bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phosphate limitation induces sporulation in the chytridiomyceteBlastocladiella emersonii
Authors: Bongiorno Vagner Alexandre , Ferreira da Cruz Angela , Nunis da Silva Antonio , Corrêa Luiz Carlos 
Published: August 2012

The cell cycle is controlled by numerous mechanisms that ensure correct cell division. If growth is not possible, cells may eventually promote autophagy, differentiation, or apoptosis. Microorganisms interrupt their growth and differentiate under general nutrient limitation. We analyzed the effects of phosphate limitation on growth and sporulation in the chytridiomycete Blastocladiella emersonii using kinetic data, phase-contrast, and laser confocal microscopy. Under phosphate limitation, zoospores germinated and subsequently formed 2–4 spores, regardless of the nutritional content of the medium. The removal of phosphate at any time during growth induced sporulation of vegetative cells. If phosphate was later added to the same cultures, growth was restored if the cells were not yet committed to sporulation. The cycles of addition and withdrawal of phosphate from growth medium resulted in cycles of germination–growth, germination–sporulation, or germination–growth–sporulation. These results show that phosphate limitation is sufficient to interrupt cell growth and to induce complete sporulation in B. emersonii. We concluded that the determination of growth or sporulation in this microorganism is linked to phosphate availability when other nutrients are not limiting. This result provides a new tool for the dissection of nutrient–energy and signal pathways in cell growth and differentiation.
Permissive-nominal logic
Authors: Dowek Gilles , Gabbay Murdoch J. 
Published: August 2012

Permissive-Nominal Logic (PNL) is an extension of first-order predicate logic in which term-formers can bind names in their arguments.
This allows for direct axiomatizations with binders, such as of the λ-binder of the lambda-calculus or the ∀-binder of first-order logic. It also allows us to finitely axiomatize arithmetic, and similarly to axiomatize “nominal” datatypes-with-binding.
Just like first- and higher-order logic, equality reasoning is not necessary to α-rename.
This gives PNL much of the expressive power of higher-order logic, but models and derivations of PNL are first-order in character, and the logic seems to strike a good balance between expressivity and simplicity.
Calculus of cooperation and game-based reasoning about protocol privacy
Authors: More Sara Miner , Naumov Pavel 
Published: August 2012

The article introduces a new formal system, the calculus of cooperation, for reasoning about coalitions of players in a certain class of games. The calculus is an extension of the propositional intuitionistic logic that adds a coalition parameter to intuitionistic implication. The system is shown to be sound and complete with respect to a game semantics.
One intended application of the calculus of cooperation is the verification of privacy properties in multiparty computation protocols. The article argues that such properties can be established by providing a set of strategies for a non-zero-sum, perfect information game based on the protocol. It concludes with several examples of such verifications formalized in the calculus of cooperation.
CD24 Is an Effector of HIF-1–Driven Primary Tumor Growth and Metastasis
Authors: Thomas Shibu , Harding Michael A. , Smith Steven C. , Overdevest Jonathan B. , Nitz Matthew D. , Frierson Henry F. , Tomlins Scott A. , Kristiansen Glen , Theodorescu Dan 
Published: August 2012

Abstract
Hypoxia drives malignant progression in part by promoting accumulation of the oncogenic transcription factor hypoxia inducible factor–1α (HIF-1α) in tumor cells. Tumor aggressiveness also relates to elevation of the cancer stem cell–associated membrane protein CD24, which has been causally implicated in tumor formation and metastasis in experimental models. Here, we link these two elements by showing that hypoxia induces CD24 expression through a functional hypoxia responsive element in the CD24 promoter. HIF-1α overexpression induced CD24 mRNA and protein under normoxic conditions, with this effect traced to a recruitment of endogenous HIF-1α to the CD24 promoter. Short hairpin RNA–mediated attenuation of HIF-1α or CD24 expression reduced cancer cell survival in vitro and in vivo at the levels of primary and metastatic tumor growth. CD24 overexpression in HIF-1α–depleted cancer cells rescued this decrease, whereas HIF-1α overexpression in CD24-depleted cells did not. Analysis of clinical tumor specimens revealed a correlation between HIF-1α and CD24 levels and an association of their coexpression to decreased patient survival. Our results establish a mechanistic linkage between 2 critically important molecules in cancer, identifying CD24 as a critical HIF-1α transcriptional target and biologic effector, strengthening the rationale to target CD24 for cancer therapy. Cancer Res; 72(21); 5600–12. ©2012 AACR.
Multilevel Whole-Genome Analysis Reveals Candidate Biomarkers in Clear Cell Renal Cell Carcinoma
Authors: Girgis Andrew H. , Iakovlev Vladimir V. , Beheshti Ben , Bayani Jane , Squire Jeremy A. , Bui Anna , Mankaruos Marina , Youssef Youssef , Khalil Bishoy , Khella Heba , Pasic Maria , Yousef George M. 
Published: August 2012

