bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lagrangian Time Series Models for Ocean Surface Drifter Trajectories
Authors: Sykulski Adam M. , Olhede Sofia C. , Lilly Jonathan M. , Danioux Eric 
Published: June 2015

SummaryThe paper proposes stochastic models for the analysis of ocean surface trajectories obtained from freely drifting satellite-tracked instruments. The time series models proposed are used to summarize large multivariate data sets and to infer important physical parameters of inertial oscillations and other ocean processes. Non-stationary time series methods are employed to account for the spatiotemporal variability of each trajectory. Because the data sets are large, we construct computationally efficient methods through the use of frequency domain modelling and estimation, with the data expressed as complex-valued time series. We detail how practical issues related to sampling and model misspecification may be addressed by using semiparametric techniques for time series, and we demonstrate the effectiveness of our stochastic models through application to both real world data and to numerical model output.
Effect of Cardiac Resynchronization Therapy on Inflammation in Congestive Heart Failure: A Review
Authors: Lappegård K. T. , Bjørnstad H. , Mollnes T. E. , Hovland A. 
Published: June 2015

AbstractCongestive heart failure is associated with increased levels of several inflammatory mediators, and animal studies have shown that infusion of a number of cytokines can induce heart failure. However, several drugs with proven efficacy in heart failure have failed to affect inflammatory mediators, and anti‐inflammatory therapy in heart failure patients has thus far been disappointing. Hence, to what extent heart failure is caused by or responsible for the increased inflammatory burden in the patient is still unclear. Over the past couple of decades, resynchronization therapy with a biventricular pacemaker has emerged as an effective treatment in a subset of heart failure patients, reducing both morbidity and mortality. Such treatment has also been shown to affect the inflammation associated with heart failure. In this study, we review recent data on the association between heart failure and inflammation, and in particular how resynchronization therapy can affect the inflammatory process.
Effect of Perfusion Fluids on Recovery of Inflammatory Mediators in Microdialysis
Authors: Khan F. , Pharo A. , Lindstad J. K. , Mollnes T. E. , Tønnessen T. I. , Pischke S. E. 
Published: June 2015

AbstractMicrodialysis is an excellent tool to assess tissue inflammation in patients, but in vitro systems to evaluate recovery of inflammatory mediators have not been standardized. We aimed to develop a reference plasma preparation and evaluate different perfusion fluids with respect to recovery of metabolic and inflammatory markers. The reference preparation was produced by incubation of human blood with lipopolysaccharide and cobra venom factor to generate cytokines and activate complement, respectively. Microdialysis with 100 kDa catheters was performed using different colloid and crystalloid perfusion fluids (hydroxyethyl starch (HES) 130/0.4, HES 200/0.5, hyperosmolar HES 200/0.5, albumin 200 g/l, T1 perfusion fluid and Ringer's acetate) compared to today's recommended dextran 60 solution. Recovery of glucose, glycerol and pyruvate was not significantly different between the perfusion fluids, whereas lactate had lower recovery in HES 200/0.5 and albumin perfusion fluids. Recovery rates for the inflammatory proteins in comparison with the concentration in the reference preparation differed substantially: IL‐6 = 9%, IL‐1β = 18%, TNF = 0.3%, MCP‐1 = 45%, IL‐8 = 48%, MIG = 48%, IP‐10 = 25%, C3a = 53% and C5a = 12%. IL‐10 was not detectable in microdialysis dialysate. HES 130/0.4 and HES 200/0.5 yielded a recovery not significantly different from dextran 60. Hyperosmolar HES 200/0.5 and albumin showed significantly different pattern of recovery with increased concentration of MIG, IP‐10, C3a and C5a and decreased concentration of IL‐1β, TNF, MCP‐1 and IL‐8 in comparison with dextran 60. In conclusion, microdialysis perfusion fluid dextran 60 can be replaced by the commonly used HES 130/0.4, whereas albumin might be used if specific immunological variables are in focus. The present reference plasma preparation is suitable for in vitro evaluation of microdialysis systems.
Disease mapping for informing targeted health interventions: childhood pneumonia in Bohol, Philippines
Authors: Thomas Deborah S. K. , Anthamatten Peter , Root Elisabeth Dowling , Lucero Marilla , Nohynek Hanna , Tallo Veronica , Williams Gail M. , Simões Eric A. F. ,   the ARIVAC Consortium
Published: June 2015

