transfer of convalescent-phase immune serum but not naive IgM toRag1−/−mice infected with CM001 significantly increased the survival time, while transfer of naive B cells completely rescuedRag1−/−mice from CM001 lethality. Protection was associated with a significant reduction in the lung chlamydial burden of genitally infected mice. These data reveal an important cooperation between T cell-independent B cell responses and innate IFN-γ in chlamydial host defense and suggest that interactions between T cell-independent antibody and IFN-γ are essential for limiting extragenital dissemination.
Research priority setting in childhood chronic disease: a systematic review
Authors: Odgers Harrison Lindsay , Tong Allison , Lopez-Vargas Pamela , Davidson Andrew , Jaffe Adam , McKenzie Anne , Pinkerton Ross , Wake Melissa , Richmond Peter , Crowe Sally , Caldwell Patrina Ha Yuen , Hill Sophie , Couper Jennifer , Haddad Suzy , Kassai Behrouz , Craig Jonathan C 
Published: April 2018

ObjectiveTo evaluate research priority setting approaches in childhood chronic diseases and to describe the priorities of stakeholders including patients, caregivers/families and health professionals.DesignWe conducted a systematic review of MEDLINE, Embase, PsycINFO and CINAHL from inception to 16 October 2016. Studies that elicited stakeholder priorities for paediatric chronic disease research were eligible for inclusion. Data on the prioritisation process were extracted using an appraisal checklist. Generated priorities were collated into common topic areas.ResultsWe identified 83 studies (n=15 722). Twenty (24%) studies involved parents/caregivers and four (5%) children. The top three health areas were cancer (11%), neurology (8%) and endocrine/metabolism (8%). Priority topic areas were treatment (78%), disease trajectory (48%), quality of life/psychosocial impact (48%), disease onset/prevention (43%), knowledge/self-management (33%), prevalence (30%), diagnostic methods (28%), access to healthcare (25%) and transition to adulthood (12%). The methods included workshops, Delphi techniques, surveys and focus groups/interviews. Specific methods for collecting and prioritising research topics were described in only 60% of studies. Most reviewed studies were conducted in high-income nations.ConclusionsResearch priority setting activities in paediatric chronic disease cover many discipline areas and have elicited a broad range of topics. However, child/caregiver involvement is uncommon, and the methods often lack clarity. A systematic and explicit process that involves patients and families in partnership may help to inform a more patient and family-relevant research agenda in paediatric chronic disease.
Patient-reported outcome measures for patients with meniscal tears: a systematic review of measurement properties and evaluation with the COSMIN checklist
Authors: Abram Simon GF , Middleton Robert , Beard David J , Price Andrew J , Hopewell Sally 
Published: April 2018

ObjectiveMeniscal tears occur frequently in the population and the most common surgical treatment, arthroscopic partial meniscectomy, is performed in approximately two million cases worldwide each year. The purpose of this systematic review is to summarise and critically appraise the evidence for the use of patient-reported outcome measures (PROMs) in patients with meniscal tears.DesignA systematic review was undertaken. Data on reported measurement properties were extracted and the quality of the studies appraised according to Consensus-based Standards for the Selection of Health Measurement Instruments.Data sourcesA search of MEDLINE, Embase, AMED and PsycINFO, unlimited by language or publication date (last search 20 February 2017).Eligibility criteria for selecting studiesDevelopment and validation studies reporting the measurement properties of PROMs in patients with meniscal tears were included.Results11 studies and 10 PROMs were included. The overall quality of studies was poor. For measurement of symptoms and functional status, there is only very limited evidence supporting the selection of either the Lysholm Knee Scale, International Knee Documentation Committee Subjective Knee Form or the Dutch version of the Knee injury and Osteoarthritis Outcome Score. For measuring health-related quality of life, only limited evidence supports the selection of the Western Ontario Meniscal Evaluation Tool (WOMET). Of all the PROMs evaluated, WOMET has the strongest evidence for content validity.ConclusionFor patients with meniscal tears, there is poor quality and incomplete evidence regarding the validity of the currently available PROMs. Further research is required to ensure these PROMs truly reflect the symptoms, function and quality of life of patients with meniscal tears.PROSPERO registration numberCRD42017056847.
Rate of adherence to urate-lowering therapy among patients with gout: a systematic review and meta-analysis
Authors: Yin Rulan , Li Lin , Zhang Guo , Cui Yafei , Zhang Lijuan , Zhang Qiuxiang , Fu Ting , Cao Haixia , Li Liren , Gu Zhifeng 
Published: April 2018

