bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of the Kinematic Lower Boundary Condition on the Spectral and Autocorrelation Structure of Annular Variability in the Troposphere
Authors: Kunz Torben , Greatbatch Richard J. 
Published: January 2014

Abstract
The dynamical origin of the spectral and autocorrelation structure of annular variability in the troposphere is investigated by a deductive approach. Specifically, the structure of the power spectrum and autocorrelation function of the zonal-mean geopotential is analyzed for the case of a quasigeostrophic spherical atmosphere subject to a white noise mechanical forcing applied in a single Hough mode and concentrated at a particular level in the vertical, with vertically uniform Newtonian cooling and Rayleigh drag concentrated at a rigid lower boundary. Analytic expressions for the power spectrum are presented together with expressions for an approximate red noise (i.e., a Lorentzian-shaped) power spectrum. It is found that for an infinitely deep atmosphere the power spectrum can be well approximated by a red noise process for the first few Hough modes (associated with large Rossby heights), provided the distance from the forcing is not larger than about one Rossby height. When a frictional rigid lower boundary is included, however, the approximation is generally bad. The high-frequency part of the power spectrum exhibits near-exponential behavior and the autocorrelation function shows a transition from a rapid decay at short lags to a much slower decay at longer lags, if the thermal and mechanical damping time scales are sufficiently well separated. Since observed annular variability exhibits the same characteristics, the above results lead to the hypothesis that these characteristics may, to some extent, be intrinsic to the linear zonal-mean response problem—although the need for an additional contribution from eddy feedbacks is also implied by the results.
Diurnal Spatial Variability of Great Plains Summer Precipitation Related to the Dynamics of the Low-Level Jet
Authors: Pu Bing , Dickinson Robert E. 
Published: January 2014

Abstract
Diurnal variations of the Great Plains low-level jet (GPLLJ) and vertical motions have been related to the development of summer precipitation individually, but their underlying connection and consequences for the nocturnal and afternoon precipitation peaks are less discussed. This paper examines how together they help explain the spatial pattern of the frequency of summer convective precipitation over the Great Plains. A one-layer linearized boundary layer model is used to reproduce the diurnal cycle of the GPLLJ. Its periodic rising and sinking motions compare favorably with those of the North American Regional Reanalysis (NARR) climatology.
Its development of rising motion is also consistent with the enhanced occurrence of nocturnal convective precipitation over the central and eastern Great Plains (90°–100°W) and afternoon maximum over the western Great Plains (100°–105°W). The diurnal phasing of the vertical motions can be captured by the model only if the diurnal oscillation of the jet is forced by both near surface geopotential gradients and friction with observed diurnal variability.
The diurnal variation of the vertical velocity (or boundary layer convergence and divergence) is explained by local vorticity balance; that is, following the diurnal oscillation of the jet, the zonal gradient of the meridional wind oscillates and, thus, relative vorticity and its tendency. The slowing down of the jet after midnight decreases the anticyclonic (cyclonic) vorticity and consequently gives a positive (negative) vorticity tendency to the east (west) of the jet core; anomalous rising (sinking) motions occur to balance these positive (negative) vorticity tendencies. The pattern reverses when the jet is relatively weak.
Understanding Thermal Drift in Liquid Nitrogen Loads Used for Radiometric Calibration in the Field
Authors: Paine Scott N. , Turner David D. , Küchler Nils 
Published: January 2014

Abstract
An absorbing load in a liquid nitrogen bath is commonly used as a radiance standard for calibrating radiometers operating at microwave to infrared wavelengths. It is generally assumed that the physical temperature of the load is stable and equal to the boiling point temperature of pure N2 at the ambient atmospheric pressure. However, this assumption will fail to hold when air movement, as encountered in outdoor environments, allows O2 gas to condense into the bath. Under typical conditions, initial boiling point drift rates of order 25 mK min−1 can occur, and the boiling point of a bath maintained by repeated refilling with pure N2 can eventually shift by approximately 2 K. Laboratory bench tests of a liquid nitrogen bath under simulated wind conditions are presented together with an example of an outdoor radiometer calibration that demonstrates the effect, and the physical processes involved are explained in detail. A key finding is that in windy conditions, changes in O2 volume fraction are related accurately to fractional changes in bath volume due to boiloff, independent of wind speed. This relation can be exploited to ensure that calibration errors due to O2 contamination remain within predictable bounds.
YC-1 enhances the anti-tumor activity of sorafenib through inhibition of signal transducer and activator of transcription 3 (STAT3) in hepatocellular carcinoma
Authors: Kong Jian , Kong Fandong , Gao Jun , Zhang Qiangbo , Dong Shuying , Gu Fang , Ke Shan , Pan Bing , Shen Qiang , Sun Huichuan , Zheng Lemin , Sun Wenbing 
Published: January 2014