Abstract
Renal cell carcinoma (RCC) is the most common neoplasm of the kidney. We conducted an integrated analysis of copy number, gene expression (mRNA and miRNA), protein expression, and methylation changes in clear cell renal cell carcinoma (ccRCC). We used a stepwise approach to identify the most significant copy number aberrations (CNA) and identified regions of peak and broad copy number gain and loss, including peak gains (3q21, 5q32, 5q34-q35, 7p11, 7q21, 8q24, 11q13, and 12q14) and deletions (1p36, 2q34-q37, 3p25, 4q33-q35, 6q23-q27, and 9p21). These regions harbor novel tumor-related genes and miRNAs not previously reported in renal carcinoma. Integration of genome-wide expression data and gene set enrichment analysis revealed 75 gene sets significantly altered in tumors with CNAs compared with tumors without aberration. We also identified genes located in peak CNAs with concordant methylation changes (hypomethylated in copy number gains such as STC2 and CCND1 and hypermethylated in deletions such as CLCNKB, VHL, and CDKN2A/2B). For other genes, such as CA9, expression represents the net outcome of opposing forces (deletion and hypomethylation) that also significantly influences patient survival. We also validated the prognostic value of miRNA let-7i in RCCs. miR-138, located in chromosome 3p deletion, was also found to have suppressive effects on tumor proliferation and migration abilities. Our findings provide a significant advance in the delineation of the ccRCC genome by better defining the impact of CNAs in conjunction with methylation changes on the expression of cancer-related genes, miRNAs, and proteins and their influence on patient survival. Cancer Res; 72(20); 5273–84. ©2012 AACR.
Natural Product Triptolide Mediates Cancer Cell Death by Triggering CDK7-Dependent Degradation of RNA Polymerase II
Authors: Manzo Stefano Giustino , Zhou Zhao-Li , Wang Ying-Qing , Marinello Jessica , He Jin-Xue , Li Yuan-Chao , Ding Jian , Capranico Giovanni , Miao Ze-Hong 
Published: August 2012

Abstract
Triptolide is a bioactive ingredient in traditional Chinese medicine that exhibits diverse biologic properties, including anticancer properties. Among its many putative targets, this compound has been reported to bind to XPB, the largest subunit of general transcription factor TFIIH, and to cause degradation of the largest subunit Rpb1 of RNA polymerase II (RNAPII). In this study, we clarify multiple important questions concerning the significance and basis for triptolide action at this core target. Triptolide decreased Rpb1 levels in cancer cells in a manner that was correlated tightly with its cytotoxic activity. Compound exposure blocked RNAPII at promoters and decreased chromatin-bound RNAPII, both upstream and within all genes that were examined, also leading to Ser-5 hyperphosphorylation and increased ubiqutination within the Rbp1 carboxy-terminal domain. Notably, cotreatment with inhibitors of the proteasome or the cyclin-dependent kinase CDK7 inhibitors abolished the ability of triptolide to ablate Rpb1. Together, our results show that triptolide triggers a CDK7-mediated degradation of RNAPII that may offer an explanation to many of its therapeutic properties, including its robust and promising anticancer properties. Cancer Res; 72(20); 5363–73. ©2012 AACR.
A Pilot Study of Low-Cost, High-Resolution Microendoscopy as a Tool for Identifying Women with Cervical Precancer
Authors: Pierce Mark C. , Guan YaoYao , Quinn Mary Kate , Zhang Xun , Zhang Wen-Hua , Qiao You-Lin , Castle Philip , Richards-Kortum Rebecca 
Published: August 2012