IntroductionReported adherence to urate-lowering therapy (ULT) in gout varies widely (17%–83.5%). Variability may partly be due to different adherence measurement methods. This review aimed to quantify ULT adherence in adult patients with gout.MethodsThis analysis examined studies in PubMed, Web of Science, CNKI Scholar and WanFang databases from inception to January 2017. Papers were selected by inclusion and exclusion criteria in the context. Random-effect meta-analysis estimated adherence.Results22 studies were found by the inclusion criteria, which involved 1 37 699 patients with gout. Four ways to define adherence were reported. Meta-analysis revealed that the overall adherence rate was 47% (95% CI 42% to 52%, I2=99.7%). Adherence rate to ULT was 42% (95% CI 37% to 47%, I2=99.8%) for prescription claims, 71% (95% CI 63% to 79%) for pill count, 66% (95% CI 50% to 81%, I2=86.3%) for self-report and 63% (95% CI 42% to 83%, I2=82.9%) for interview, respectively. The influential factor on adherence rate was country of origin.ConclusionsAmong adult patients with gout, overall adherence rate to ULT was as low as 47%, which suggested that clinicians should pay more attention to medication adherence in patients with gout to effectively improve adherence to ULT.
Refugee maternal and perinatal health in Ontario, Canada: a retrospective population-based study
Authors: Wanigaratne Susitha , Shakya Yogendra , Gagnon Anita J , Cole Donald C , Rashid Meb , Blake Jennifer , Dastoori Parisa , Moineddin Rahim , Ray Joel G , Urquia Marcelo L 
Published: April 2018

ObjectivesImmigrants are thought to be healthier than their native-born counterparts, but less is known about the health of refugees or forced migrants. Previous studies often equate refugee status with immigration status or country of birth (COB) and none have compared refugee to non-refugee immigrants from the same COB. Herein, we examined whether: (1) a refugee mother experiences greater odds of adverse maternal and perinatal health outcomes compared with a similar non-refugee mother from the same COB and (2) refugee and non-refugee immigrants differ from Canadian-born mothers for maternal and perinatal outcomes.DesignThis is a retrospective population-based database study. We implemented two cohort designs: (1) 1:1 matching of refugees to non-refugee immigrants on COB, year and age at arrival (±5 years) and (2) an unmatched design using all data.Setting and participantsRefugee immigrant mothers (n=34 233), non-refugee immigrant mothers (n=243 439) and Canadian-born mothers (n=615 394) eligible for universal healthcare insurance who had a hospital birth in Ontario, Canada, between 2002 and 2014.Primary outcomesNumerous adverse maternal and perinatal health outcomes.ResultsRefugees differed from non-refugee immigrants most notably for HIV, with respective rates of 0.39% and 0.20% and an adjusted OR (AOR) of 1.82 (95% CI 1.19 to 2.79). Other elevated outcomes included caesarean section (AOR 1.04, 95% CI 1.00 to 1.08) and moderate preterm birth (AOR 1.08, 95% CI 0.99 to 1.17). For the majority of outcomes, refugee and non-refugee immigrants experienced similar AORs when compared with Canadian-born mothers.ConclusionsRefugee status was associated with a few adverse maternal and perinatal health outcomes, but the associations were not strong except for HIV. The definition of refugee status used herein may not sensitively identify refugees at highest risk. Future research would benefit from further refining refugee status based on migration experiences.
Complications in breast augmentation with textured versus smooth breast implants: a systematic review protocol
Authors: Wang Chenglong , Luan Jie , Panayi Adriana C , Orgill Dennis P , Xin Minqiang 
Published: April 2018

