bluuebunny/crossref_metadata_2025_split huggingface dataset:
All-in-One Bacmids: an Efficient Reverse Genetics Strategy for Influenza A Virus Vaccines
Authors: Chen Hongjun , Angel Matthew , Li Weizhong , Finch Courtney , Gonzalez Ana Silvia , Sutton Troy , Santos Jefferson , Perez Daniel R. 
Published: June 2014

ABSTRACT

Vaccination is the first line of defense against influenza virus infection, yet influenza vaccine production methods are slow, antiquated, and expensive as a means to effectively reduce the virus burden during epidemic or pandemic periods. There is a great need for alternative influenza vaccines and vaccination methods with a global scale of impact. We demonstrate here a strategy to generate influenza A virus
in vivo
by using bacmid DNAs. Compared to the classical reverse genetics system, the “eight-in-one” bacmids (bcmd-RGFlu) showed higher efficiency of virus rescue in various cell types. Using a transfection-based inoculation (TBI) system, intranasal delivery to DBA/2J and BALB/c mice of bcmd-RGFlu plus 293T cells led to the generation of lethal PR8 virus
in vivo
. A prime-boost intranasal vaccination strategy using TBI in the context of a bcmd-RGFlu carrying a temperature-sensitive H1N1 virus resulted in protection of mice against lethal challenge with the PR8 strain. Taken together, these studies provide proof of principle to highlight the potential of vaccination against influenza virus by using
in vivo
reverse genetics.

IMPORTANCE
Vaccination is the first line of defense against influenza virus infections. A major drawback in the preparation of influenza vaccines is that production relies on a heavily time-consuming process of growing the viruses in eggs. We propose a radical change in the way influenza vaccination is approached, in which a recombinant bacmid, a shuttle vector that can be propagated in both
Escherichia coli
and insect cells, carries an influenza virus infectious clone (bcmd-RGFlu). Using a surrogate cell system, we found that intranasal delivery of bcmd-RGFlu resulted in generation of influenza virus in mice. Furthermore, mice vaccinated with this system were protected against lethal influenza virus challenge. The study serves as a proof of principle of a potentially universal vaccine platform against influenza virus and other pathogens.
Evidence of Extensive DNA Transfer between
Bacteroidales
Species within the Human Gut
Authors: Coyne Michael J. , Zitomersky Naamah Levy , McGuire Abigail Manson , Earl Ashlee M. , Comstock Laurie E. 
Published: June 2014

ABSTRACT

The genome sequences of intestinal
Bacteroidales
strains reveal evidence of extensive horizontal gene transfer.
In vitro
studies of
Bacteroides
and other bacteria have addressed mechanisms of conjugative transfer and some phenotypic outcomes of these DNA acquisitions in the recipient, such as the acquisition of antibiotic resistance. However, few studies have addressed the horizontal transfer of genetic elements between bacterial species coresident in natural microbial communities, especially microbial ecosystems of humans. Here, we examine the genomes of
Bacteroidales
species from two human adults to identify genetic elements that were likely transferred among these
Bacteroidales
while they were coresident in the intestine. Using seven coresident
Bacteroidales
species from one individual and eight from another, we identified five large chromosomal regions, each present in a minimum of three of the coresident strains at near 100% DNA identity. These five regions are not found in any other sequenced
Bacteroidetes
genome at this level of identity and are likely all integrative conjugative elements (ICEs). Such highly similar and unique regions occur in only 0.4% of phylogenetically representative mock communities, providing strong evidence that these five regions were transferred between coresident strains in these subjects. In addition to the requisite proteins necessary for transfer, these elements encode proteins predicted to increase fitness, including orphan DNA methylases that may alter gene expression, fimbriae synthesis proteins that may facilitate attachment and the utilization of new substrates, putative secreted antimicrobial molecules, and a predicted type VI secretion system (T6SS), which may confer a competitive ecological advantage to these strains in their complex microbial ecosystem.