Abstract
Cervical cancer remains one of the leading causes of death among women in developing countries. Without resources to support Pap smear cytology and colposcopy, cost-effective approaches which enable single-visit “see-and-treat” protocols offer the potential to reduce morbidity and mortality due to this preventable disease. We carried out a pilot clinical study in Shanxi province, China, to evaluate a low-cost, high-resolution microendoscope (HRME) imaging system which enables evaluation of epithelial cell morphology in vivo. HRME images were obtained at discrete sites on the cervix in 174 women, in addition to visual inspection with acetic acid (VIA) and colposcopic examination. Of 69 sites appearing abnormal on colposcopy, only 12 showed high-grade disease (CIN2+) on pathology. Quantification of the nuclear-to-cytoplasm ratio by HRME enabled an ad hoc threshold to be defined, which correctly classified all 12 sites as abnormal, whilst classifying 38 of the remaining 57 pathology normal sites as normal. All patients with biopsy confirmed high-grade disease also tested positive for high-risk human papilloma virus (HPV) DNA and were classified as abnormal by HRME. Among the remaining patients who tested positive for HPV but were either normal by colposcopy or showed &lt;CIN2 on pathology, only 6 of 32 (18.8%) were classified as abnormal by HRME.
Visual examination techniques for cervical cancer screening may overestimate the prevalence of precancerous lesions, leading to unnecessary treatment, expense, and patient stress. The results of this study suggest that evaluation of suspicious lesions by HRME may assist in ruling out immediate cryotherapy, thus increasing the efficiency of current see-and-treat programs. Cancer Prev Res; 5(11); 1273–9. ©2012 AACR.
The Effect of Chair Designs on Sitting Pressure Distribution and Tissue Perfusion
Authors: Makhsous Mohsen , Lin Fang , Hanawalt David , Kruger Shannon Lynn , LaMantia Angie 
Published: August 2012

Objective: The aim of this study was to investigate the effect of five chair designs on interface pressure distribution and tissue perfusion in the buttock-thigh region. Background: Prolonged sitting has been found to contribute to the symptoms of work-related low back pain. Studies have found that chair design affects users’ sitting posture and comfort. As sitting applies pressure to the user, it is necessary to investigate how chair design affects sitting pressure and tissue perfusion during sitting. Method: We tested five chair designs (Suspension A, Suspension B, Foam A, Foam B, and bicompliant) on 15 young, healthy females. Sitting interface pressure and buttock-thigh tissue perfusion (in terms of transcutaneous partial pressure of oxygen and carbon dioxide, tcPO2 and tcPCO2, respectively) were measured during 10-min sitting on each chair. Results: We found that chair design significantly affected the distribution of the sitting pressure ( p < .001) and buttock-thigh tissue perfusion ( p < .023). Average pressure and total contact area were found highest in both foam designs, and the average pressure was the lowest in one of the suspension designs. Across all tested chair designs, the anterior portion of the seat sustained the lowest contact pressure. It was also found that tcPO2 was the lowest ( p < .003) and tcPCO2 was the highest ( p < .001) in tissue around ischial tuberosity for all chair designs. Conclusion: Chair design and materials of the seat significantly affect the sitting interface pressure distribution and tissue perfusion in sitting area. Further evaluation of these outcomes may provide useful information to correlate chair design with sitting comfort.
Retraction of Supraspinatus Muscle and Tendon as Predictors of Success of Rotator Cuff Repair
Authors: Meyer Dominik C. , Wieser Karl , Farshad Mazda , Gerber Christian 
Published: August 2012

Background: The structural failure rate of rotator cuff repair can exceed 50%. Important predictors for repair failure are preoperative fatty muscle infiltration and myotendinous retraction. Purpose: To quantitatively assess the prognostic value of preoperative retraction of both the supraspinatus muscle and tendon for the outcome of supraspinatus repair. Study Design: Cohort study; Level of evidence, 3. Methods: In 33 shoulders with complete supraspinatus tendon ruptures subjected to arthroscopic repair, magnetic resonance imaging (MRI) scans taken preoperatively and after a mean follow-up of 24 months were studied. The exact position of the lateral extension of the supraspinatus muscle and of the tendon end was evaluated and correlated with the preoperative stage of fatty infiltration (Goutallier) and the failure rate of tendon repair. Results: The mean lengthening of the muscle and tendon end was −3 mm and 4 mm in the failed repairs (n = 19) and 14 mm and 8 mm in the successful repairs (n = 14). If the supraspinatus had preoperative Goutallier stages 2 to 3 and a tendon length of less than 15 mm, the failure rate was 92%, but if the tendon length was greater than 15 mm, the failure rate was only 33%. With Goutallier stages 0 to 1, the corresponding failure rates were 57% and 25%, respectively. Conclusion: Rotator cuff repair lengthens the tendon, even if the repair fails. The possibility to lengthen the myotendinous unit is related to the preoperative length of the tendon. The combination of Goutallier grading and preoperative tendon length appears to be a more powerful predictor for the reparability of a tendon tear than Goutallier grading alone.
A Comparison of Objective Biomarkers With a Subjective Health Status Measure Among Children in the Philippines
Authors: Butrick Elizabeth , Peabody John W. , Solon Orville , DeSalvo Karen B. , Quimbo Stella A. 
Published: August 2012