IntroductionBreast augmentation is one of the most popular aesthetic plastic surgeries worldwide. There are various types of breast implants, and these can be categorised into different broad groups based on their content, shape or surface, to name a few. When looking at the surface of the shell, they can be categorised into two main kinds: textured and smooth implants. To our knowledge, a literature review and meta-analysis of the complications of these two types of implants when used for aesthetic breast augmentation has yet to be written.Methods and analysisThe PubMed, EMBASE and Cochrane electronic databases will be searched from their inception to 1 October 2017. Only cohort studies, case series, case–control studies and randomised controlled trials will be included. Identification of the articles for inclusion will be carried out by two independent researchers, and data will be extracted from these studies for analysis. This protocol defines the inclusion and exclusion criteria, as well as the primary and secondary outcomes. Statistical data analysis will be conducted in Review Manager V.5.3 from Cochrane Collaboration. The methodological quality of the included studies will also be assessed.Ethics and disseminationThis review will analyse secondary data collected from studies which are not linked to any specific individual. Once completed, the conclusions of the review could prove to be a valuable resource for plastic surgeons to conduct aesthetic implant procedures. The review will be submitted for publication in a peer-reviewed journal and presented at various national and international conferences.PROSPERO registration numberCRD42017078727.
Safety and feasibility evaluation of tourniquets for total knee replacement (SAFE-TKR): study protocol
Authors: Wall Peter DH , Ahmed Imran , Metcalfe Andrew , Price Andrew J , Seers Kate , Hutchinson Charles E , Parsons Helen , Warwick Jane , Rahman Bushra , Brown Jaclyn , Underwood Martin 
Published: April 2018

IntroductionThis study is designed to determine whether a full randomised controlled trial (RCT) examining the clinical effectiveness and safety of total knee replacement surgery with or without a tourniquet is warranted and feasible.Method and analysisSingle centre, patient-blinded and assessor-blinded RCT. A computer-generated randomisation service will allocate 50 participants into one of two trial treatments, surgery with or without a tourniquet. The primary objective is to estimate recruitment, crossovers and follow-up of patients. All patients will have an MRI scan of their brain preoperatively and day 1 or 2 postoperatively to identify ischaemic cerebral emboli (primary clinical outcome). Oxford Cognitive Screen, Montreal Cognitive Assessment and Mini-Mental State Examination will be evaluated as outcome tools for measuring cognitive impairment at days 1, 2 and 7 postoperatively. Thigh pain, blood transfusion requirements, venous thromboembolism, revision surgery, surgical complications, mortality and Oxford knee and five-level EuroQol-5D scores will be collected over 12 months.Integrated qualitative research study: 30 trial patients and 20 knee surgeons will take part in semistructured interviews. Interviews will capture views regarding the pilot trial and explore barriers and potential solutions to a full trial.Multicentre cohort study: UK National Joint Registry data will be linked to Hospital Episode Statistics to estimate the relationship between tourniquet use and venous thromboembolic event, length of hospital stay, risk of revision surgery and death. The study will conclude with a multidisciplinary workshop to reach a consensus on whether a full trial is warranted and feasible.Ethics and disseminationNational Research Ethics Committee (West Midlands-Edgbaston) approved this study on 27 January 2016 (15/WM/0455). The study is sponsored by University of Warwick and University Hospitals Coventry and Warwickshire. The results will be disseminated via high-impact peer-reviewed publication.Trial registration numberISRCTN20873088; Pre-results.
Consensus Game Acceptors and Iterated Transductions
Authors: Berwanger Dietmar , van den Bogaard Marie 
Published: April 2018

