bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of Nonlinear Atmospheric Response to SST on the Asymmetric Transition Process of ENSO
Authors: Ohba Masamichi , Ueda Hiroaki 
Published: July 2008

Abstract
Physical processes that are responsible for the asymmetric transition processes between El Niño and La Niña events are investigated by using observational data and physical models to examine the nonlinear atmospheric response to SST. The air–sea coupled system of ENSO is able to remain in a weak, cold event for up to 2 yr, while the system of a relatively warm event turns into a cold phase. Through analysis of the oceanic observational data, it is found that there is a strong difference in thermocline variations in relation to surface zonal wind anomalies in the equatorial Pacific (EP) during the mature-to-decaying phase of ENSO. The atmospheric response for the warm phase of ENSO causes a rapid reduction of the EP westerlies in boreal winter, which play a role in hastening the following ENSO transition through the generation of upwelling oceanic Kelvin waves. However, the anomalous EP easterlies in the cold phase persist to the subsequent spring, which tends to counteract the turnabout from the cold to warm phase of ENSO.
A suite of idealized atmospheric general circulation model (AGCM) experiments are performed by imposing two different ENSO-related SST anomalies, which have equal amplitudes but opposite signs. The nonlinear climate response in the AGCM is found at the mature-to-decaying phase of ENSO that closely resembles the observations, including a zonal and meridional shift in the equatorial positions of the atmospheric wind. By using a simple ocean model, it is determined that the asymmetric responses of the equatorial zonal wind result in different recovery times of the thermocline in the eastern Pacific. Thus, the differences in transition processes between the warm and cold ENSO event are fundamentally due to the nonlinear atmospheric response to SST, which originates from the distribution of climatological SST and its seasonal changes. By including the asymmetric wind responses the intermediate air–sea coupled model herein demonstrates that the essential elements of the redevelopment of La Niña arise from the nonlinear atmospheric response to SST anomalies.
Acute Achilles Tendon Rupture
Authors: Metz Roderick , Verleisdonk Egbert-Jan M. M. , van der Heijden Geert J.-M.-G. , Clevers Geert-Jan , Hammacher Erik R. , Verhofstad Michiel H. J. , van der Werken Christiaan 
Published: July 2008

Background Surgical repair of acute Achilles tendon ruptures is considered superior to nonoperative treatment, but complications other than rerupture range up to 34%. Nonoperative treatment by functional bracing seems a promising alternative. Hypothesis Nonoperative treatment of acute Achilles tendon rupture with functional bracing reduces the number of complications compared with surgical treatment with a minimally invasive technique. Study Design Randomized controlled clinical trial; Level of evidence, 2. Method Using concealed random allocation, 83 patients with acute Achilles tendon rupture were assigned to nonoperative treatment by functional bracing or minimally invasive surgical treatment followed by tape bandage. Patients were allowed full weightbearing, and follow-up was 1 year. Results Complications risk other than rerupture by intention-to-treat basis was 9 in 42 patients (21 %) for surgical treatment and 15 in 41 patients (36%) for nonoperative treatment (risk ratio, 0.59; 95% confidence interval, 0.29-1.19). Reruptures risk was 5 in 41 patients after nonoperative treatment and 3 in 42 patients for surgical treatment (risk ratio, 0.59; 95% confidence interval, 0.15-2.29). The mean time to work was 59 days (SD, 82) after surgical treatment and 108 days (SD, 115) after nonoperative treatment (difference, 49 days; 95% confidence interval, 4-94; P < .05). The difference between treatments for return to sports (risk ratio, 0.55; 95% confidence interval, 0.23-1.29), pain, and treatment satisfaction did not reach statistical significance. Conclusion There appears to be a clinically important difference in the risk of complications between minimally invasive surgical treatment and nonoperative treatment for acute Achilles tendon ruptures, but this was not statistically significant.
Wound Bioburden and Infection-Related Complications in Diabetic Foot Ulcers
Authors: Gardner Sue E. , Frantz Rita A. 
Published: July 2008