Abstract

Background
Traditional systemic chemotherapy does not provide survival benefits in patients with hepatocellular carcinoma (HCC). Molecular targeted therapy shows promise for HCC treatment, however, the duration of effectiveness for targeted therapies is finite and combination therapies offer the potential for improved effectiveness.

Methods
Sorafenib, a multikinase inhibitor, and YC-1, a soluble guanylyl cyclase (sGC) activator, were tested in HCC by proliferation assay, cell cycle analysis and western blot in vitro and orthotopic and ectopic HCC models in vivo.

Results

In vitro, combination of sorafenib and YC-1 synergistically inhibited proliferation and colony formation of HepG2, BEL-7402 and HCCLM3 cells. The combination also induced S cell cycle arrest and apoptosis, as observed by activated PARP and caspase 8. Sorafenib and YC-1 respectively suppressed the expression of phosphorylated STAT3 (p-STAT3) (Y705) in a dose- and time-dependent manner. Combination of sorafenib and YC-1 significantly inhibited the expression of p-STAT3 (Y705) (S727), p-ERK1/2, cyclin D1 and survivin and SHP-1 activity compared with sorafenib or YC-1 used alone in all tested HCC cell lines. In vivo, sorafenib-YC-1 combination significantly suppressed the growth of HepG2 tumor xenografts with decreased cell proliferation and increased apoptosis observed by PCNA and PARP. Similar results were also confirmed in a HCCLM3 orthotopic model. There was a reduction in CD31-positive blood vessels and reduced VEGF expression, which suggested a combinational effect of sorafenib and YC-1 on angiogenesis. The reduced expression of p-STAT3, cyclin D1 and survivin was also observed with the combination of sorafenib and YC-1.

Conclusions
Our data show that sorafenib-YC-1 combination is a novel potent therapeutic agent that can target the STAT3 signaling pathway to inhibit HCC tumor growth.
Risk factors associated with negative in-vivodiagnostic results in bovine tuberculosis-infected cattle in Spain
Authors: Álvarez Julio , Perez Andrés , Marqués Sergio , Bezos Javier , Grau Anna , de la Cruz Maria Luisa , Romero Beatriz , Saez Jose Luis , del Rosario Esquivel Maria , del Carmen Martínez Maria , Mínguez Olga , de Juan Lucía , Domínguez Lucas 
Published: January 2014

Abstract

Background
Despite great effort and investment incurred over decades to control bovine tuberculosis (bTB), it is still one of the most important zoonotic diseases in many areas of the world. Test-and-slaughter strategies, the basis of most bTB eradication programs carried out worldwide, have demonstrated its usefulness in the control of the disease. However, in certain countries, eradication has not been achieved due in part to limitations of currently available diagnostic tests. In this study, results of in-vivo and post-mortem diagnostic tests performed on 3,614 animals from 152 bTB-infected cattle herds (beef, dairy, and bullfighting) detected in 2007–2010 in the region of Castilla y León, Spain, were analyzed to identify factors associated with positive bacteriological results in cattle that were non-reactors to the single intradermal tuberculin test, to the interferon-gamma (IFN-γ) assay, or to both tests applied in parallel (Test negative/Culture + animals, T-/C+). The association of individual factors (age, productive type, and number of herd-tests performed since the disclosure of the outbreak) with the bacteriology outcome (positive/negative) was analyzed using a mixed multivariate logistic regression model.

Results
The proportion of non-reactors with a positive post-mortem result ranged from 24.3% in the case of the SIT test to 12.9% (IFN-γ with 0.05 threshold) and 11.9% (95% CI 9.9-11.4%) using both tests in parallel. Older (>4.5 years) and bullfighting cattle were associated with increased odds of confirmed bTB infection by bacteriology, whereas dairy cattle showed a significantly lower risk. Ancillary use of IFN-γ assay reduced the proportion of T-/C + animals in high risk groups.

