bluuebunny/crossref_metadata_2025_split huggingface dataset:
Technical Note: Validation and implementation of a wireless transponder tracking system for gated stereotactic ablative radiotherapy of the liver
Authors: James Joshua , Cetnar Ashley , Dunlap Neal E. , Huffaker Corinna , Nguyen Vi Nhan , Potts Melissa , Wang Brian 
Published: May 2016

Purpose:Tracking soft‐tissue targets has recently been cleared as a new application of Calypso, an electromagnetic wireless transponder tracking system, allowing for gated treatment of the liver based on the motion of the target volume itself. The purpose of this study is to describe the details of validating the Calypso system for wireless transponder tracking of the liver and to present the clinical workflow for using it to deliver gated stereotactic ablative radiotherapy (SABR).Methods:A commercial 3D diode array motion system was used to evaluate the dynamic tracking accuracy of Calypso when tracking continuous large amplitude motion. It was then used to perform end‐to‐end tests to evaluate the dosimetric accuracy of gated beam delivery for liver SABR. In addition, gating limits were investigated to determine how large the gating window can be while still maintaining dosimetric accuracy. The gating latency of the Calypso system was also measured using a customized motion phantom.Results:The average absolute difference between the measured and expected positional offset was 0.3 mm. The 2%/2 mm gamma pass rates for the gated treatment delivery were greater than 97%. When increasing the gating limits beyond the known extent of planned motion, the gamma pass rates decreased as expected. The 2%/2 mm gamma pass rate for a 1, 2, and 3 mm increase in gating limits was measured to be 97.8%, 82.9%, and 61.4%, respectively. The average gating latency was measured to be 63.8 ms for beam‐hold and 195.8 ms for beam‐on. Four liver patients with 17 total fractions have been successfully treated at our institution.Conclusions:Wireless transponder tracking was validated as a dosimetrically accurate way to provide gated SABR of the liver. The dynamic tracking accuracy of the Calypso system met manufacturer's specification, even for continuous large amplitude motion that can be encountered when tracking liver tumors close to the diaphragm. The measured beam‐hold gating latency was appropriate for targets that will traverse the gating limit each respiratory cycle causing the beam to be interrupted constantly throughout treatment delivery.
Associations Between Objectively Assessed Components of Physical Activity and Health-Related Fitness in 10- to 14-Year-Old Children
Authors: De Baere Stijn , Philippaerts Renaat , De Martelaer Kristine , Lefevre Johan 
Published: May 2016

Background:Our aim was to investigate the association between different components of physical activity (PA) and health-related fitness in 10-to 14-year-old children.Methods:241 children were recruited from 15 primary and 15 secondary schools. PA was assessed using the SenseWear Mini and an electronic diary. Health-related fitness was assessed using Eurofit and translated into indicators of body fatness, cardiorespiratory fitness and muscular fitness. Associations between PA intensity and physical fitness components were determined using multiple linear regression models adjusted for possible confounders and the contribution of PA domains per intensity categories was calculated.Results:Associations between PA intensities and body fatness were low to moderate (|β| = 0.09 to 0.44), explaining up to 6% of the variance in boys and 17% in girls. For cardiorespiratory fitness, associations were higher (|β| = 0.17 to 0.56), with PA explaining up to 6% of the variance in boys and 31% in girls. Low-tomoderate associations (|β| = 0.06 to 0.43) were found for muscular fitness, with PA explaining up to 7% in boys and 13% in girls. Stronger associations were found for sedentary and light activities.Conclusions:Low-to-moderate associations between PA and fitness components were observed, with higher associations in girls. Sedentary and light intensity activity showed the strongest link with body fatness, cardiorespiratory fitness and muscular fitness.
Physical Activity With Alanine Aminotransferase and Gamma-Glutamyltransferase: Implications of Liver Pathology on the Relationship Between Physical Activity and Mortality
Authors: Loprinzi Paul D. 
Published: May 2016