The identification and diagnosis of diabetic foot ulcer (DFU) infections remains a complex problem. Because inflammatory responses to microbial invasion may be diminished in persons with diabetes, clinical signs of infection are often absent in persons with DFUs when infection is limited to localized tissue. In the absence of these clinical signs, microbial load is believed to be the best indicator of infection. Some researchers, however, believe microbial load to be insignificant and type of organism growing in the ulcer to be most important. Previous studies on the microbiology of DFUs have not provided enough evidence to determine the microbiological parameters of importance. Infection-related complications of DFUs include wound deterioration, osteomyelitis, and amputation. Risk factors for amputation include age, peripheral vascular disease, low transcutaneous oxygen, smoking, and poor glycemic control. These risk factors are best measured directly with physiological measures of arterial perfusion, glycemic control, sensory neuropathy, plantar pressures, and activity level and by controlling off-loading. DFU bioburden has not been examined as a risk factor for infection-related complications. To address the relationship between wound bioburden and the development of infection-related complications in DFUs, tightly controlled prospective studies based on clearly defined, valid measures of wound bioburden and wound outcomes are needed. This article reviews the literature and proposes a model of hypothesized relationships between wound bioburden—including microbial load, microbial diversity, and pathogenicity of organisms—and the development of infection-related complications.
An Aerobic Weight-Loaded Pilot Exercise Intervention for Breast Cancer Survivors: Bone Remodeling and Body Composition Outcomes
Authors: Knobf M. Tish , Insogna Karl , DiPietro Loretta , Fennie Kristopher , Thompson A. Siobhan 
Published: July 2008

Objective. Weight gain and bone loss are commonly reported in breast cancer survivors. The purpose of this pilot study is to assess feasibility and explore the effect of an aerobic weight-loaded exercise intervention on bone remodeling, weight, and body composition. Design. A one-group pre-posttest design was used to test a 16—24-week supervised walking exercise intervention among women within 2 years of menopause. Through Weeks 1—4, time and weight were progressively increased. By Week 5 and through the end of the intervention, a waist belt was loaded with 5 lb and participants spent 45 min on the treadmill 3 times/week. Bone remodeling was measured by serum biomarkers (N-terminal propeptides of type I collagen [NTX] and serum osteocalcin). Dual-energy absorptiometry scans assessed body composition. Data were collected at baseline and 16 and 24 weeks. Results. The majority of the 26 participants were married, well educated, and employed, with a mean age of 51.3 years (SD = 6.2). The high adherence (M = 88.2%, SD = 6.8) demonstrated feasiblity. There were no significant changes in serum osteocalcin (p = .67), serum NTX (p = .31), lean muscle mass (p = .08), or percent fat mass for the group as a whole (p = .14), but fat mass increased for women on adjuvant endocrine therapy (p = .04). The women maintained their weight. Conclusions. This novel exercise intervention for breast cancer survivors was feasible, and women otherwise at high risk for weight gain and bone loss maintained their weight and bone mass.
Umbilical cord blood regulatory T-cell expansion and functional effects of tumor necrosis factor receptor family members OX40 and 4-1BB expressed on artificial antigen-presenting cells
Authors: Hippen Keli L. , Harker-Murray Paul , Porter Stephen B. , Merkel Sarah C. , Londer Aryel , Taylor Dawn K. , Bina Megan , Panoskaltsis-Mortari Angela , Rubinstein Pablo , Van Rooijen Nico , Golovina Tatiana N. , Suhoski Megan M. , Miller Jeffrey S. , Wagner John E. , June Carl H. , Riley James L. , Blazar Bruce R. 
Published: July 2008

