bluuebunny/crossref_metadata_2025_split huggingface dataset:
Disease severity staging system for idiopathic pulmonary fibrosis in Japan
Authors: Kondoh Yasuhiro , Taniguchi Hiroyuki , Kataoka Kensuke , Furukawa Taiki , Ando Masahiko , Murotani Kenta , Mishima Michiaki , Inoue Yoshikazu , Ogura Takashi , Bando Masashi , Hagiwara Koichi , Suda Takafumi , Chiba Hirofumi , Takahashi Hiroki , Sugiyama Yukihiko , Homma Sakae 
Published: August 2017

ABSTRACTBackground and objectiveIn Japan, the classification of disease severity of idiopathic pulmonary fibrosis (IPF) (J‐system) has been used in making decisions on medical care subsidies. The present J‐system consists of arterial partial pressure of oxygen (PaO2) and exercise desaturation in stages of I–IV. It provides a good prognostic classification in stages III and IV, but not in stages I and II. Therefore, we propose a revised system to improve discriminative ability in stages I and II.MethodsWe compared the revised J‐system with the present J‐system using Cox proportional hazards model to predict mortality rate. We also evaluated the recently proposed GAP (Gender, Age and Physiology) system in comparison to both J‐systems.ResultsTwo‐hundred and fifteen IPF patients were studied retrospectively. A univariate model showed that the present and revised J‐systems and a modified GAP system were all significant prognostic factors. The C‐statistic for discriminating prognosis was higher in the revised J‐system than the modified GAP system and the present J‐system (0.677, 0.652 and 0.659, respectively). The C‐statistics of these models produced from the 10 000 bootstrap samples were similar to those of the original models, suggesting good internal validation (0.665 (95% CI: 0.621–0.705), 0.645 (0.600–0.686) and 0.659 (0.616–0.700), respectively). Multivariate analysis revealed that the revised J‐system (P = 0.0038) and the modified GAP system (P = 0.0029) were independent prognostic factors.ConclusionThe revised J‐system can provide a better mortality prediction than the present one. Both the revised J‐system and the modified GAP system are independent and valuable tools for prognostication and clinical management for IPF.
Modelling Time Varying Heterogeneity in Recurrent Infection Processes: An Application to Serological Data
Authors: Abrams Steven , Wienke Andreas , Hens Niel 
Published: August 2017

SummaryFrailty models are often used in survival analysis to model multivariate time-to-event data. In infectious disease epidemiology, frailty models have been proposed to model heterogeneity in the acquisition of infection and to accommodate association in the occurrence of multiple types of infection. Although traditional frailty models rely on the assumption of lifelong immunity after recovery, refinements have been made to account for reinfections with the same pathogen. Recently, Abrams and Hens quantified the effect of misspecifying the underlying infection process on the basic and effective reproduction number in the context of bivariate current status data on parvovirus B19 and varicella zoster virus. Furthermore, Farrington, Unkel and their co-workers introduced and applied time varying shared frailty models to paired bivariate serological data. In this paper, we consider an extension of the proposed frailty methodology by Abrams and Hens to account for age-dependence in individual heterogeneity through the use of age-dependent shared and correlated gamma frailty models. The methodology is illustrated by using two data applications.
Bayesian Non-Parametric Conditional Copula Estimation of Twin Data
Authors: Valle Luciana Dalla , Leisen Fabrizio , Rossini Luca 
Published: August 2017

SummarySeveral studies on heritability in twins aim at understanding the different contribution of environmental and genetic factors to specific traits. Considering the national merit twin study, our purpose is to analyse correctly the influence of socio-economic status on the relationship between twins’ cognitive abilities. Our methodology is based on conditional copulas, which enable us to model the effect of a covariate driving the strength of dependence between the main variables. We propose a flexible Bayesian non-parametric approach for the estimation of conditional copulas, which can model any conditional copula density. Our methodology extends the work of Wu, Wang and Walker in 2015 by introducing dependence from a covariate in an infinite mixture model. Our results suggest that environmental factors are more influential in families with lower socio-economic position.
Shelf‐margin clinothem progradation, degradation and readjustment: Tanqua depocentre, Karoo Basin (South Africa)
Authors: Gomis‐Cartesio Luz E. , Poyatos‐Moré Miquel , Hodgson David M. , Flint Stephen S. 
Published: August 2017