IMPORTANCE
By analyzing
Bacteroidales
strains coresident in the gut microbiota of two human adults, we provide strong evidence for extensive interspecies and interfamily transfer of integrative conjugative elements within the intestinal microbiota of individual humans. In the recipient strain, we show that the conjugative elements themselves can be modified by the transposition of insertion sequences and retroelements from the recipient’s genome, with subsequent transfer of these modified elements to other members of the microbiota. These data suggest that the genomes of our gut bacteria are substantially modified by other, coresident members of the ecosystem, resulting in highly personalized
Bacteroidales
strains likely unique to that individual. The genetic content of these ICEs suggests that their transfer from successful adapted members of an ecosystem confers beneficial properties to the recipient, increasing its fitness and allowing it to better compete within its particular personalized gut microbial ecosystem.
Motion Patterns in Acupuncture Needle Manipulation
Authors: Seo Yoonjeong , Lee In-Seon , Jung Won-Mo , Ryu Ho-Sun , Lim Jinwoong , Ryu Yeon-Hee , Kang Jung-Won , Chae Younbyoung 
Published: June 2014

Background In clinical practice, acupuncture manipulation is highly individualised for each practitioner. Before we establish a standard for acupuncture manipulation, it is important to understand completely the manifestations of acupuncture manipulation in the actual clinic. To examine motion patterns during acupuncture manipulation, we generated a fitted model of practitioners’ motion patterns and evaluated their consistencies in acupuncture manipulation. Methods Using a motion sensor, we obtained real-time motion data from eight experienced practitioners while they conducted acupuncture manipulation using their own techniques. We calculated the average amplitude and duration of a sampled motion unit for each practitioner and, after normalisation, we generated a true regression curve of motion patterns for each practitioner using a generalised additive mixed modelling (GAMM). Results We observed significant differences in rotation amplitude and duration in motion samples among practitioners. GAMM showed marked variations in average regression curves of motion patterns among practitioners but there was strong consistency in motion parameters for individual practitioners. The fitted regression model showed that the true regression curve accounted for an average of 50.2% of variance in the motion pattern for each practitioner. Conclusions Our findings suggest that there is great inter-individual variability between practitioners, but remarkable intra-individual consistency within each practitioner.
Current practice of venous thromboembolism prevention in acute trusts: a qualitative study
Authors: McFarland L , Murray E , Harrison S , Heneghan C , Ward A , Fitzmaurice D , Greenfield S 
Published: June 2014

ObjectiveTo explore the current practice of venous thromboembolism (VTE) prevention in acute trusts.DesignA qualitative research design was used to explore the perceived current practice of thromboprophylaxis, and knowledge and experience of VTE prevention. Data were collected via interviews with personnel from acute trusts and other relevant organisations and charities. Constant comparison was used to generate themes grounded in the data.SettingThe UK.Participants17 participants, sampled due to their expertise and knowledge in the field of VTE, were interviewed for the study.ResultsNo one felt directly responsible for VTE risk assessment and treatment in acute trusts. There were concerns whether any action takes place based on the risk assessment. Low levels of VTE knowledge existed throughout the system.ConclusionsOur study highlights the importance of continuous training to prevent VTE risk assessment being considered a tick box exercise and for clinicians to understand the significance of the procedure to ensure that VTE preventative measures are administered. It is essential that acute trust staff acknowledge that VTE prevention is the responsibility of everyone involved in a patient's care. Concerns remain around prophylaxis treatment, administration and contraindications.
Reliability of demographic and socioeconomic variables in predicting early initiation of breastfeeding: a replication analysis using the Kenya Demographic and Health Survey data
Authors: Matanda Dennis J , Mittelmark Maurice B , Urke Helga B , Amugsi Dickson A 
Published: June 2014