AbstractBackgroundAcute lower respiratory tract infections (ALRI) are the leading cause of childhood mortality worldwide. Currently, most developing countries assign resources at a district level, and yet District Medical Officers have few tools for directing targeted interventions to high mortality or morbidity areas. Mapping of ALRI at the local level can guide more efficient allocation of resources, coordination of efforts and targeted interventions, which are particularly relevant for health management in resource‐scarce settings.MethodsAn efficacy study of 11‐valent pneumococcal vaccine was conducted in six municipalities in the Bohol Province of central Philippines from July 2000 to December 2004. Geocoded under‐five pneumonia cases (using WHO classifications) were mapped to create spatial patterns of pneumonia at the local health unit (barangay) level.ResultsThere were 2951 children with WHO‐defined clinical pneumonia, of whom 1074 were severe or very severely ill, 278 were radiographic, and 219 were hypoxaemic. While most children with pneumonia were from urban barangays, there was a disproportionately higher distribution of severe/very severe pneumonia in rural barangays and the most severe hypoxaemic children were concentrated in the northern barangays most distant from the regional hospital.ConclusionsMapping of ALRI at the local administrative health level can be performed relatively simply. If these principles are applied to routinely collected IMCI classification of disease at the district level in developing countries, such efforts can form the basis for directing public health and healthcare delivery efforts in a targeted manner.
Physical Activity Level and Associated Factors Among Higher Secondary School Students in Banke, Nepal: A Cross-Sectional Study
Authors: Paudel Susan , Subedi Narayan , Mehata Suresh 
Published: June 2015

Background:This study was carried out to assess physical activity level and identify associated factors among higher secondary school students in Banke district, Nepal.Methods:A school-based, cross-sectional descriptive study was conducted among 405 students studying in grades 11 and 12 in 7 higher secondary schools selected randomly. A self-administered questionnaire based on the International Physical Activity Questionnaire was used to measure physical activity level.Results:Only 5% of students were found to be inactive, and domestic and transport-related activities were major contributors to total physical activity score. No significant difference existed for total physical activity and domain-specific and activity-specific scores across different age groups when males and females were tested separately. Being male (P = .046), lower economic status (P = .026), living at a distance of less than 30 minutes (P = .007), walking/cycling to school (P < .001), and studying in government school (P < .001) were associated with increased physical activity scores on multivariate logistic regression analysis.Conclusion:Routine activities such as transport and household chores contributed greatly to total physical activity among students. This study highlights the need for physical activity promotion interventions at school addressing the associated factors and a need for greater focus on leisure-time physical activities.
Validity of Activity Monitor Step Detection Is Related to Movement Patterns
Authors: Hickey Amanda , John Dinesh , Sasaki Jeffer E. , Mavilia Marianna , Freedson Patty 
Published: June 2015

Background:There is a need to examine step-counting accuracy of activity monitors during different types of movements. The purpose of this study was to compare activity monitor and manually counted steps during treadmill and simulated free-living activities and to compare the activity monitor steps to the StepWatch (SW) in a natural setting.Methods:Fifteen participants performed laboratory-based treadmill (2.4, 4.8, 7.2 and 9.7 km/h) and simulated free-living activities (eg, cleaning room) while wearing an activPAL, Omron HJ720-ITC, Yamax Digi-Walker SW-200, 2 ActiGraph GT3Xs (1 in “low-frequency extension” [AGLFE] and 1 in “normal-frequency” mode), an ActiGraph 7164, and a SW. Participants also wore monitors for 1-day in their free-living environment. Linear mixed models identified differences between activity monitor steps and the criterion in the laboratory/free-living settings.Results:Most monitors performed poorly during treadmill walking at 2.4 km/h. Cleaning a room had the largest errors of all simulated free-living activities. The accuracy was highest for forward/rhythmic movements for all monitors. In the free-living environment, the AGLFE had the largest discrepancy with the SW.Conclusion:This study highlights the need to verify step-counting accuracy of activity monitors with activities that include different movement types/directions. This is important to understand the origin of errors in step-counting during free-living conditions.
Variation in Resistance Traits, Phylogenetic Backgrounds, and Virulence Genotypes among Escherichia coli Clinical Isolates from Adjacent Hospital Campuses Serving Distinct Patient Populations
Authors: Drawz Sarah M. , Porter Stephen , Kuskowski Michael A. , Johnston Brian , Clabots Connie , Kline Susan , Ferrieri Patricia , Johnson James R. 
Published: June 2015