Large health surveys use subjective (self-reported) and objective (biomarkers) measures to assess heath status. However, the linkage or disparity of these measures has not been systematically studied in developing countries. Method: Using data from the Philippine Quality Improvement Demonstration Study, QIDS, this study evaluated the associations between General Self-Reported Health Status (GSRH) and height, weight, hemoglobin, red blood cell folate, C-reactive protein, and blood lead levels. The authors modeled each biomarker as a function of GSRH controlling for socioeconomic status and selection effects. Changes in biomarkers and GSRH in children who had previously been hospitalized were also examined. Results: GSRH independently predicted hemoglobin, C-reactive protein, stunting, and wasting. GSRH did not vary significantly with folate deficiency and blood lead levels. Conclusions: In addition to being a measure of overall child health status, GSRH may be a useful and inexpensive screening tool for identifying children that need further health testing.
Consensus Statement
Authors: Chan Siew Pheng , Chui William C. , Lo Kwok Wing , Huang Kuo-Chin , Leyesa Normita D. , Lin Wen-Yuan , Mirasol Roberto C. , Robles Yolanda R. , Tey Beng Hea , Paraidathathu Thomas 
Published: August 2012

Background and aim The increasing prevalence of overweight and obesity worldwide demands increased efforts in the prevention and management of obesity. This article aims to present consensus statements promoting appropriate consumer education and communication programs for weight-loss agents in Asia. Methods Panel members from various disciplines developed consensus statements based on an expert meeting on the benefits of consumer education and communication programs for over-the-counter weight-loss agents. Key opinion leaders discussed relevant data that served as the basis of the recommendations. Results Obesity is a growing epidemic in Asia, turning the region into a potential market for weight-loss products and services. Current trends in direct-to-consumer advertising demonstrate the pervasiveness of false representations lacking adequate substantiation. Relevant issues and recommendations were established. Conclusions Public education on weight management is a shared responsibility; there is a need to raise public awareness of obesity and its health-related consequences. Advertising guidelines should ensure responsible direct-to-consumer advertising of weight-loss agents.
The Effects of Evacuation on Nursing Home Residents With Dementia
Authors: Brown Lisa M. , Dosa David M. , Thomas Kali , Hyer Kathryn , Feng Zhanlian , Mor Vincent 
Published: August 2012

Background: In response to the hurricane-related deaths of nursing home residents, there has been a steady increase in the number of facilities that evacuate under storm threat. This study examined the effects of evacuation during Hurricane Gustav on residents who were cognitively impaired. Methods: Nursing homes in counties located in the path of Hurricane Gustav were identified. The Minimum Data Set resident assessment files were merged with the Centers for Medicare enrollment file to determine date of death for residents in identified facilities. Difference-in-differences analyses were conducted adjusting for residents' demographic characteristics and acuity. Results: The dataset included 21,255 residents living in 119 at risk nursing homes over three years of observation. Relative to the two years before the storm, there was a 2.8 percent increase in death at 30 days and a 3.9 percent increase in death at 90 days for residents with severe dementia who evacuated for Hurricane Gustav, controlling for resident demographics and acuity. Conclusions: The findings of this research reveal the deleterious effects of evacuation on residents with severe dementia. Interventions need to be developed and tested to determine the best methods for protecting this at risk population when there are no other options than to evacuate the facility.
Choosing Sides: HIV Health Care Practices among Shared Populations of HIV-Positive Latinos Living near the US-Mexico Border
Authors: Servin Argentina E. , Muñoz Fátima A. , Strathdee Steffanie A. , Kozo Justine , Zúñiga María Luisa 
Published: August 2012