ObjectivesExamine the reliability of sociodemographic variables in predicting initiation of breastfeeding within an hour of birth (EarlyBF), using data from 1998, 2003 and 2008–2009.Study designA replication analysis using the Kenya Demographic and Health Survey (KDHS) data collected in 1998, 2003 and 2008–2009. The candidate predictor variables were child's gender, home or health facility place of birth, vaginal or caesarean mode of birth, urban or rural setting, province of residence, Wealth Index and maternal education, occupation, literacy and media exposure.SettingKenya.Participants6375 dyads of mothers aged 15–49 and their children aged 0–23 months (2125 dyads in each of the survey years).ResultsMode of birth and province were statistically significant predictors of EarlyBF in 1998, 2003 and 2008–2009. Children delivered through caesarean section were non-EarlyBF in 1998 (OR 2.63, 95% CI 1.72 to 4.04), 2003 (OR 3.36, 95% CI 1.83 to 6.16) and 2008 (OR 3.51, 95% CI 2.17 to 5.69). The same was true of those living in the Western province in 1998 (OR 2.67, 95% CI 1.61 to 4.43), 2003 (OR 4.92, 95% CI 3.01 to 8.04) and 2008 (OR 6.07, 95% CI 3.54 to 10.39).ConclusionsThe 1998 KDHS data do not provide the basis for reliable prediction of EarlyBF, with reliability conceptualised as replicability of findings using highly similar data sets from 2003 and 2008–2009. Most of the demographic and socioeconomic variables were unreliable predictors of EarlyBF. We speculate that activities in parts or all of Kenya changed the analysis context in the period between 1998 and 2008–2009, and these changes were of a sufficient magnitude to affect the relationships under investigation. The degree to which this is a general problem in child health research is not known, calling for further research to investigate this methodological issue with other health end points and other data.
The effect on physical performance of a functional assessment and immediate rehabilitation of acutely admitted elderly patients with reduced functional performance: the design of a randomised clinical trial
Authors: Bruun Inge Hansen , Nørgaard Birgitte , Maribo Thomas , Schiøttz-Christensen Berit , Mogensen Christian Backer 
Published: June 2014

IntroductionIllness and hospitalisation, even of short duration, pose separate risks for permanently reduced functional performance in elderly medical patients. Functional assessment in the acute pathway will ensure early detection of declining performance and form the basis for mobilisation during hospitalisation and subsequent rehabilitation. For optimal results rehabilitation should begin immediately after discharge.The aim of this study is to investigate the effect of a systematic functional assessment in the emergency department (ED) of elderly medical patients with reduced functional performance when combined with immediate postdischarge rehabilitation.Method and analysisThe study is a two-way factorial randomised clinical trial. Participants will be recruited among patients admitted to the ED who are above 65 years of age with reduced functional performance. Patients will be randomly assigned to one of four groups: (1) functional assessment and immediate rehabilitation; (2) functional assessment and rehabilitation as usual; (3) assessment as usual and immediate rehabilitation; (4) assessment and rehabilitation as usual.Primary outcome30 s chair-stand test administered at admission and 3 weeks after discharge.Ethics and disseminationThe study has been approved by the Regional Scientific Ethical Committees of Southern Denmark in February 2014. The study findings will be published in peer-reviewed journals and presented at national and international conferences.Trial registration number:ClinicalTrials.gov Identifier:NCT02062541.
Use of a rotary battery‐powered device for the collection of bone marrow in dogs and cats
Authors: Tappin S. W. , Lorek A. , Villiers E. J. 
Published: June 2014

Bone marrow biopsies form an important part of investigations into a large number of conditions in veterinary patients. In the human field, powered drivers specifically designed for the collection of bone marrow have become available. These systems have been shown to obtain better quality bone marrow, more quickly and with less pain. This study showed that a powered rotary bone marrow collection system could be used in dogs and cats to collect bone marrow, easily and without complications. Good quality bone marrow aspirates were obtained in the majority of patients; where aspirates could not be collected it was not possible to obtain aspirates from alternative sites using a standard manual technique. Bone marrow core samples were of increased size (mean useable area 16.5 mm2), compared to samples obtained using a standard manual technique (mean useable area 4.1 mm2, P<0.001). Samples obtained using the powered system were also judged to be of significantly better diagnostic quality. The use of a powered system for bone marrow collection may aid the collection of better quality bone marrow samples in small animal patients.
The Feynman problem and fermionic entanglement: Fermionic theory versus qubit theory
Authors: D'Ariano Giacomo Mauro , Manessi Franco , Perinotti Paolo , Tosini Alessandro 
Published: June 2014