Objective:Examine the association between objectively-measured moderate-to-vigorous physical activity (MVPA) and engagement in self-reported muscle strengthening activities (MSA) with alanine aminotransferase (ALT) and gamma-glutamyltransferase (GGT), and in turn, how each of these parameters associate with of all-cause mortality.Methods:Data from the 2003–2006 NHANES were employed, with follow-up through December 31, 2011 (N = 5030; 20+ yrs). Physical activity was assessed via accelerometry; MSA was assessed via survey; and ALT and GGT were assessed via a blood sample. Linear regression and Cox proportional hazard models were used.Results:MVPA (βadjusted = 0.15; 95% CI: –0.45 to 0.76; P = .60) was not associated with ALT, but MSA was (β adjusted = –0.31; 95% CI: –0.56 to –0.05; P = .02). With regard to GGT, MSA was not significant (β adjusted = –0.12; 95% CI: –0.71 to 0.47; P = .67), nor was MVPA (β adjusted = –1.10; 95% CI: –2.20 to 0.06; P = .06). Higher ALT levels were associated with increased allcause mortality risk (HRadjusted = 1.05; 95% CI: 1.02 to 1.06; P < .001).Conclusion:Physical activity is favorably associated with markers of hepatic inflammation, and higher levels of markers of hepatic inflammation are associated with increased mortality risk. These findings suggest that physical activity may help protect against premature mortality through its influence on liver pathology.
Sensory Impairment, Functional Balance and Physical Activity With All-Cause Mortality
Authors: Loprinzi Paul D. , Crush Elizabeth 
Published: May 2016

Objective:No study has comprehensively examined the independent and combined effects of sensory impairment, physical activity and balance on mortality risk, which was this study’s purpose.Methods:Data from the population-based 2003–2004 National Health and Nutrition Examination Survey (NHANES) was used, with follow-up through 2011. Physical activity was assessed via accelerometry. Balance was assessed via the Romberg test. Peripheral neuropathy was assessed objectively using a standard monofilament. Visual impairment was objectively assessed using an autorefractor. Hearing impairment was assessed via self-report. A 5-level index variable (higher score is worse) was calculated based on the participant’s degree of sensory impairment, dysfunctional balance and physical inactivity.Results:Among the 1658 participants (age 40–85 yrs), 228 died during the median follow-up period of 92 months. Hearing (Hazard Ratio [HR] = 1.18; P = .40), vision (HR = 1.17; P = .58) and peripheral neuropathy (HR = 1.06; P = .71) were not independently associated with all-cause mortality, but physical activity (HR = 0.97; P = .01) and functional balance (HR = 0.59; P = .03) were. Compared with those with an index score of 0, the HR (95% CI) for those with an index score of 1 to 3, respectively, were 1.20 (0.46–3.13), 2.63 (1.08–6.40) and 2.88 (1.36–6.06).Conclusions:Physical activity and functional balance are independent contributors to survival.
Study of Two Separate Types of Macrolide-Resistant Mycoplasma pneumoniae Outbreaks
Authors: Wang Yingshuo , Ye Qian , Yang Dehua , Ni Zhimin , Chen Zhimin 
Published: May 2016

ABSTRACT

To study the complete natural process of a
Mycoplasma pneumoniae
outbreak in a semiclosed room such as a primary school room, we investigated two separate
M. pneumoniae
outbreaks involving 81 students in total in two primary schools in Hangzhou, China.
M. pneumoniae
isolates from pharyngeal swabs were detected by fluorescence quantitative real-time PCR (RT-PCR) and culture. The class in school M had 39 students, with 12 (30.8%) with positive
M. pneumoniae
detection results. The class from school J had 42 students, with 13 (31.0%) positive. The strains from two classes were confirmed to represent two clones (3/4/5/7/2 and 5/4/5/7/2) and to be macrolide resistant (A2063G) according to P1 and multilocus variable-number tandem-repeat analysis (MLVA) genotyping, determination of MIC of antibiotics, and sequencing. Students with
M. pneumoniae
isolates detected were divided into three groups: those carrying the isolates, those with upper respiratory tract infection (URI), and those with pneumonia. Longitudinal sampling performed using pharyngeal swabs showed that the persistence of
M. pneumoniae
was longest in the group of students with pneumonia.
M. pneumoniae
causes pneumonia outbreaks in schools, and the incidence of pneumonia has a higher rate than that of URI. The persistence of
M. pneumoniae
, with a median duration of 79.50 days in the group of students with pneumonia, differs from that of the infection state.
Efavirenz and Metabolites in Cerebrospinal Fluid: Relationship with
CYP2B6
c.516G→T Genotype and Perturbed Blood-Brain Barrier Due to Tuberculous Meningitis
Authors: Nightingale Sam , Chau Tran Thi Hong , Fisher Martin , Nelson Mark , Winston Alan , Else Laura , Carr Daniel F. , Taylor Steven , Ustianowski Andrew , Back David , Pirmohamed Munir , Solomon Tom , Farrar Jeremy , Törok M. Estée , Khoo Saye 
Published: May 2016