Conclusions
These results demonstrate the likelihood of positive bacteriological results in non-reactor cattle is influenced by individual epidemiological factors of tested animals. Increased surveillance on non-reactors with an increased probability of being false negative could be helpful to avoid bTB persistence, particularly in chronically infected herds. These findings may aid in the development of effective strategies for eradication of bTB in Spain.
Long-term functional donor site morbidity of the free radial forearm flap in head and neck cancer survivors
Authors: Orlik Jason R , Horwich Peter , Bartlett Clark , Trites Jonathan , Hart Robert , Taylor S Mark 
Published: January 2014

Background To assess the functional donor site morbidity of the forearm free flap in patients surviving at least 2 years after ablative head and neck cancer surgery in a tertiary care centre. Methods This study involved nine long-term survivors (2 year post-operative) who had forearm free flaps to reconstruct head and neck defects. All flaps were raised from the non-dominant arm. The non-donor side acted as a control for all patients. Objective measurements were as follows: grip, tip pinch and key pinch strength measured with dynamometers; flexion, extension, radial and ulnar deviation and pronation and supination range of motion at the wrist measured with goniometry; A timed manual dexterity task was performed with a grooved pegboard test, and sensation of the radial nerve was tested with Semmes Weinstein monofilaments. Subjective measurements included a validated patient questionnaire of hand function and opinions of scar appearance as well as a validated scar assessment from two different observers. Results Pronation at the wrist, manual dexterity and sensation were found to be significantly reduced in the donor side compared to the non-donor side. Inter-rater agreement between the two observers was found to be poor, except for an acceptable correlation between overall scar opinions. No correlations were found between any subjective or objective items or between the patient's and the observers’ subjective evaluations. Conclusions Donor site morbidity can be demonstrated with objective testing however this is accepted and well tolerated by head and neck cancer patients.
Genome sequencing accuracy by RCA-seq versus long PCR template cloning and sequencing in identification of human papillomavirus type 58
Authors: Wang Xiaohong , Li Yang , Ni Ting , Xie Xing , Zhu Jun , Zheng Zhi-Ming 
Published: January 2014

Abstract

Background
Genome variations in human papillomaviruses (HPVs) are common and have been widely investigated in the past two decades. HPV genotyping depends on the finding of the viral genome variations in the L1 ORF. Other parts of the viral genome variations have also been implicated as a possible genetic factor in viral pathogenesis and/or oncogenicity.

Results
In this study, the HPV58 genome in cervical lesions was completely sequenced both by rolling-circle amplification of total cell DNA and deep sequencing (RCA-seq) and by long PCR template cloning and sequencing. By comparison of three HPV58 genome sequences decoded from three clinical samples to reference HPV-58, we demonstrated that RCA-seq is much more accurate than long-PCR template cloning and sequencing in decoding HPV58 genome. Three HPV58 genomes decoded by RCA-seq displayed a total of 52 nucleotide substitutions from reference HPV58, which could be verified by long PCR template cloning and sequencing. However, the long PCR template cloning and sequencing led to additional nucleotide substitutions, insertions, and deletions from an authentic HPV58 genome in a clinical sample, which vary from one cloned sequence to another. Because the inherited error-prone nature of Tgo DNA polymerase used in preparation of the long PCR templates of HPV58 genome from the clinical samples, the measurable error rate in incorporation of nucleotide into an elongating DNA template was about 0.149% ±0.038% in our studies.

Conclusions
Since PCR template cloning and sequencing is widely used in identification of single nucleotide polymorphism (SNP), our data indicate that a serious caution should be taken in finding of true SNPs in various genetic studies.
Differential protein occupancy profiling of the mRNA transcriptome
Authors: Schueler Markus , Munschauer Mathias , Gregersen Lea Haarup , Finzel Ana , Loewer Alexander , Chen Wei , Landthaler Markus , Dieterich Christoph 
Published: January 2014

Abstract
Background
RNA-binding proteins (RBPs) mediate mRNA biogenesis, translation and decay. We recently developed an approach to profile transcriptome-wide RBP contacts on polyadenylated transcripts by next-generation sequencing. A comparison of such profiles from different biological conditions has the power to unravel dynamic changes in protein-contacted cis-regulatory mRNA regions without a priori knowledge of the regulatory protein component.