AbstractPreviously, we showed that human umbilical cord blood (UCB) regulatory T cells (Tregs) could be expanded approximately 100-fold using anti-CD3/28 monoclonal antibody (mAb)–coated beads to provide T-cell receptor and costimulatory signals. Because Treg numbers from a single UCB unit are limited, we explored the use of cell-based artificial antigen-presenting cells (aAPCs) preloaded with anti-CD3/28 mAbs to achieve higher levels of Treg expansion. Compared with beads, aAPCs had similar expansion properties while significantly increasing transforming growth factor β (TGF-β) secretion and the potency of Treg suppressor function. aAPCs modified to coexpress OX40L or 4-1BBL expanded UCB Tregs to a significantly greater extent than bead- or nonmodified aAPC cultures, reaching mean expansion levels exceeding 1250-fold. Despite the high expansion and in contrast to studies using other Treg sources, neither OX40 nor 4-1BB signaling of UCB Tregs reduced in vitro suppression. UCB Tregs expanded with 4-1BBL expressing aAPCs had decreased levels of proapoptotic bim. UCB Tregs expanded with nonmodified or modified aAPCs versus beads resulted in higher survival associated with increased Treg persistence in a xeno-geneic graft-versus-host disease lethality model. These data offer a novel approach for UCB Treg expansion using aAPCs, including those coexpressing OX40L or 4-1BBL.
Genes related to apoptosis predict necrosis of the liver as a phenotype observed in rats exposed to a compendium of hepatotoxicants
Authors: Huang Lingkang , Heinloth Alexandra N , Zeng Zhao-Bang , Paules Richard S , Bushel Pierre R 
Published: July 2008

Abstract

Background
Some of the biochemical events that lead to necrosis of the liver are well-known. However, the pathogenesis of necrosis of the liver from exposure to hepatotoxicants is a complex biological response to the injury. We hypothesize that gene expression profiles can serve as a signature to predict the level of necrosis elicited by acute exposure of rats to a variety of hepatotoxicants and postulate that the expression profiles of the predictor genes in the signature can provide insight to some of the biological processes and molecular pathways that may be involved in the manifestation of necrosis of the rat liver.

Results
Rats were treated individually with one of seven known hepatotoxicants and were analyzed for gene expression by microarray. Liver samples were grouped by the level of necrosis exhibited in the tissue. Analysis of significantly differentially expressed genes between adjacent necrosis levels revealed that inflammation follows programmed cell death in response to the agents. Using a Random Forest classifier with feature selection, 21 informative genes were identified which achieved 90%, 80% and 60% prediction accuracies of necrosis against independent test data derived from the livers of rats exposed to acetaminophen, carbon tetrachloride, and allyl alcohol, respectively. Pathway and gene network analyses of the genes in the signature revealed several gene interactions suggestive of apoptosis as a process possibly involved in the manifestation of necrosis of the liver from exposure to the hepatotoxicants. Cytotoxic effects of TNF-α, as well as transcriptional regulation by JUN and TP53, and apoptosis-related genes possibly lead to necrosis.

Conclusion
The data analysis, gene selection and prediction approaches permitted grouping of the classes of rat liver samples exhibiting necrosis to improve the accuracy of predicting the level of necrosis as a phenotypic end-point observed from the exposure. The strategy, along with pathway analysis and gene network reconstruction, led to the identification of 1) expression profiles of genes as a signature of necrosis and 2) perturbed regulatory processes that exhibited biological relevance to the manifestation of necrosis from exposure of rat livers to the compendium of hepatotoxicants.
Growth rate regulated genes and their wide involvement in the Lactococcus lactis stress responses
Authors: Dressaire Clémentine , Redon Emma , Milhem Helene , Besse Philippe , Loubière Pascal , Cocaign-Bousquet Muriel 
Published: July 2008

Abstract

Background
The development of transcriptomic tools has allowed exhaustive description of stress responses. These responses always superimpose a general response associated to growth rate decrease and a specific one corresponding to the stress. The exclusive growth rate response can be achieved through chemostat cultivation, enabling all parameters to remain constant except the growth rate.