ABSTRACT

Efavirenz (EFZ) has been associated with neuropsychiatric side effects. Recently, the 8-hydroxy-EFZ (8OH-EFZ) metabolite has been shown to be a potent neurotoxin
in vitro
, inducing neuronal damage at concentrations of 3.3 ng/ml. EFZ induced similar neuronal damage at concentrations of 31.6 ng/ml. We investigated the effect of genotype and blood-brain barrier integrity on EFZ metabolite concentrations in cerebrospinal fluid (CSF). We measured CSF drug concentrations in subjects from two separate study populations: 47 subjects with tuberculous meningitis (TBM) coinfection in Vietnam receiving 800 mg EFZ with standard antituberculous treatment and 25 subjects from the PARTITION study in the United Kingdom without central nervous system infection receiving 600 mg EFZ. EFZ and metabolite concentrations in CSF and plasma were measured and compared with estimates of effectiveness and neurotoxicity from available published
in vitro
and
in vivo
data. The effect of the
CYP2B6
c.516G→T genotype (GG genotype, fast EFV metabolizer status; GT genotype, intermediate EFV metabolizer status; TT genotype, slow EFV metabolizer status) was examined. The mean CSF concentrations of EFZ and 8OH-EFZ in the TBM group were 60.3 and 39.3 ng/ml, respectively, and those in the no-TBM group were 15.0 and 5.9 ng/ml, respectively. Plasma EFZ and 8OH-EFZ concentrations were similar between the two groups. CSF EFZ concentrations were above the
in vitro
toxic concentration in 76% of samples (GG genotype, 61%; GT genotype, 90%; TT genotype, 100%) in the TBM group and 13% of samples (GG genotype, 0%; GT genotype, 18%; TT genotype, 50%) in the no-TBM group. CSF 8OH-EFZ concentrations were above the
in vitro
toxic concentration in 98% of the TBM group and 87% of the no-TBM group; levels were independent of genotype but correlated with the CSF/plasma albumin ratio. Potentially neurotoxic concentrations of 8OH-EFZ are frequently observed in CSF independently of the
CYP2B6
genotype, particularly in those with impaired blood-brain barrier integrity.
Copresence of
tet
(K) and
tet
(M) in Livestock-Associated Methicillin-Resistant Staphylococcus aureus Clonal Complex 398 Is Associated with Increased Fitness during Exposure to Sublethal Concentrations of Tetracycline
Authors: Larsen Jesper , Clasen Julie , Hansen Julie E. , Paulander Wilhelm , Petersen Andreas , Larsen Anders R. , Frees Dorte 
Published: May 2016

ABSTRACT

The tetracycline resistance gene
tet
(K) was shown to be integrated within the predominant staphylococcal cassette chromosome
mec
(SCC
mec
) element of Danish livestock-associated methicillin-resistant
Staphylococcus aureus
CC398 (LA-MRSA CC398). These LA-MRSA CC398 isolates already possessed
tet
(M), but the acquisition of
tet
(K) significantly improved their fitness at sublethal concentrations of tetracycline. Because
tet
(K) is genetically linked to SCC
mec
, the use of tetracycline in food animals may have contributed to the successful spread of LA-MRSA CC398.
Genetic Features of MCR-1-Producing Colistin-Resistant Escherichia coli Isolates in South Africa
Authors: Poirel Laurent , Kieffer Nicolas , Brink Adrian , Coetze Jennifer , Jayol Aurélie , Nordmann Patrice 
Published: May 2016

ABSTRACT

A series of colistin-resistant
Escherichia coli
clinical isolates was recovered from hospitalized and community patients in South Africa. Seven clonally unrelated isolates harbored the
mcr-1
gene located on different plasmid backbones. Two distinct plasmids were fully sequenced, and identical 2,600-bp-long DNA sequences defining a
mcr-1
cassette were identified. Promoter sequences responsible for the expression of
mcr-1
, deduced from the precise identification of the +1 transcription start site for
mcr-1
, were characterized.
Combination Chemotherapy with Suboptimal Doses of Benznidazole and Pentoxifylline Sustains Partial Reversion of Experimental Chagas' Heart Disease
Authors: Vilar-Pereira Glaucia , Resende Pereira Isabela , de Souza Ruivo Leonardo Alexandre , Cruz Moreira Otacilio , da Silva Andrea Alice , Britto Constança , Lannes-Vieira Joseli 
Published: May 2016