The present paper is both a review on the Feynman problem, and an original research presentation on the relations between Fermionic theories and qubits theories, both regarded in the novel framework of operational probabilistic theories. The most relevant results about the Feynman problem of simulating Fermions with qubits are reviewed, and in the light of the new original results, the problem is solved. The answer is twofold. On the computational side, the two theories are equivalent, as shown by Bravyi and Kitaev [S. B. Bravyi and A. Y. Kitaev, Ann. Phys. 298, 210 (2002)]. On the operational side, the quantum theory of qubits and the quantum theory of Fermions are different, mostly in the notion of locality, with striking consequences on entanglement. Thus the emulation does not respect locality, as it was suspected by Feynman [R. Feynman, Int. J. Theor. Phys. 21, 467 (1982)].
Serum CA19-9 Is Significantly Upregulated up to 2 Years before Diagnosis with Pancreatic Cancer: Implications for Early Disease Detection
Authors: O'Brien Darragh P. , Sandanayake Neomal S. , Jenkinson Claire , Gentry-Maharaj Aleksandra , Apostolidou Sophia , Fourkala Evangelia-Ourania , Camuzeaux Stephane , Blyuss Oleg , Gunu Richard , Dawnay Anne , Zaikin Alexey , Smith Ross C. , Jacobs Ian J. , Menon Usha , Costello Eithne , Pereira Stephen P. , Timms John F. 
Published: June 2014

Abstract
Purpose: Biomarkers for the early detection of pancreatic cancer are urgently needed. The primary objective of this study was to evaluate whether increased levels of serum CA19-9, CA125, CEACAM1, and REG3A are present before clinical presentation of pancreatic cancer and to assess the performance of combined markers for early detection and prognosis.
Experimental Design: This nested case–control study within the UKCTOCS included 118 single and 143 serial serum samples from 154 postmenopausal women who were subsequently diagnosed with pancreatic cancer and 304 matched noncancer controls. Samples were split randomly into independent training and test sets. CA19-9, CA125, CEACAM1, and REG3A were measured using ELISA and/or CLIA. Performance of markers to detect cancers at different times before diagnosis and for prognosis was evaluated.
Results: At 95% specificity, CA19-9 (&gt;37 U/mL) had a sensitivity of 68% up to 1 year, and 53% up to 2 years before diagnosis. Combining CA19-9 and CA125 improved sensitivity as CA125 was elevated (&gt;30 U/mL) in approximately 20% of CA19-9–negative cases. CEACAM1 and REG3A were late markers adding little in combined models. Average lead times of 20 to 23 months were estimated for test-positive cases. Prediagnostic levels of CA19-9 and CA125 were associated with poor overall survival (HR, 2.69 and 3.15, respectively).
Conclusions: CA19-9 and CA125 have encouraging sensitivity for detecting preclinical pancreatic cancer, and both markers can be used as prognostic tools. This work challenges the prevailing view that CA19-9 is upregulated late in the course of pancreatic cancer development. Clin Cancer Res; 21(3); 622–31. ©2014 AACR.
Sobre o espaço e a profundidade
Authors: Strathern Marilyn 
Published: June 2014

traduzido de:STRATHERN, Marilyn. “On Space and Depth”. In: LAW, J.; MOL, A-M. (Eds.), Complexities: Social studies of knowledge practices. Durham: Duke University Press, 2002. pp. 88-115. Copyright, 2002. All rights reserved. Reprinted by permission of the publisher. tradução: PRISCILA SANTOS DA COSTArevisão técnica: RENATO SZTUTMAN, DIANA PAOLA GÓMEZ MATEUS
Memantine Enhances Recovery From Stroke
Authors: López-Valdés Héctor E. , Clarkson Andrew N. , Ao Yan , Charles Andrew C. , Carmichael Stanley Thomas , Sofroniew Michael V. , Brennan Kevin C. 
Published: June 2014

Background and Purpose—

Stroke treatment is constrained by limited treatment windows and the clinical inefficacy of agents that showed preclinical promise. Yet animal and clinical data suggest considerable poststroke plasticity, which could allow treatment with recovery-modulating agents. Memantine is a well-tolerated N-methyl-
D
-aspartate glutamate receptor antagonist in common use for Alzheimer disease.

Methods—
Memantine, 30 mg/kg per day, or vehicle, was delivered chronically in drinking water beginning >2 hours after photothrombotic stroke.

Results—
Although there was no difference in infarct size, behavior, or optical intrinsic signal maps in the first 7 days after stroke, mice treated chronically with memantine showed significant improvements in motor control, measured by cylinder test and grid-walking performance, compared with vehicle-treated animals. Optical intrinsic signal revealed an increased area of forepaw sensory maps at 28 days after stroke. There was decreased reactive astrogliosis and increased vascular density around the infarcted cortex. Peri-infarct Western blots revealed increased brain-derived neurotrophic factor and phosphorylated-tropomyosin–related kinase-B receptor expression.

