bluuebunny/crossref_metadata_2025_split huggingface dataset:
A compiled and systematic reference map of nucleosome positions across the Saccharomyces cerevisiae genomes
Authors: Jiang Cizhong , Pugh B Franklin 
Published: October 2009

AbstractNucleosomes have position-specific functions in controlling gene expression. A complete systematic genome-wide reference map of absolute and relative nucleosome positions is needed to minimize potential confusion when referring to the function of individual nucleosomes (or nucleosome-free regions) across datasets. We compiled six high-resolution genome-wide maps of Saccharomyces cerevisiae nucleosome positions from multiple labs and detection platforms, and report new insights. Data downloads, reference position assignment software, queries, and a visualization browser are available online http://atlas.bx.psu.edu/.
Determination of Time Required for Materials Exposed to Oxygen to Return to Reduced Flammability
Authors: Harper Susana , Hirsch David , Smith Sarah 
Published: October 2009

Abstract
Increased material flammability due to exposure to high oxygen concentrations is a concern from both safety and operational perspectives. Localized high oxygen concentrations can occur when exiting a higher oxygen concentration environment due to material saturation as well as oxygen entrapment between barrier materials. Understanding of oxygen diffusion and its correlation to flammability risks can reduce the likelihood of fires while improving procedures as NASA moves to longer missions with increased extravehicular activities in both spacecraft and off-Earth habitats. This paper examines the time required for common spacecraft materials exposed to oxygen to return to reduced flammability after removal from the increased oxygen concentration environment. Specifically, NASA-STD-6001A maximum oxygen concentration testing and ASTM Standard F1927 diffusion testing were performed on Nomex®®Nomex is a registered trademark of E. I. Du Pont de Nemours and Co., Wilmington, DE. HT90-40, Tiburon®®Tiburon is a registered trademark of Allegiance Corporation, McGraw Park, IL. surgical drape, cotton, Extravehicular Mobility Unit (EMU) Liquid-Cooled Ventilation Garment, EMU Thermal Comfort Undergarment, EMU Mosite foam with spandex covering, Advanced Crew Escape Suit (ACES) outer cross-section, ACES Liquid-Cooled Garment, ACES O2 hose material, Minicel®®Minicel is a registered trademark of Sekisui Voltek, Lawrence, MA. polyethylene foam, Minicel® polyethylene foam with Nomex® covering, Pyrell polyurethane foam, and Zotek®®Zotek is a registered trademark of Zotefoams plc, Walton, KY. F-30 foam.
Severe XIST hypomethylation clearly distinguishes (SRY+) 46,XX-maleness from Klinefelter syndrome
Authors: Poplinski Andreas , Wieacker Peter , Kliesch Sabine , Gromoll Jörg 
Published: October 2009

Objective46,XX-maleness affects 1 in 20 000 live male newborns resulting in infertility and hypergonadotrophic hypogonadism. Although the phenotypes of XX-males have been well described, the molecular nature of the X chromosomes remains elusive. We assessed the X inactivation status by DNA methylation analysis of four informative loci and compared those to Klinefelter syndrome (KS) and Turner syndrome.Design and methodsPatient cohort consisted of ten sex-determining region of the Y (SRY+) XX-males, two (SRY−) XX-males, ten 47,XXY Klinefelter men, six 45,X Turner females and ten male and female control individuals each. Methylation analysis was carried out by bisulphite sequencing of DNA from peripheral blood lymphocytes analysing X-inactive-specific transcript (XIST), phosphoglycerate kinase 1 (PGK1), ferritin, heavy peptide-like 17 (FTHL17) and short stature homeobox (SHOX).ResultsXIST methylation was 18% in (SRY+) XX-males, and thus they were severely hypomethylated compared to (SRY−) XX-males (48%; P<0.01), Klinefelter men (44%; P<0.01) and female controls (47%; P<0.01). Turner females and male controls displayed a high degree of XIST methylation of 98 and 94% respectively. Methylation of PGK1, undergoing X inactivation, was not significantly reduced in (SRY+) XX-males compared to female controls in spite of severe XIST hypomethylation (51 vs 69%; P>0.05). FTHL17, escaping X inactivation, but undergoing cell-type-specific inactivation was similarly methylated in XX-males (89%), KS patients (87%) and female controls (90%). SHOX, an X inactivation escapee located in the pseudoautosomal region, displays similarly low degrees of methylation for XX-males (7%), KS patients (7%) and female controls (9%).ConclusionsXIST hypomethylation clearly distinguishes (SRY+) XX-males from Klinefelter men. It does not, however, impair appropriate epigenetic regulation of representative X-linked loci.
A New Inversion Method To Interpret Flow Profiles From Distributed Temperature and Pressure Measurements in Horizontal Wells
Authors: Yoshioka K. , Zhu D. , Hill A. D. , Lake Larry W. 
Published: October 2009