ABSTRACT

Escherichia coli
sequence type 13 (ST131), an emergent cause of multidrug-resistant extraintestinal infections, has important phylogenetic subsets, notably the
H
30 and
H
30Rx subclones, with distinctive resistance profiles and, possibly, clinical associations. To clarify the local prevalence of these ST131 subclones and their associations with antimicrobial resistance, ecological source, and virulence traits, we extensively characterized 233 consecutive
E. coli
clinical isolates (July and August 2013) from the University of Minnesota Medical Center-Fairview Infectious Diseases and Diagnostic Laboratory, Minneapolis, MN, which serves three adjacent facilities (a children's hospital and low- and high-acuity adult facilities). ST131 accounted for 26% of the study isolates (more than any other clonal group), was distributed similarly by facility, and was closely associated with ciprofloxacin resistance and extended-spectrum β-lactamase (ESBL) production. The
H
30 and
H
30Rx subclones accounted for most ST131 isolates and for the association of ST131 with fluoroquinolone resistance and ESBL production. Unlike ST131
per se
, these subclones were distributed differentially by hospital, being most prevalent at the high-acuity adult facility and were absent from the children's hospital. The virulence gene profiles of ST131 and its subclones were distinctive and more extensive than those of other fluoroquinolone-resistant or ESBL-producing isolates. Within ST131,
bla
CTX-M-15
was confined to
H
30Rx isolates and other
bla
CTX-M
variants to non-Rx
H
30 isolates. Pulsed-field gel electrophoresis documented a predominance of globally distributed pulsotypes and no local outbreak pattern. These findings help clarify the epidemiology, ecology, and bacterial correlates of the
H
30 and
H
30Rx ST131 subclones by documenting a high overall prevalence but significant segregation by facility, strong associations with fluoroquinolone resistance and specific ESBL variants, and distinctive virulence gene associations that may confer fitness advantages over other resistant
E. coli
.
Mutations in Genes for the F
420
Biosynthetic Pathway and a Nitroreductase Enzyme Are the Primary Resistance Determinants in Spontaneous
In Vitro
-Selected PA-824-Resistant Mutants of Mycobacterium tuberculosis
Authors: Haver Hana L. , Chua Adeline , Ghode Pramila , Lakshminarayana Suresh B. , Singhal Amit , Mathema Barun , Wintjens René , Bifani Pablo 
Published: June 2015

ABSTRACT

Alleviating the burden of tuberculosis (TB) requires an understanding of the genetic basis that determines the emergence of drug-resistant mutants. PA-824 (pretomanid) is a bicyclic nitroimidazole class compound presently undergoing the phase III STAND clinical trial, despite lacking identifiable genetic markers for drug-specific resistant
Mycobacterium tuberculosis
. In the present study, we aimed to characterize the genetic polymorphisms of spontaneously generated PA-824-resistant mutant strains by surveying drug metabolism genes for potential mutations. Of the 183 independently selected PA-824-resistant
M. tuberculosis
mutants, 83% harbored a single mutation in one of five nonessential genes associated with either PA-824 prodrug activation (
ddn
, 29%;
fgd1
, 7%) or the tangential F
420
biosynthetic pathway (
fbiA
, 19%;
fbiB
, 2%;
fbiC
, 26%). Crystal structure analysis indicated that identified mutations were specifically located within the protein catalytic domain that would hinder the activity of the enzymes required for prodrug activation. This systematic analysis conducted of genotypes resistant to PA-824 may contribute to future efforts in monitoring clinical strain susceptibility with this new drug therapy.
Innate Inflammatory Response and Immunopharmacologic Activity of Micafungin, Caspofungin, and Voriconazole against Wild-Type and
FKS
Mutant Candida glabrata Isolates
Authors: Beyda Nicholas D. , Liao Guangling , Endres Bradley T. , Lewis Russell E. , Garey Kevin W. 
Published: June 2015