Results
We analysed metabolic and transcriptomic responses of Lactococcus lactis in continuous cultures at different growth rates ranging from 0.09 to 0.47 h-1. Growth rate was conditioned by isoleucine supply. Although carbon metabolism was constant and homolactic, a widespread transcriptomic response involving 30% of the genome was observed. The expression of genes encoding physiological functions associated with biogenesis increased with growth rate (transcription, translation, fatty acid and phospholipids metabolism). Many phages, prophages and transposon related genes were down regulated as growth rate increased. The growth rate response was compared to carbon and amino-acid starvation transcriptomic responses, revealing constant and significant involvement of growth rate regulations in these two stressful conditions (overlap 27%).
Two regulators potentially involved in the growth rate regulations, llrE and yabB, have been identified. Moreover it was established that genes positively regulated by growth rate are preferentially located in the vicinity of replication origin while those negatively regulated are mainly encountered at the opposite, thus indicating the relationship between genes expression and their location on chromosome. Although stringent response mechanism is considered as the one governing growth deceleration in bacteria, the rigorous comparison of the two transcriptomic responses clearly indicated the mechanisms are distinct.

Conclusion
This work of integrative biology was performed at the global level using transcriptomic analysis obtained in various growth conditions. It raised the importance of growth rate regulations in bacteria but also participated to the elucidation of the involved mechanism. Though the mechanism controlling growth rate is not yet fully understood in L. lactis, one expected regulatory mechanism has been ruled out, two potential regulators have been pointed out and the involvement of gene location on the chromosome has also been found to be involved in the expression regulation of these growth related genes.
Advantages of the nested case-control design in diagnostic research
Authors: Biesheuvel Cornelis J , Vergouwe Yvonne , Oudega Ruud , Hoes Arno W , Grobbee Diederick E , Moons Karel GM 
Published: July 2008

Abstract

Background
Despite its benefits, it is uncommon to apply the nested case-control design in diagnostic research. We aim to show advantages of this design for diagnostic accuracy studies.

Methods
We used data from a full cross-sectional diagnostic study comprising a cohort of 1295 consecutive patients who were selected on their suspicion of having deep vein thrombosis (DVT). We draw nested case-control samples from the full study population with case:control ratios of 1:1, 1:2, 1:3 and 1:4 (per ratio 100 samples were taken). We calculated diagnostic accuracy estimates for two tests that are used to detect DVT in clinical practice.

Results
Estimates of diagnostic accuracy in the nested case-control samples were very similar to those in the full study population. For example, for each case:control ratio, the positive predictive value of the D-dimer test was 0.30 in the full study population and 0.30 in the nested case-control samples (median of the 100 samples). As expected, variability of the estimates decreased with increasing sample size.

Conclusion
Our findings support the view that the nested case-control study is a valid and efficient design for diagnostic studies and should also be (re)appraised in current guidelines on diagnostic accuracy research.
Identification of new HIV-1 Gag-specific cytotoxic T lymphocyte responses in BALB/c mice
Authors: Cellini Silvia , Fortini Cinzia , Gallerani Eleonora , Destro Federica , Cofano Egidio Brocca , Caputo Antonella , Gavioli Riccardo 
Published: July 2008

AbstractBackgroundAs HIV-specific cytotoxic T cells play a key role during acute and chronic HIV-1 infection in humans, the ability of potential anti-HIV vaccines to elicit strong, broad T cell responses is likely to be crucial. The HIV-1 Gag antigen is widely considered a relevant antigen for the development of an anti-HIV vaccine since it is one of the most conserved viral proteins and is also known to induce T cell responses. In the majority of studies reporting Gag-specific cellular immune responses induced by Gag-based vaccines, only a small number of Gag T cell epitopes were tested in preclinical mouse models, thus giving an incomplete picture of the numerous possible cellular immune responses against this antigen. As is, this partial knowledge of epitope-specific T cell responses directed to Gag will unavoidably result in a limited preclinical evaluation of Gag-based vaccines.ResultsIn this study we identified new Gag CD8+ T cell epitopes in BALB/c mice vaccinated with the HIV-1 Gag antigen alone or in combination with the HIV-1 Tat protein, which was recently shown to broaden T cell responses directed to Gag. Specifically, we found that CTL responses to Gag may be directed to nine different CTL epitopes, and four of these were mapped as minimal CTL epitopes.ConclusionThese newly identified CTL epitopes should be considered in the preclinical evaluation of T cell responses induced by Gag-based vaccines in mice.
Cryptic genomic imbalances in patients with de novo or familial apparently balanced translocations and abnormal phenotype
Authors: Sismani Carolina , Kitsiou-Tzeli Sofia , Ioannides Marios , Christodoulou Christodoulos , Anastasiadou Violetta , Stylianidou Goula , Papadopoulou Eleftheria , Kanavakis Emanuel , Kosmaidou-Aravidou Zoe , Patsalis Philippos C 
Published: July 2008