Conclusions—
Our results suggest that memantine improves stroke outcomes in an apparently non-neuroprotective manner involving increased brain-derived neurotrophic factor signaling, reduced reactive astrogliosis, and improved vascularization, associated with improved recovery of sensory and motor cortical function. The clinical availability and tolerability of memantine make it an attractive candidate for clinical translation.
Routine Clinical Evaluation of Cerebrovascular Reserve Capacity Using Carbogen in Patients With Intracranial Stenosis
Authors: Donahue Manus J. , Dethrage Lindsey M. , Faraco Carlos C. , Jordan Lori C. , Clemmons Paul , Singer Robert , Mocco J , Shyr Yu , Desai Aditi , O’Duffy Anne , Riebau Derek , Hermann Lisa , Connors John , Kirshner Howard , Strother Megan K. 
Published: June 2014

Background and Purpose—
A promising method for identifying hemodynamic impairment that may serve as a biomarker for stroke risk in patients with intracranial stenosis is cerebrovascular reactivity (CVR) mapping using noninvasive MRI. Here, abilities to measure CVR safely in the clinic using hypercarbic hyperoxic (carbogen) gas challenges, which increase oxygen delivery to tissue, are investigated.

Methods—
In sequence with structural and angiographic imaging, blood oxygenation level–dependent carbogen-induced CVR scans were performed in patients with symptomatic intracranial stenosis (n=92) and control (n=10) volunteers, with a subgroup of patients (n=57) undergoing cerebral blood flow–weighted pseudocontinuous arterial spin labeling CVR. Subjects were stratified for 4 substudies to evaluate relationships between (1) carbogen and hypercarbic normoxic CVR in healthy tissue (n=10), (2) carbogen cerebral blood flow CVR and blood oxygenation level–dependent CVR in intracranial stenosis patients (n=57), (3) carbogen CVR and clinical measures of disease in patients with asymmetrical intracranial atherosclerotic (n=31) and moyamoya (n=29) disease, and (4) the CVR scan and immediate and longer-term complications (n=92).

Results—

Noninvasive blood oxygenation level–dependent carbogen-induced CVR values correlate with (1) lobar hypercarbic normoxic gas stimuli in healthy tissue (
R
=0.92;
P
<0.001), (2) carbogen-induced cerebral blood flow CVR in patients with intracranial stenosis (
R
=0.30–0.33;
P
<0.012), and (3) angiographic measures of disease severity both in atherosclerotic and moyamoya patients after appropriate processing. No immediate stroke-related complications were reported in response to carbogen administration; longer-term neurological events fell within the range for expected events in this patient population.

Conclusions—
Carbogen-induced CVR elicited no added adverse events and provided a surrogate marker of cerebrovascular reserve consistent with intracranial vasculopathy.
Time, Probe Type, and Temperature Variable Bias Corrections to Historical Expendable Bathythermograph Observations
Authors: Cheng Lijing , Zhu Jiang , Cowley Rebecca , Boyer Tim , Wijffels Susan 
Published: June 2014

Abstract
Systematic biases in historical expendable bathythermograph (XBT) data are examined using two datasets: 4151 XBT–CTD side-by-side pairs from 1967 to 2011 and 218 653 global-scale XBT–CTD pairs (within one month and 1°) extracted from the World Ocean Database 2009 (WOD09) from 1966 to 2010. Using the side-by-side dataset, it was found that both the pure thermal bias and the XBT fall rate (from which the depth of observation is calculated) increase with water temperature. Correlations between the terminal velocity A and deceleration B terms of the fall-rate equation (FRE) and between A and the offset from the surface terms are obtained, with A as the dominant term in XBT fall-rate behavior. To quantify the time variation of the XBT fall-rate and pure temperature biases, global-scale XBT–CTD pairs are used. Based on the results from the two datasets, a new correction scheme for historical XBT data is proposed for nine independent probe-type groups. The scheme includes corrections for both temperature and depth records, which are all variable with calendar year, water temperature, and probe type. The results confirm those found in previous studies: a slowing in fall rate during the 1970s and 2000s and the large pure thermal biases during 1970–85. The performance of nine different correction schemes is compared. After the proposed corrections are applied to the XBT data in the WOD09 dataset, global ocean heat content from 1967 to 2010 is reestimated.