ABSTRACT

The direct or indirect interactions that antifungals have with the host immune response may play a significant role in defining their activity
in vivo
. However, the impact that acquired antifungal resistance has on the immunopharmacologic activity of antifungals is not well described. We assessed the immunopharmacologic activity of caspofungin, micafungin, and voriconazole among isolates of
Candida glabrata
with or without FKS-mediated echinocandin resistance. Clinical bloodstream isolates of
C. glabrata
from patients who did (
n
= 5) or did not (
n
= 3) develop persistent candidemia and who did (
n
= 2) or did not (
n
= 11) harbor FKS gene mutations were included. A cell-based assay was used to compare differences in macrophage activation among isolates when grown in the presence or absence of subinhibitory concentrations of caspofungin, micafungin, or voriconazole. In the absence of antifungals, macrophage activation was significantly lower for index
C. glabrata
isolates obtained from persistent candidemia patients than for those from nonpersistent patients (33% versus 79% increase over negative controls, respectively;
P
< 0.01). Growth of isolates possessing wild-type
FKS
genes in subinhibitory concentrations of micafungin or caspofungin, but not voriconazole, significantly increased macrophage inflammatory responses compared to untreated controls (1.25- to 2.75-fold increase,
P
< 0.01). For isolates harboring the
FKS2
hot spot 1 (HS1) S663P mutation, however, a significant increase was observed only with micafungin treatment (1.75-fold increase versus negative control,
P
< 0.01). Macrophage activation correlated with the level of unmasking of β-glucan in the cell wall. The diminished macrophage inflammatory response to isolates that caused persistent candidemia and differential immunopharmacologic activity of echinocandins among
FKS
mutants suggest that certain strains of
C. glabrata
may have a higher propensity for immunoevasion and development of antifungal resistance during treatment.
An
In Vitro
Combined Antibiotic-Antibody Treatment Eliminates Toxicity from Shiga Toxin-Producing Escherichia coli
Authors: Skinner Craig , Zhang Guodong , Patfield Stephanie , He Xiaohua 
Published: June 2015

ABSTRACT

Treating Shiga toxin-producing
Escherichia coli
(STEC) gastrointestinal infections is difficult. The utility of antibiotics for STEC treatment is controversial, since antibiotic resistance among STEC isolates is widespread and certain antibiotics dramatically increase the expression of Shiga toxins (Stxs), which are some of the most important virulence factors in STEC. Stxs contribute to life-threatening hemolytic uremic syndrome (HUS), which develops in considerable proportions of patients with STEC infections. Understanding the antibiotic resistance profiles of STEC isolates and the Stx induction potential of promising antibiotics is essential for evaluating any antibiotic treatment of STEC. In this study, 42 O157:H7 or non-O157 STEC isolates (including the “big six” serotypes) were evaluated for their resistance against 22 antibiotics by using an antibiotic array. Tigecycline inhibited the growth of all of the tested STEC isolates and also inhibited the production of Stxs (Stx2 in particular). In combination with neutralizing antibodies to Stx1 and Stx2, the tigecycline-antibody treatment fully protected Vero cells from Stx toxicity, even when the STEC bacteria and the Vero cells were cultured together. The combination of an antibiotic such as tigecycline with neutralizing antibodies presents a promising strategy for future STEC treatments.
The Times They Are a-Changin': Carbapenems for Extended-Spectrum-β-Lactamase-Producing Bacteria
Authors: Rodríguez-Baño Jesús 
Published: June 2015

ABSTRACT

Several antimicrobial agents are being investigated as alternatives to carbapenems in the treatment of infections caused by ESBL-producing
Enterobacteriaceae
, which may be useful in avoiding overuse of carbapenems in the context of recent global spread of carbapenem-resistant
Enterobacteriaceae
. The most promising candidates for invasive infections so far are β-lactam/β-lactamase inhibitor combinations and cephamycins.
Case-Control Study of the Risk Factors for Acquisition of Pseudomonas and Proteus Species during Tigecycline Therapy
Authors: Park Ga Eun , Kang Cheol-In , Wi Yu Mi , Ko Jae-Hoon , Lee Woo Joo , Lee Ji Yong , Cho Sun Young , Ha Young Eun , Chung Doo Ryeon , Peck Kyong Ran , Song Jae-Hoon 
Published: June 2015