Results
We compared protein occupancy profiles of polyadenylated transcripts in MCF7 and HEK293 cells. Briefly, we developed a bioinformatics workflow to identify differential crosslinking sites in cDNA reads of 4-thiouridine crosslinked polyadenylated RNA samples. We identified 30,000 differential crosslinking sites between MCF7 and HEK293 cells at an estimated false discovery rate of 10%. 73% of all reported differential protein-RNA contact sites cannot be explained by local changes in exon usage as indicated by complementary RNA-seq data. The majority of differentially crosslinked positions are located in 3′ UTRs, show distinct secondary-structure characteristics and overlap with binding sites of known RBPs, such as ELAVL1. Importantly, mRNA transcripts with the most significant occupancy changes show elongated mRNA half-lives in MCF7 cells.

Conclusions
We present a global comparison of protein occupancy profiles from different cell types, and provide evidence for altered mRNA metabolism as a result of differential protein-RNA contacts. Additionally, we introduce POPPI, a bioinformatics workflow for the analysis of protein occupancy profiling experiments. Our work demonstrates the value of protein occupancy profiling for assessing cis-regulatory RNA sequence space and its dynamics in growth, development and disease.
The Robustness Case for Proportional Liability
Authors: Stremitzer Alexander , Tabbach Avraham D. 
Published: January 2014

AbstractIn important areas like medical malpractice and environmental torts, injurers are potentially insolvent and courts may make errors in determining liability (e.g. due to hindsight bias). We show that proportional liability, which holds a negligent injurer liable for harm discounted with the probability that the harm was caused by the injurer’s negligence, is less susceptible to these imperfections and therefore socially preferable to all other liability rules currently contemplated by courts. We also provide a result which might be useful to regulators when calculating minimum capital requirements or minimum mandatory insurance for different industries.
Thyroid hormones and the heart
Authors: Vargas-Uricoechea Hernando , Sierra-Torres Carlos Hernán 
Published: January 2014

Abstract
Thyroid hormones have a significant impact on heart function, mediated by genomic and non-genomic effects. Consequently, thyroid hormones deficit as well as excess are expected to result in profound changes in cardiac function regulation and cardiovascular hemodynamics. Thyroid hormones upregulate the expression of the sarcoplasmic reticulum calcium-activated ATPase and downregulate the expression of phospholamban. Overall, hyperthyroidism is characterized by an increase in resting heart rate, blood volume, stroke volume, myocardial contractility, and ejection fraction. The development of “high-output heart failure” in hyperthyroidism may be due to “tachycardia-mediated cardiomyopathy.” In contrast, in the hypothyroid state, thyroid hormone deficiency results in lower heart rate and weakening of myocardial contraction and relaxation, with prolonged systolic and early diastolic times. Cardiac preload is decreased owing to impaired diastolic function, cardiac afterload is increased, and chronotropic and inotropic functions are reduced. Subclinical thyroid dysfunction is relatively common in patients >65 years of age. In general, subclinical hypothyroidism increases the risk of cardiovascular heart disease (CHD) mortality and CHD events, but not of total mortality. The risk of CHD mortality and atrial fibrillation (but not other outcomes) in subclinical hyperthyroidism is higher among patients with very low levels of thyrotropin. Finally, medications such as amiodarone may induce hypothyroidism (mediated by the Wolff-Chaikoff effect) as well as hyperthyroidism (mediated by the Jod-Basedow effect). In both instances, the underlying cause is the high concentration of iodine in this medication. The purpose of this review is to assess the effects of thyroid hormones on the heart, and their clinical repercussions.
Silent chorioamnionitis and associated pregnancy outcomes: a review of clinical data gathered over a 16-year period
Authors: Horvath Boldizsár , Lakatos Ferenc , Tóth Csaba , Bödecs Tamás , Bódis József 
Published: January 2014

Abstract

Objective: To assess neonatal outcomes and associated findings in pregnant women identified after delivery as having had underlying subclinical chorioamnionitis by either histology or bacterial culture.

Methods: In 16 years, 8974 clinical, histological, and bacterial culture data were obtained retrospectively.