AbstractDegradation of basin‐margin clinothems around the shelf‐edge rollover zone may lead to the generation of conduits through which gravity flows transport sediment downslope. Many studies from seismic‐reflection data sets show these features, but they lack small‐scale (centimetre to metre) sedimentary and stratigraphic observations on process interactions. Exhumed basin‐margin clinothems in the Tanqua depocentre (Karoo Basin) provide seismic‐reflection‐scale geometries and internal details of architecture with depositional dip and strike control. At the Geelhoek locality, clinothem parasequences comprise siltstone‐rich offshore deposits overlain by heterolithic prodelta facies and sandstone‐dominated deformed mouth bars. Three of these parasequences are truncated by a steep (6 to 22°), 100 m deep and 1·5 km wide asymmetrical composite erosion surface that delineates a shelf‐incised canyon. The fill, from base to top comprises: (i) thick‐bedded sandstone with intrabasinal clasts and multiple erosion surfaces; (ii) scour‐based interbedded sandstone and siltstone with tractional structures; and (iii) inverse‐graded to normal‐graded siltstone beds. An overlying 55 m thick coarsening‐upward parasequence fills the upper section of the canyon and extends across its interfluves. Younger parasequences display progressively shallower gradients during progradation and healing of the local accommodation. The incision surface resulted from initial oversteepening and high sediment supply triggering deformation and collapse at the shelf edge, enhanced by a relative sea‐level fall that did not result in subaerial exposure of the shelf edge. Previous work identified an underlying highly incised, sandstone‐rich shelf‐edge rollover zone across‐margin strike, suggesting that there was migration in the zone of shelf edge to upper‐slope incision over time. This study provides an unusual example of clinothem degradation and readjustment with three‐dimensional control in an exhumed basin‐margin succession. The work demonstrates that large‐scale erosion surfaces can develop and migrate due to a combination of factors at the shelf‐edge rollover zone and proposes additional criteria to predict clinothem incision and differential sediment bypass in consistently progradational systems.
Automated counting of sand‐sized particles in marine records
Authors: Becker Lukas W. M. , Hjelstuen Berit O. , Støren Eivind W. N. , Sejrup Hans Petter 
Published: August 2017

AbstractContent and fluxes of ice‐transported sand‐sized and gravel‐sized, lithic particles in marine sediment cores are a common tool used to reconstruct glacial variability. Ice‐rafted debris data sets are currently acquired in several different and often time‐consuming ways, and within various grain‐size fractions. This article proposes a novel workflow using an automated method to count ice‐rafted debris to reduce analysis time and subjectivity. The described method is based on the instrument ‘Morphologi G3’ from Malvern Instruments Limited and includes all pre‐processing and post‐processing steps. This particle characterization tool is an automated microscope combined with a proprietary software package. In this study, the analysis was performed on the 150 to 1000 μm fraction. If desired, grain counts can be carried out on the entire sand and silt fractions. However, this would result in a considerably greater turnover time. A total of 350 sediment samples from core MD99‐2283, taken on the upper continental slope at the southern part of the north‐east Atlantic margin, were counted with this automated method. In addition, a total of 161 samples were counted manually as a control on the reliability of the scanning. The comparison of automated versus manually counted biogenic and lithic material shows a convincing correlation between the two methods. The turnover time per automatically counted sample is around 20 min, the method requiring less experience and skills than manual counting. The results yield a promising, time‐saving new technique to achieve high‐resolution ice‐rafted debris counting records with acceptable error margins.
Median preoptic glutamatergic neurons promote thermoregulatory heat loss and water consumption in mice
Authors: Abbott Stephen B. G. , Saper Clifford B. 
Published: August 2017