ABSTRACT

Tigecycline is an important agent in clinical practice because of its broad-spectrum activity. However, it has no activity against
Pseudomonas
or
Proteus
species. We conducted a case-control study to analyze risk factors for the acquisition of
Pseudomonas
or
Proteus
spp. during tigecycline therapy. Placement of suction drainage at infected wound sites, ICU stay, and neurologic disease were identified as independent risk factors for the acquisition of
Pseudomonas
and
Proteus
spp.
Characterization of Epidemic IncI1-Iγ Plasmids Harboring Ambler Class A and C Genes in Escherichia coli and Salmonella enterica from Animals and Humans
Authors: Smith Hilde , Bossers Alex , Harders Frank , Wu Guanghui , Woodford Neil , Schwarz Stefan , Guerra Beatriz , Rodríguez Irene , van Essen-Zandbergen Alieda , Brouwer Michael , Mevius Dik 
Published: June 2015

ABSTRACT

The aim of the study was to identify the plasmid-encoded factors contributing to the emergence and spread of epidemic IncI1-Iγ plasmids obtained from
Escherichia coli
and
Salmonella enterica
isolates from animal and human reservoirs. For this, 251 IncI1-Iγ plasmids carrying various extended-spectrum β-lactamase (ESBL) or AmpC β-lactamase genes were compared using plasmid multilocus sequence typing (pMLST). Thirty-two of these plasmids belonging to different pMLST types were sequenced using Roche 454 and Illumina platforms. Epidemic IncI1-Iγ plasmids could be assigned to various dominant clades, whereas rarely detected plasmids clustered together as a distinct clade. Similar phylogenetic trees were obtained using only the plasmid backbone sequences, showing that the differences observed between the plasmids belonging to distinct clades resulted mainly from differences between their backbone sequences. Plasmids belonging to the various clades differed particularly in the presence/absence of genes encoding partitioning and addiction systems, which contribute to stable inheritance during cell division and plasmid maintenance. Despite this, plasmids belonging to the various phylogenetic clades also showed marked resistance gene associations, indicating the circulation of successful plasmid-gene combinations. The variation in
traY
and
excA
genes found in IncI1-Iγ plasmids is conserved within pMLST sequence types and plays a role in incompatibility, although functional study is needed to elucidate the role of these genes in plasmid epidemiology.
The Periplasmic Nitrate Reductase NapABC Supports Luminal Growth of Salmonella enterica Serovar Typhimurium during Colitis
Authors: Lopez Christopher A. , Rivera-Chávez Fabian , Byndloss Mariana X. , Bäumler Andreas J. 
Published: June 2015

ABSTRACT

The food-borne pathogen
Salmonella enterica
serovar Typhimurium benefits from acute inflammation in part by using host-derived nitrate to respire anaerobically and compete successfully with the commensal microbes during growth in the intestinal lumen. The
S
. Typhimurium genome contains three nitrate reductases, encoded by the
narGHI
,
narZYV
, and
napABC
genes. Work on homologous genes present in
Escherichia coli
suggests that nitrate reductase A, encoded by the
narGHI
genes, is the main enzyme promoting growth on nitrate as an electron acceptor in anaerobic environments. Using a mouse colitis model, we found, surprisingly, that
S
. Typhimurium strains with defects in either nitrate reductase A (
narG
mutant) or the regulator inducing its transcription in the presence of high concentrations of nitrate (
narL
mutant) exhibited growth comparable to that of wild-type
S
. Typhimurium. In contrast, a strain lacking a functional periplasmic nitrate reductase (
napA
mutant) exhibited a marked growth defect in the lumen of the colon. In
E. coli
, the
napABC
genes are transcribed maximally under anaerobic growth conditions in the presence of low nitrate concentrations. Inactivation of
narP
, encoding a response regulator that activates
napABC
transcription in response to low nitrate concentrations, significantly reduced the growth of
S
. Typhimurium in the gut lumen. Cecal nitrate measurements suggested that the murine cecum is a nitrate-limited environment. Collectively, our results suggest that
S
. Typhimurium uses the periplasmic nitrate reductase to support its growth on the low nitrate concentrations encountered in the gut, a strategy that may be shared with other enteric pathogens.