Results: Placental histology was analyzed in 4237 pregnancies (2785 term and 1452 preterm) and 4737 amniotic cavity cultures were obtained during 5446 cesarean deliveries (3268 term and 1469 preterm). Histological results and bacterial cultures were both available in 1270 of the preterm deliveries. Histology revealed inflammation, suggestive of infection, in 13.6% of placentas. Subclinical acute chorioamnionic inflammation was confirmed in 142 out of 2785 term pregnancies (5.1%) and in 436 out of 1452 preterm pregnancies (30.0%, P<0.001). Bacteriological culture of the intrauterine cavity was obtained from the lower uterine segment of the uterus during cesarean section. A positive culture was found in 19.9% of all cases (941/4737), this proportion was significantly higher in preterm deliveries (343/1273, 26.9%) than in term (17.3%, P<0.001). The lower the birth-weight or gestational age, the higher the frequency of silent infections in the uterine cavity.

Conclusions: Our study findings support the association between intra-amniotic infections and preterm delivery.
Influence of Parstatin on Experimental Periodontal Disease and Repair in Rats
Authors: Spolidorio Luís Carlos , Ramalho Lucas Pablo Dallari , Steffens Joao Paulo , da Silva Henrique Aparecido Bueno , Tubero Euzebio Alves Vanessa , Palomari Spolidorio Denise M. , Holzhausen Marinella 
Published: January 2014

Background: Parstatin is a 41‐amino acid peptide, formed by proteolytic cleavage on activation of the protease activated receptor‐1, with antiangiogenic properties. The purpose of this study is to evaluate the influence of synthetic parstatin on experimental periodontal disease and repair in rats.Methods: Ligature‐induced periodontitis was established in rats and the influence of parstatin administration was assessed after 8 and 15 days for periodontal disease and 24 hours and 8 days after repair after ligature removal.Results: Parstatin administration significantly inhibited gingival myeloperoxidase activity, interleukin (IL)‐1β, tumor necrosis factor‐α, and IL‐6 levels and led to suppression of macrophages and collagen degradation. At periodontal tissues under repair, parstatin increased the gingival levels of endostatin and decreased vascular endothelial growth factor expression and blood vessel number but did not influence histologic healing. In addition, the tomographic linear bone loss was significantly reduced at 15 days of periodontitis when the rats were treated with parstatin compared to their respective phosphate‐buffered saline–treated controls.Conclusions: Parstatin suppresses the periodontal tissue breakdown followed by experimental periodontitis in rats and did not impair periodontal tissue repair, despite its antiangiogenic effect. Parstatin may represent a novel approach to modulate host response in chronic periodontal disease.
Risk Factors for Infection Following Total Joint Arthroplasty in Rheumatoid Arthritis
Authors: Somayaji Ranjani , Barnabe Cheryl , Martin Liam 
Published: January 2014

Objectives:
Determine risk factors for infection following hip or knee total joint arthroplasty in patients with
rheumatoid arthritis.

Methods:
All rheumatoid arthritis patients with a hip or knee arthroplasty between years 2000 and 2010 were identified
from population-based administrative data from the Calgary Zone of Alberta Health Services. Clinical data from patient
charts during the hospital admission and during a one year follow-up period were extracted to identify incident infections.

Results:
We identified 381 eligible procedures performed in 259 patients (72.2% female, mean age 63.3 years, mean body
mass index 27.6 kg/m2). Patient comorbidities were hypertension (43.2%), diabetes (10.4%), coronary artery disease
(13.9%), smoking (10.8%) and obesity (32%). Few infectious complications occurred: surgical site infections occurred
within the first year after 5 procedures (2 joint space infections, 3 deep incisional infections). Infections of non-surgical
sites (urinary tract, skin or respiratory, n=4) complicated the hospital admission. The odds ratio for any post-arthroplasty
infection was increased in patients using prednisone doses exceeding 15 mg/day (OR 21.0, 95%CI 3.5-127.2, p=<0.001),
underweight patients (OR 6.0, 95%CI 1.2-30.9, p=0.033) and those with known coronary artery disease (OR 5.1, 95%CI
1.3-19.8, p=0.017). Types of disease-modifying therapy, age, sex, and other comorbidities were not associated with an
increased risk for infection.

Conclusion:
Steroid doses over 15 mg/day, being underweight and having coronary artery disease were associated with
significant increases in the risk of post-arthroplasty infection in rheumatoid arthritis. Maximal tapering of prednisone and
comorbidity risk reduction must be addressed in the peri-operative management strategy.