Key points
Glutamatergic neurons in the median preoptic area were stimulated using genetically targeted Channelrhodopsin 2 in transgenic mice.
Stimulation of glutamatergic median preoptic area neurons produced a profound hypothermia due to cutaneous vasodilatation.
Stimulation also produced drinking behaviour that was inhibited as water was ingested, suggesting pre‐systemic feedback gating of drinking.
Anatomical mapping of the stimulation sites showed that sites associated with hypothermia were more anteroventral than those associated with drinking, although there was substantial overlap.
AbstractThe median preoptic nucleus (MnPO) serves an important role in the integration of water/electrolyte homeostasis and thermoregulation, but we have a limited understanding these functions at a cellular level. Using Cre–Lox genetic targeting of Channelrhodospin 2 in VGluT2 transgenic mice, we examined the effect of glutamatergic MnPO neuron stimulation in freely behaving mice while monitoring drinking behaviour and core temperature. Stimulation produced a strong hypothermic response in 62% (13/21) of mice (core temperature: −4.6 ± 0.5°C, P = 0.001 vs. controls) caused by cutaneous vasodilatation. Stimulating glutamatergic MnPO neurons also produced robust drinking behaviour in 82% (18/22) of mice. Mice that drank during stimulation consumed 912 ± 163 μl (n = 8) during a 20 min trial in the dark phase, but markedly less during the light phase (421 ± 83 μl, P = 0.0025). Also, drinking during stimulation was inhibited as water was ingested, suggesting pre‐systemic feedback gating of drinking. Both hypothermia and drinking during stimulation occurred in 50% of mice tested. Anatomical mapping of the stimulation sites showed that sites associated with hypothermia were more anteroventral than those associated with drinking, although there was substantial overlap. Thus, activation of separate but overlapping populations of glutamatergic MnPO neurons produces effects on drinking and autonomic thermoregulatory mechanisms, providing a structural basis for their frequently being coordinated (e.g. during hyperthermia).
The Long-Term Impact of Osteoarthritis Following Knee Surgery in Former College Athletes
Authors: Simon Janet E. , Grooms Dustin R. , Docherty Carrie L. 
Published: August 2017

Context: Individuals who sustain a knee surgery have been shown to have an increased likelihood to develop osteoarthritis (OA). Objective: Identify the consequences of knee surgery in a cohort of former college athletes. Design: Cross-sectional. Setting: Research laboratory. Participants: A group of 100 former Division I college athletes aged 40–65 years (60 males and 40 females) participated in the study. Interventions: All individuals self-reported whether they sustained a knee injury during college requiring surgery and if they have been diagnosed with knee OA by a medical physician post knee injury. Individuals were categorized into 3 groups: no history of knee injury requiring surgery (33 males and 24 females; 54.53 [5.95] y), history of knee surgery in college with no diagnosis of OA later in life (4 males and 6 females; 51.26 [7.29] y), and history of knee surgery in college with physician diagnosed OA later in life (23 males and 10 females; 54.21 [7.64] y). All individuals completed the knee injury and osteoarthritis outcome score (KOOS) and short form-36 version 2. Main Outcome Measures: Scores on the KOOS and short form-36 version 2. Results: A majority (76.7%) of individuals who had a knee surgery in college did develop OA. The largest mean differences were between the healthy knee and surgical knee/OA groups on the KOOS-quality of life scale (mean difference: 49.76; χ2(3) = 44.65; P < .001) and KOOS-sports scale (mean difference: 43.69; χ2(3) = 28.69; P < .001), with the surgical knee/OA group scoring worse. Conclusions: Later in life functional limitations were observed in individuals who sustained a knee injury requiring surgery and developed OA. These findings support increased efforts toward prevention of knee injuries and consideration of the long-term implication when making treatment and return to activity decisions.
Comparison of a Vibration Roller and a Nonvibration Roller Intervention on Knee Range of Motion and Pressure Pain Threshold: A Randomized Controlled Trial
Authors: Cheatham Scott W. , Stull Kyle R. , Kolber Morey J. 
Published: August 2017

Background: Roller massage (RM) has become a common intervention among health and fitness professionals. Recently, manufacturers have merged the science of vibration therapy and RM with the development of vibration rollers. Of interest, is the therapeutic effects of such RM devices. Purpose: The purpose of this study was to compare the effects of a vibration roller and nonvibration roller intervention on prone knee-flexion passive range of motion (ROM) and pressure pain threshold (PPT) of the quadriceps musculature. Methods: Forty-five recreationally active adults were randomly allocated to one of 3 groups: vibration roller, nonvibration roller, and control. Each roller intervention lasted a total of 2 minutes. The control group did not roll. Dependent variables included prone knee-flexion ROM and PPT measures. Statistical analysis included parametric and nonparametric tests to measure changes among groups. Results: The vibration roller demonstrated the greatest increase in PPT (180 kPa, P < .001), followed by the nonvibration roller (112 kPa, P < .001) and control (61 kPa, P < .001). For knee flexion ROM, the vibration roller demonstrated the greatest increase in ROM (7°, P < .001), followed by the nonvibration roller (5°, P < .001) and control (2°, P < .001). Between groups, there was a significant difference in PPT between the vibration and nonvibration roller (P = .03) and vibration roller and control (P < .001). There was also a significant difference between the nonvibration roller and control (P < .001). For knee ROM, there was no significant difference between the vibration and nonvibration roller (P = .31). A significant difference was found between the vibration roller and control group (P < .001) and nonvibration roller and control group (P < .001). Conclusion: The results suggest that a vibration roller may increase an individual’s tolerance to pain greater than a nonvibration roller. This investigation should be considered a starting point for future research on this technology.
Hip Flexor and Knee Extensor Muscularity Are Associated With Sprint Performance in Sprint-Trained Preadolescent Boys
Authors: Tottori Nobuaki , Suga Tadashi , Miyake Yuto , Tsuchikane Ryo , Otsuka Mitsuo , Nagano Akinori , Fujita Satoshi , Isaka Tadao 
Published: August 2017