Background: We compared HIV-positive patients receiving care in the border cities of San Diego, United States, with Tijuana, Mexico. Methods: Participants were HIV-positive Latinos (n = 233) receiving antiretroviral therapy (ART) from San Diego–Tijuana clinics (2009-2010). Logistic regression identified correlates of receiving HIV care in San Diego versus Tijuana. Results: Those with their most recent HIV visit in San Diego (59%) were more likely to be older, have at least a high school education, and were less likely to have been deported than those with last visits in Tijuana. Despite reporting better patient–provider relationships and less HIV-related stigma than those with visits in Tijuana, San Diego patients were twice as likely to make unsupervised changes in their ART regimen. Conclusions: We observed poorer relative adherence among HIV-positive Latinos receiving care in San Diego, despite reports of good clinical relationships. Further study is needed to ascertain underlying reasons to avoid ART-related resistance.
Cytosolic sensing of extracellular self-DNA transported into monocytes by the antimicrobial peptide LL37
Authors: Chamilos Georgios , Gregorio Josh , Meller Stephan , Lande Roberto , Kontoyiannis Dimitrios P. , Modlin Robert L. , Gilliet Michel 
Published: August 2012

AbstractThe intracellular location of nucleic acid sensors prevents recognition of extracellular self-DNA released by dying cells. However, on forming a complex with the endogenous antimicrobial peptide LL37, extracellular DNA is transported into endosomal compartments of plasmacytoid dendritic cells, leading to activation of Toll-like receptor-9 and induction of type I IFNs. Whether LL37 also transports self-DNA into nonplasmacytoid dendritic cells, leading to type I IFN production via other intracellular DNA receptors is unknown. Here we found that LL37 very efficiently transports self-DNA into monocytes, leading the production of type I IFNs in a Toll-like receptor-independent manner. This type I IFN induction was mediated by double-stranded B form DNA, regardless of its sequence, CpG content, or methylation status, and required signaling through the adaptor protein STING and TBK1 kinase, indicating the involvement of cytosolic DNA sensors. Thus, our study identifies a novel link between the antimicrobial peptides and type I IFN responses involving DNA-dependent activation of cytosolic sensors in monocytes.
Final results of a multicenter trial addressing role of CSF flow cytometric analysis in NHL patients at high risk for CNS dissemination
Authors: Benevolo Giulia , Stacchini Alessandra , Spina Michele , Ferreri Andrés J. M. , Arras Marcella , Bellio Laura , Botto Barbara , Bulian Pietro , Cantonetti Maria , Depaoli Lorella , Di Renzo Nicola , Di Rocco Alice , Evangelista Andrea , Franceschetti Silvia , Godio Laura , Mannelli Francesco , Pavone Vincenzo , Pioltelli Pietro , Vitolo Umberto , Pogliani Enrico M. 
Published: August 2012

AbstractThis prospective study compared diagnostic and prognostic value of conventional cytologic (CC) examination and flow cytometry (FCM) of baseline samples of cerebrospinal fluid (CSF) in 174 patients with newly diagnosed aggressive non-Hodgkin lymphoma (NHL). FCM detected a neoplastic population in the CSF of 18 of 174 patients (10%), CC only in 7 (4%; P < .001); 11 patients (14%) were discordant (FCM+/CC−). At a median follow-up of 46 months, there were 64 systemic progressions and 10 CNS relapses, including 2 patients with both systemic and CNS relapses. Two-year progression-free and overall survival were significantly higher in patients with FCM− CSF (62% and 72%) compared with those FCM+ CSF (39% and 50%, respectively), with a 2-year CNS relapse cumulative incidence of 3% (95% confidence interval [CI], 0-7) versus 17% (95% CI, 0-34; P = .004), respectively. The risk of CNS progression was significantly higher in FMC+/CC− versus FCM−/CC− patients (hazard ratio = 8.16, 95% CI, 1.45-46). In conclusion, FCM positivity in the CSF of patients with high-risk NHL is associated with a significantly higher CNS relapse risk and poorer outcome. The combination of IV drugs with a higher CNS bioavailability and intrathecal chemotherapy is advisable to prevent CNS relapses in FCM+ patients.