Summary
The increasing deployment of distributed temperature- and pressure-measuring devices in intelligent-well completions is providing the means to monitor the inflow profiles of wells without any well intervention. If the profiles of pressure and/or temperature are affected by the inflow profiles of the various phases being produced, it is possible to estimate these flow profiles by inverting the measured temperature and pressure profiles. This inversion process is particularly challenging for horizontal wells because the pressure drop along the well is usually small, and temperature changes, caused primarily by Joule-Thomson effects, are also small.
This paper presents an inversion method that interprets distributed temperature and pressure data to obtain flow-rate profiles along horizontal wells. The inversion method, which is based on the Levenberg-Marquardt algorithm (Marquardt 1963), is applied to minimize the differences between the measured profiles and the profiles calculated from a forward model of the well and reservoir-flow system.
We present synthetic and field examples in this paper to illustrate how to use the inversion model to interpret the flow profile of a horizontal well. The synthetic examples show that even with single-phase oil production, the inflow profile can be estimated in many cases with the inversion method developed. The method is even more robust when water or gas is produced along discrete intervals in an oil production well because of the unique temperature signature of water or gas production. We applied the inversion method to temperature and pressure profiles measured with production logs in a North Sea horizontal oil-producing well. The method successfully inverted pressure and temperature profiles, and the profiles of oil- and water-flow rates determined compared well with the flowmeter-derived profiles.
Cesarean section in relation to self‐esteem and parenting among new mothers in southwestern Nigeria
Authors: LOTO OLABISI MOREBISE , ADEWUYA ABIODUN O. , AJENIFUJA OLUSEGUN K. , ORJI ERNEST O. , AYANDIRAN EMMANUEL OLUFEMI , OWOLABI ALEXANDER T. , ADE‐OJO IDOWU PIUS 
Published: October 2009

AbstractBackground. Maternal psychopathology and self‐esteem during childbirth may have an effect on maternal parenting self‐efficacy. Objective. This study aimed to asses the self‐esteem of newly delivered primiparous mothers who had cesarean section (CS) in relation to their parenting self‐efficacy. Methods. A total of 115 primiparous women who delivered by CS were compared with 97 matched controls who had vaginal delivery during the same period. They completed the Rosenberg self‐esteem scale prior to discharge. They also completed the parent–child relationship questionnaire at six weeks postpartum, together with the Rosenberg self‐esteem scale. Results. The mean score on the Rosenberg self‐esteem scale was significantly lower for the CS group, both prior to discharge (p = 0.006) and at six weeks (p < 0.001), than the vaginal delivery group. The mean score on the parent–child relationship questionnaire was also lower in those who had CS compared with those who had vaginal delivery (p < 0.001, OR 4.71, 95% CI 1.75–14.71). Conclusion. CS in Nigerian women is associated with lowered self‐esteem and predicts poor parenting self‐efficacy in the postnatal period. Psychological support and techniques to improve self‐esteem and parenting should be incorporated into the management of women having CS.
Epidural analgesia for labor pain: whose choice?
Authors: SCHYTT ERICA , WALDENSTRÖM ULLA 
Published: October 2009