ABSTRACT

Chronic chagasic cardiomyopathy (CCC) progresses with parasite persistence, fibrosis, and electrical alterations associated with an unbalanced immune response such as high plasma levels of tumor necrosis factor (TNF) and nitric oxide (NO). Presently, the available treatments only mitigate the symptoms of CCC. To improve CCC prognosis, we interfered with the parasite load and unbalanced immune response using the trypanocidal drug benznidazole (Bz) and the immunoregulator pentoxifylline (PTX). C57BL/6 mice chronically infected with the Colombian strain of
Trypanosoma cruzi
and with signs of CCC were treated for 30 days with a suboptimal dose of Bz (25 mg/kg of body weight), PTX (20 mg/kg), or their combination (Bz plus PTX) and analyzed for electrocardiographic, histopathological, and immunological changes. Bz (76%) and Bz-plus-PTX (79%) therapies decreased parasite loads. Although the three therapies reduced myocarditis and fibrosis and ameliorated electrical alterations, only Bz plus PTX restored normal heart rate-corrected QT (QTc) intervals. Bz-plus-PTX-treated mice presented complementary effects of Bz and PTX, which reduced TNF expression (37%) in heart tissue and restored normal TNF receptor 1 expression on CD8
+
T cells, respectively. Bz (85%) and PTX (70%) therapies reduced the expression of inducible nitric oxide synthase (iNOS/NOS2) in heart tissue, but only Bz (58%) reduced NO levels in serum. These effects were more pronounced after Bz-plus-PTX therapy. Moreover, 30 to 50 days after treatment cessation, reductions of the prolonged QTc and QRS intervals were sustained in Bz-plus-PTX-treated mice. Our findings support the importance of interfering with the etiological agent and immunological abnormalities to improve CCC prognosis, opening an opportunity for a better quality of life for Chagas' disease (CD) patients.
The UbiI (VisC) Aerobic Ubiquinone Synthase Is Required for Expression of Type 1 Pili, Biofilm Formation, and Pathogenesis in Uropathogenic Escherichia coli
Authors: Floyd Kyle A. , Mitchell Courtney A. , Eberly Allison R. , Colling Spencer J. , Zhang Ellisa W. , DePas William , Chapman Matthew R. , Conover Matthew , Rogers Bridget R. , Hultgren Scott J. , Hadjifrangiskou Maria 
Published: May 2016

ABSTRACTUropathogenicEscherichia coli(UPEC), which causes the majority of urinary tract infections (UTI), uses pilus-mediated adherence to initiate biofilm formation in the urinary tract. Oxygen gradients withinE. colibiofilms regulate expression and localization of adhesive type 1 pili. A transposon mutant screen for strains defective in biofilm formation identified theubiI(formerlyvisC) aerobic ubiquinone synthase gene as critical for UPEC biofilm formation. In this study, we characterized a nonpolarubiIdeletion mutant and compared its behavior to that of wild-type bacteria grown under aerobic and anoxic conditions. Consistent with its function as an aerobic ubiquinone-8 synthase, deletion ofubiIin UPEC resulted in reduced membrane potential, diminished motility, and reduced expression of chaperone-usher pathway pili. Loss of aerobic respiration was previously shown to negatively impact expression of type 1 pili. To determine whether this reduction in type 1 pili was due to an energy deficit, wild-type UPEC and theubiImutant were compared for energy-dependent phenotypes under anoxic conditions, in which quinone synthesis is undertaken by anaerobic quinone synthases. Under anoxic conditions, the two strains exhibited wild-type levels of motility but produced diminished numbers of type 1 pili, suggesting that the reduction of type 1 pilus expression in the absence of oxygen is not due to a cellular energy deficit. Acute- and chronic-infection studies in a mouse model of UTI revealed a significant virulence deficit in theubiImutant, indicating that UPEC encounters enough oxygen in the bladder to induce aerobic ubiquinone synthesis during infection.IMPORTANCEThe majority of urinary tract infections are caused by uropathogenicE. coli, a bacterium that can respire in the presence and absence of oxygen. The bladder environment is hypoxic, with oxygen concentrations ranging from 4% to 7%, compared to 21% atmospheric oxygen. This work provides evidence that aerobic ubiquinone synthesis must be engaged during bladder infection, indicating that UPEC bacteria sense and use oxygen as a terminal electron acceptor in the bladder and that this ability drives infection potential despite the fact that UPEC is a facultative anaerobe.
Pleistocene megaflood landscapes of the Channeled Scabland
Authors: Baker Victor R. , Bjornstad Bruce N. , Gaylord David R. , Smith Gary A. , Meyer Scott E. , Alho Petteri , Breckenridge Roy M. , Sweeney Mark R. , Zreda Marek 
Published: May 2016