Purpose: We attempted to determine the relationships between the cross-sectional area (CSA) of the trunk and lower limb muscles and sprint performance in male preadolescent sprinters. Methods: Fifteen sprint-trained preadolescent boys (age 11.6 ± 0.4 y) participated in this study. The CSAs of the participants’ trunk and lower limb muscles were measured using magnetic resonance imaging, and these muscles were normalized with free-fat mass. To assess participants’ sprint performance, sprint time and variables during the 50-m sprint test were measured. The sprint variables were expressed as their indices by normalizing with body height. Results: The relative CSAs of psoas major, adductors, and quadriceps femoris were significantly correlated with sprint time (r = −.802, −.643, and −.639). Moreover, the relative CSAs of these muscles were significantly correlated with indices of sprint velocity (r = .694, .612, and .630) and step frequency (r = .687, .740, and .590) but not with that of step length. Conclusions: These findings suggest that greater hip flexor and knee extensor muscularity in male preadolescent sprinters may help achieve superior sprint performance by potentially enhancing their moments, which may be induced by increased step frequency rather than step length during sprinting.
Pharmacokinetic-Pharmacodynamic Target Attainment Analyses To Determine Optimal Dosing of Ceftazidime-Avibactam for the Treatment of Acute Pulmonary Exacerbations in Patients with Cystic Fibrosis
Authors: Bensman Timothy J. , Wang Joshua , Jayne Jordanna , Fukushima Lynn , Rao Adupa P. , D'Argenio David Z. , Beringer Paul M. 
Published: August 2017

ABSTRACT

Acute pulmonary exacerbations (APE) involving
Pseudomonas aeruginosa
are associated with increased morbidity and mortality in cystic fibrosis (CF) patients. Drug resistance is a significant challenge to treatment. Ceftazidime-avibactam (CZA) demonstrates excellent
in vitro
activity against isolates recovered from CF patients, including drug-resistant strains. Altered pharmacokinetics (PK) of several beta-lactam antibiotics have been reported in CF patients. Therefore, this study sought to characterize the PK of CZA and perform target attainment analyses to determine the optimal treatment regimen. The PK of CZA in 12 adult CF patients administered 3 intravenous doses of 2.5 g every 8 h infused over 2 h were determined. Population modeling utilized the maximum likelihood expectation method. Monte Carlo simulations determined the probability of target attainment (PTA). An exposure target consisting of the cumulative percentage of a 24-h period that the free drug concentration exceeds the MIC under steady-state pharmacokinetic conditions (
fT
>MIC
) was evaluated for ceftazidime (CAZ), and an exposure target consisting of the cumulative percentage of a 24-h period that the free drug concentration exceeds a 1-mg/liter threshold concentration (
fT
>1 mg/liter
) was evaluated for avibactam (AVI). Published CAZ and CZA MIC distributions were incorporated to evaluate cumulative response probabilities. CAZ and AVI were best described by one-compartment models. The values of total body clearance (CL; CAZ CL, 7.53 ± 1.28 liters/h; AVI CL, 12.30 ± 1.96 liters/h) and volume of distribution (
V
; CAZ
V
, 18.80 ± 6.54 liters; AVI
V
, 25.30 ± 4.43 liters) were broadly similar to published values for healthy adults. CZA achieved a PTA (
fT
>MIC
, 50%) of >0.9 for MICs of ≤16 mg/liter. The overall likelihood of a treatment response was 0.82 for CZA, whereas it was 0.42 for CAZ. These data demonstrate improved pharmacodynamics of CZA in comparison with those of CAZ and provide guidance on the optimal dosing of CZA for future studies. (This study has been registered at ClinicalTrials.gov under registration no. NCT02504827.)
In Vitro
Activities of Gepotidacin (GSK2140944) and Other Antimicrobial Agents against Human Mycoplasmas and Ureaplasmas
Authors: Waites Ken B. , Crabb Donna M. , Xiao Li , Duffy Lynn B. 
Published: August 2017