We study a game for recognising formal languages, in which two players with imperfect information should coordinate on a common decision, given private input words correlated by a finite graph. The players have a common objective to avoid an inadmissible decision, in spite of the uncertainty induced by the input.We show that the acceptor model based on consensus games characterises context-sensitive languages. Further, we describe the expressiveness of these games in terms of iterated synchronous transductions and identify a subclass that characterises context-free languages.
Temporal exploration in sequential movements shapes efficient neuromuscular control
Authors: Furuya Shinichi , Yokota Sayuri 
Published: April 2018

The interaction of early and deliberate practice with genetic predisposition endows experts with virtuosic motor performance. However, it has not been known whether ways of practicing shape motor virtuosity. Here, we addressed this issue by comparing the effects of rhythmic variation in motor practice on neuromuscular control of the finger movements in pianists. With the use of a novel electromyography system with miniature active electrodes, we recorded the activity of the intrinsic hand muscles of 27 pianists while they played the piano and analyzed it by using a nonnegative matrix factorization algorithm and cluster analysis. The result demonstrated that practicing a target movement sequence with various rhythms reduced muscular activity, whereas neither practicing a sequence with a single rhythm nor taking a rest without practicing changed the activity. In addition, practice with rhythmic variation changed the patterns of simultaneous activations across muscles. This alteration of muscular coordination was associated with decreased activation of muscles not only relevant to, but also irrelevant to the task performance. In contrast, piano practice improved the maximum speed of the performance, the amount of which was independent of whether rhythmic variation was present. These results suggest that temporal variation in movement sequences during practice co-optimizes both movement speed and neuromuscular efficiency, which emphasizes the significance of ways of practice in the acquisition of motor virtuosity.NEW & NOTEWORTHY A key question in motor neuroscience is whether “ways of practicing” contribute to shaping motor virtuosity. We found both attenuation of activities and alteration of coordination of the intrinsic hand muscles of pianists, specifically through practicing a movement sequence with various rhythms. The maximum speed of the finger movements was also enhanced following the practice. These results emphasize the importance of ways of practicing in facilitating multiple skills: efficiency and speed.
Early Ambulation Among Hospitalized Heart Failure Patients Is Associated With Reduced Length of Stay and 30-Day Readmissions
Authors: Fleming Lisa M. , Zhao Xin , DeVore Adam D. , Heidenreich Paul A. , Yancy Clyde W. , Fonarow Gregg C. , Hernandez Adrian F. , Kociol Robb D. 
Published: April 2018

Background:
Early ambulation (EA) is associated with improved outcomes for mechanically ventilated and stroke patients. Whether the same association exists for patients hospitalized with acute heart failure is unknown. We sought to determine whether EA among patients hospitalized with heart failure is associated with length of stay, discharge disposition, 30-day post discharge readmissions, and mortality.

Methods and Results:

The study population included 369 hospitals and 285 653 patients with heart failure enrolled in the Get With The Guidelines-Heart Failure registry. We used multivariate logistic regression with generalized estimating equations at the hospital level to identify predictors of EA and determine the association between EA and outcomes. Sixty-five percent of patients ambulated by day 2 of the hospital admission. Patient-level predictors of EA included younger age, male sex, and hospitalization outside of the Northeast (
P
<0.01 for all). Hospital size and academic status were not predictive. Hospital-level analysis revealed that those hospitals with EA rates in the top 25% were less likely to have a long length of stay (defined as >4 days) compared with those in the bottom 25% (odds ratio, 0.83; confidence interval, 0.73–0.94;
P
=0.004). Among a subgroup of fee-for-service Medicare beneficiaries, we found that hospitals in the highest quartile of rates of EA demonstrated a statistically significant 24% lower 30-day readmission rates (
P
<0.0001). Both end points demonstrated a dose–response association and statistically significant
P
for trend test.