Abstract
The Channeled Scabland of east-central Washington comprises a complex of anastomosing fluvial channels that were eroded by Pleistocene megaflooding into the basalt bedrock and overlying sediments of the Columbia Plateau and Columbia Basin regions of eastern Washington State, U.S.A. The cataclysmic flooding produced huge coulees (dry river courses), cataracts, streamlined loess hills, rock basins, butte-and-basin scabland, potholes, inner channels, broad gravel deposits, and immense gravel bars. Giant current ripples (fluvial dunes) developed in the coarse gravel bedload. In the 1920s, J Harlen Bretz established the cataclysmic flooding origin for the Channeled Scabland, and Joseph Thomas Pardee subsequently demonstrated that the megaflooding derived from the margins of the Cordilleran Ice Sheet, notably from ice-dammed glacial Lake Missoula, which had formed in western Montana and northern Idaho. More recent research, to be discussed on this field trip, has revealed the complexity of megaflooding and the details of its history.
To understand the scabland one has to throw away textbook treatments of river work.
—J. Hoover Mackin, as quoted in Bretz et al. (1956, p. 960)
Mesozoic tectonics west of the accretionary boundary in west-central Idaho
Authors: Schmidt Keegan L. , Gray Keith D. , Lewis Reed S. , Steven Cody J. , Isakson Vince H. 
Published: May 2016

Abstract
The late Mesozoic accretionary boundary in west-central Idaho has played a critical role in tectonic models proposed for the northwestern U.S. Cordillera. From west-to-east, major elements include the Permian to Jurassic Wallowa island-arc terrane, a poorly understood transition zone consisting of the Riggins Group assemblage and deformation belt along the west side of the island arc-continent boundary, Late Jurassic to Cretaceous arc-continent boundary, and Precambrian North American margin intruded by the Cretaceous–Paleogene Idaho batholith. We focus on the transition zone in the area between White Bird and Riggins, Idaho, which includes a contractional belt in variously deformed and metamorphosed rocks of island-arc affinity. We propose that the rocks of the entire transition zone, including those originally defined as the Riggins Group, are likely of Wallowa terrane origin and/or related basinal assemblages. Ultramafic rocks in the transition zone are possibly related to a Jurassic or Cretaceous basinal assemblage that includes the Squaw Creek Schist of the Riggins Group. Our recent work addresses the kinematic history of structures in the contractional belt. The belt was reactivated in the Neogene to accommodate mostly brittle normal faulting that strongly influenced preservation of the Miocene Columbia River Basalt Group at this location along the eastern margin of the flood basalt province. This field guide provides a road log for examining the geology between Moscow and New Meadows, Idaho, along U.S. Highway 95.
Development and validation of an instrument to assess treatment adherence for each individual drug taken by a patient
Authors: Sidorkiewicz Stéphanie , Tran Viet-Thi , Cousyn Cécile , Perrodeau Elodie , Ravaud Philippe 
Published: May 2016

ObjectiveTo develop and validate an instrument to assess adherence to each individual drug taken by patients undergoing long-term treatment.DesignMulticentre prospective observational validation study.SettingSix general practitioners' clinics and 6 university hospitals in Paris, France.ParticipantsPatients 18 years and older receiving at least one long-term treatment.MethodsThe instrument was developed from a literature search and interviews with experts. Clarity and wording were assessed during pilot testing with 51 patients. The tool was validated in a sample of consecutive patients. We assessed agreement between adherence measured with our tool and drug diaries and compared measurements from our instrument with (1) the Lu instrument; (2) the Adherence Estimator (AE); (3) patient's adherence assessed by physicians; (4) the Morisky Medication Adherence Scale-4 items (MMAS-4); and (5) the Treatment Burden Questionnaire (TBQ). Reliability was assessed by a test–retest method.ResultsA total of 243 patients taking 961 drugs were recruited in 2014. We found good agreement between adherence measured by our tool and drug diaries (intraclass correlation coefficient (ICC) 0.69, 95% CI 0.34 to 0.91) and a linear relationship between measurement with our tool and (1) the Lu instrument (p<0.01); (2) 2 items of the AE (perceived need for medication (p<0.01) and concerns about medication (p<0.01)); (3) patients' adherence assessed by their physicians (p<0.01); (4) the MMAS-4 (p<0.01) and (5) the TBQ (p<0.01). Reliability of the retest was good (ICC 0.67, 95% CI 0.42 to 0.85).ConclusionsWe developed an instrument with acceptable validity and reliability to assess adherence for each drug taken by patients, usable in hospital and primary care settings.