ABSTRACT

Gepotidacin, a novel first-in-class triazaacenaphthylene topoisomerase II inhibitor, was tested against 85 type strains and clinical isolates of
Mycoplasma pneumoniae
,
Mycoplasma hominis
,
Mycoplasma genitalium
,
Ureaplasma parvum
, and
Ureaplasma urealyticum
in comparison to levofloxacin, moxifloxacin, azithromycin or clindamycin, and tetracycline. Gepotidacin MIC
90
s (μg/ml) were 0.125 (
M. pneumoniae
), 0.032 (
M. genitalium
), 2 (
M. hominis
), and 8 (
Ureaplasma
species). Gepotidacin activity was not affected by resistance to fluoroquinolones, tetracyclines, or macrolides in the strains tested. Gepotidacin merits further study for treating infections caused by these organisms.
Identification of Plasmid-Mediated Quinolone Resistance in Salmonella Isolated from Swine Ceca and Retail Pork Chops in the United States
Authors: Tyson Gregory H. , Tate Heather P. , Zhao Shaohua , Li Cong , Dessai Uday , Simmons Mustafa , McDermott Patrick F. 
Published: August 2017

ABSTRACT

Fluoroquinolones are important antimicrobial drugs used to treat human
Salmonella
infections, and resistance is rare in the United States for isolates from human and animal sources. Recently, a number of
Salmonella
isolates from swine cecal contents and retail pork products from National Antimicrobial Resistance Monitoring System (NARMS) surveillance exhibited decreased susceptibility to ciprofloxacin. We identified two
qnrB19
quinolone resistance plasmids that are predominantly responsible for this phenomenon and found them distributed among several
Salmonella
serotypes isolated throughout the United States.
Cystic Fibrosis Transmembrane Conductance Regulator Reduces Microtubule-Dependent Campylobacter jejuni Invasion
Authors: Kido Junko , Shimohata Takaaki , Amano Sachie , Hatayama Sho , Nguyen Anh Quoc , Sato Yuri , Kanda Yuna , Tentaku Aya , Fukushima Shiho , Nakahashi Mutsumi , Uebanso Takashi , Mawatari Kazuaki , Takahashi Akira 
Published: August 2017

ABSTRACT

Campylobacter
jejuni
is a foodborne pathogen that induces gastroenteritis. Invasion and adhesion are essential in the process of
C. jejuni
infection leading to gastroenteritis. The mucosal layer plays a key role in the system of defense against efficient invasion and adhesion by bacteria, which is modulated by several ion channels and transporters mediated by water flux in the intestine. The cystic fibrosis transmembrane conductance regulator (CFTR) plays the main role in water flux in the intestine, and it is closely associated with bacterial clearance. We previously reported that
C. jejuni
infection suppresses CFTR channel activity in intestinal epithelial cells; however, the mechanism and importance of this suppression are unclear. This study sought to elucidate the role of CFTR in
C. jejuni
infection. Using HEK293 cells that stably express wild-type and mutated CFTR, we found that CFTR attenuated
C. jejuni
invasion and that it was not involved in bacterial adhesion or intracellular survival but was associated with microtubule-dependent intracellular transport. Moreover, we revealed that CFTR attenuated the function of the microtubule motor protein, which caused inhibition of
C. jejuni
invasion, but did not affect microtubule stability. Meanwhile, the CFTR mutant G551D-CFTR, which had defects in channel activity, suppressed
C. jejuni
invasion, whereas the ΔF508-CFTR mutant, which had defects in maturation, did not suppress
C. jejuni
invasion, suggesting that CFTR suppression of
C. jejuni
invasion is related to CFTR maturation but not channel activity. When these findings are taken together, it may be seen that mature CFTR inhibits
C. jejuni
invasion by regulating microtubule-mediated pathways. We suggest that CFTR plays a critical role in cellular defenses against
C. jejuni
invasion and that suppression of CFTR may be an initial step in promoting cell invasion during
C. jejuni
infection.