Conclusions:
Multivariable-adjusted hospital-level analysis suggests an association between EA and both shorter length of stay and lower 30-day readmissions. Further prospective studies are needed to validate these findings.
Necessity and Future-Dependence: ‘Ockhamist’ Accounts of Abraham’s Faith at Paris around 1200
Authors: Wciórka Wojciech 
Published: April 2018

Abstract
This article aims to show that the so-called ‘Ockhamist’ solution to the determinist challenge was a commonplace among Parisian scholastics around 1200. On the ‘Ockhamist’ view, some propositions about the past do not fall under the necessity of the past, since their truth-value depends on the future. The paper focuses on two puzzles involving Abraham’s belief in the future Incarnation. The author discusses the ‘Ockhamist’ strategies adopted by theologians of the period, including Simon of Tournai, Peter of Poitiers, Praepositinus of Cremona, Stephen Langton, Geoffrey of Poitiers, and William of Auxerre. Langton draws an analogy between Abraham’s faith and Christ’s statement “Thou shalt deny me thrice” and suggests (while weighing alternatives) that past movements of faith are counterfactually flexible with regard to content. In order to interpret Langton’s statements, the author sketches a model of empty slots in the supernatural layer of the past, retrospectively infused with grace.
Looking at the “Qu qie” Chapter of the Zhuangzi from the Guodian *Yucong iv Bamboo Slip Manuscript (從郭店簡《語叢四》看《莊子·胠篋》)
Authors: Xueqin (李學勤) Li 
Published: April 2018

The *Yucong
iv manuscript, part of the Guodian bamboo manuscript corpus, has an excerpt from the “Qu qie” chapter of the Zhuangzi. Since the date of the Guodian materials is no later than 300 b.c.e., the date of the composition of the “Qu qie” chapter must have been earlier than this. Since “Qu qie” is assigned to the Outer Chapters in the Zhuangzi, modern scholars have often regarded it as a later product. Now that *Yucong
iv has an excerpt from this chapter, we know that this traditional interpretation is by no means accurate. Information in “Qu qie” provides additional clues to further determine that the date of this chapter is earlier than 300 b.c.e. Because of this, “Qu qie” must have been from the hand of Zhuangzi himself or from one of his immediate pupils. However, since the philosophical perspective and many terms and language of “Qu qie” are drawn from the Laozi, we can also learn more about the issue of whether or not the Laozi and early Daoism and Confucianism were philosophically differentiated.
郭店簡《語叢四》摘錄了《莊子 · 胠篋》篇的文句，而這批楚簡的時代不晚於公元前300年，故《胠篋》篇的時代要早於這一時間。由於《胠篋》列於《莊子》外篇，近代學者多以爲晚出，現在知道《語叢四》已經引用該篇，可知以往的這一認識幷不正確。根據《胠篋》篇中一些可供判斷年代的地方，也能看出該篇的時代在公元前300年以前，因此《胠篋》篇應當是出自莊子或其及門弟子之手。而《胠篋》的思想觀點和許多詞語是由《老子》引申而來，對於瞭解《老子》及早期道家與儒家是否有思想分歧的問題也有重要的幫助。
Non-Chu Characteristics in the Guodian *Wu xing 五行 Manuscript (談談郭店簡《五行》篇中的非楚文字因素)
Authors: Shengjun (馮勝君) Feng 
Published: April 2018

The Guodian *Wu xing 五行 is a Chu 楚 manuscript that contains a number of non-Chu scribal characteristics. In some cases we can identify which regional script the characteristics were inherited from. The *Wu xing manuscript provides a unique opportunity to help us better understand the process of how ancient Chinese texts were copied.
郭店簡《五行》篇，總體來説是一篇楚文字抄本，但其中夾雜了一些非楚文字因素。這些因素有的能夠斷定其地域特征，有的則不能。這篇簡文爲我們認識古書傳抄過程中的一些現象，提供了難得的樣本。