Abstract

Background
Carriers of apparently balanced translocations are usually phenotypically normal; however in about 6% of de novo cases, an abnormal phenotype is present. In the current study we investigated 12 patients, six de novo and six familial, with apparently balanced translocations and mental retardation and/or congenital malformations by applying 1 Mb resolution array-CGH. In all de novo cases, only the patient was a carrier of the translocation and had abnormal phenotype. In five out of the six familial cases, the phenotype of the patient was abnormal, although the karyotype appeared identical to other phenotypically normal carriers of the family. In the sixth familial case, all carriers of the translocations had an abnormal phenotype.

Results
Chromosomal and FISH analyses suggested that the rearrangements were "truly balanced" in all patients. However, array-CGH, revealed cryptic imbalances in three cases (3/12, 25%), two de novo (2/12, 33.3%) and one familial (1/12, 16.6%). The nature and type of abnormalities differed among the cases. In the first case, what was identified as a de novo t(9;15)(q31;q26.1), a complex rearrangement was revealed involving a ~6.1 Mb duplication on the long arm of chromosome 9, an ~10 Mb deletion and an inversion both on the long arm of chromosome 15. These imbalances were located near the translocation breakpoints. In the second case of a de novo t(4;9)(q25;q21.2), an ~6.6 Mb deletion was identified on the short arm of chromosome 7 which is unrelated to the translocation. In the third case, of a familial, t(4;7)(q13.3;p15.3), two deletions of ~4.3 Mb and ~2.3 Mb were found, each at one of the two translocation breakpoints. In the remaining cases the translocations appeared balanced at 1 Mb resolution.

Conclusion
This study investigated both de novo and familial apparently balanced translocations unlike other relatively large studies which are mainly focused on de novo cases. This study provides additional evidence that cryptic genomic imbalances are common in patients with abnormal phenotype and "apparently balanced" translocations not only in de novo but can also occur in familial cases. The use of microarrays with higher resolution such as oligo-arrays may reveal that the frequency of cryptic genomic imbalances among these patients is higher.
Increased chemotactic migration and growth in heparanase-overexpressing human U251n glioma cells
Authors: Hong Xin , Jiang Feng , Kalkanis Steven N , Zhang Zheng Gang , Zhang Xuepeng , Zheng Xuguang , Jiang Hao , Mikkelsen Tom , Chopp Michael 
Published: July 2008

Abstract
Heparanase is an endoglycosidase that degrades heparan sulfate, the main polysaccharide constituent of the extracellular matrix (ECM) and basement membrane. Expression of the heparanase gene is associated with the invasion and metastatic potential of a variety of tumor-derived cell types. However, the roles of heparanase in the regulation of gene expression and the subsequent cell function changes other than invasion are not clear. In the current study, we overexpressed the human heparanase gene in a human U251n glioma cell line. We found that heparanase-overexpression significantly increased cell invasion, proliferation, anchorage-independent colony formation and chemotactic migration towards fetal bovine serum (FBS)-supplied medium and stromal cell-derived factor-1 (SDF-1). These phenotypic appearances were accompanied by enhanced protein kinase B (AKT) phosphorylation. Focal adhesion kinase (FAK) and extracellular signal-regulated kinase 1 (ERK1) signaling were not altered by heparanase-overexpression. These results indicate that heparanase has pleiotropic effects on tumor cells.