AbstractObjective. To test the hypothesis that the decision to use epidural analgesia during labor is influenced not only by the woman and her background but also by the local cultural practice in the delivery unit. Design. Population‐based cohort study. Setting. All delivery units in Sweden. Population. A nationwide sample of 2,529 women. Methods. Data were collected by questionnaires in early pregnancy and two months after birth, and from the Swedish Medical Birth Register. Logistic regression analysis was conducted, adjusted for gestational age, induction of labor and infant birthweight. Main outcome measures. Epidural analgesia during labor. Results. The odds of having an epidural analgesia were more than twice as high in the Stockholm region (odds ratio (OR) 2.4; 95% confidence interval (CI) 1.7–3.4) and three times higher in middle‐north Sweden (OR 3.0; 95% CI 1.7–5.3) compared with the south of Sweden. Of the maternal factors, nulliparity was the strongest predictor (OR 6.3; 95% CI 5.1–7.9), followed by a prenatal belief that epidural analgesia would be needed (OR 3.5; 95% CI 2.8–4.4). Conclusion. The hypothesis of the study was confirmed. The woman and her background as well as the local cultural practice in the delivery unit matter with regard to the use of epidural analgesia.
The Gene History of Zebrafish tlr4a and tlr4b Is Predictive of Their Divergent Functions
Authors: Sullivan Con , Charette Jeremy , Catchen Julian , Lage Christopher R. , Giasson Gregory , Postlethwait John H. , Millard Paul J. , Kim Carol H. 
Published: October 2009

Abstract
Mammalian immune responses to LPS exposure are typified by the robust induction of NF-κB and IFN-β responses largely mediated by TLR4 signal transduction pathways. In contrast to mammals, Tlr4 signal transduction pathways in nontetrapods are not well understood. Comprehensive syntenic and phylogenetic analyses support our hypothesis that zebrafish tlr4a and tlr4b genes are paralogous rather than orthologous to human TLR4. Furthermore, we provide evidence to support our assertion that the in vivo responsiveness of zebrafish to LPS exposure is not mediated by Tlr4a and Tlr4b paralogs because they fail to respond to LPS stimulation in vitro. Zebrafish Tlr4a and Tlr4b paralogs were also unresponsive to heat-killed Escherichia coli and Legionella pneumophila. Using chimeric molecules in which portions of the zebrafish Tlr4 proteins were fused to portions of the mouse TLR4 protein, we show that the lack of responsiveness to LPS was most likely due to the inability of the extracellular portions of zebrafish Tlr4a and Tlr4b to recognize the molecule, rather than to changes in their capacities to transduce signals through their Toll/IL-1 receptor (TIR) domains. Taken together, these findings strongly support the notion that zebrafish tlr4a and tlr4b paralogs have evolved to provide alternative ligand specificities to the Tlr immune defense system in this species. These data demonstrate that intensive examination of gene histories when describing the Tlr proteins of basally diverging vertebrates is required to obtain fuller appreciation of the evolution of their function. These studies provide the first evidence for the functional evolution of a novel Tlr.
Targeting to Static Endosome Is Required for Efficient Cross-Presentation of Endoplasmic Reticulum-Resident Oxygen-Regulated Protein 150-Peptide Complexes
Authors: Kutomi Goro , Tamura Yasuaki , Okuya Koichi , Yamamoto Takashi , Hirohashi Yoshihiko , Kamiguchi Kenjiro , Oura Jun , Saito Keita , Torigoe Toshihiko , Ogawa Satoshi , Hirata Koichi , Sato Noriyuki 
Published: October 2009

Abstract
Heat shock proteins (HSPs) such as Hsp70, gp96, and Hsp90 have been shown to elicit intriguing, efficient CTL responses by cross-presentation via an as yet entirely unknown mechanism. Oxygen-regulated protein 150 (ORP150), also known as grp170, is an endoplasmic reticulum-resident HSP and is up-regulated by hypoxia. It has been demonstrated that ORP150 binds tumor-associated Ag peptides within cancer cells. Immunization with an ORP150-tumor Ag complex has been shown to generate tumor-specific CTLs. Most recently, it has been shown that exogenous ORP150 induces cross-presentation of a chaperoned Ag, thereby stimulating Ag-specific CTLs. However, the mechanism underlying this efficient cross-presentation is still unsolved. In this study, we show that the ORP150-precursor peptide complex can elicit CTL response through cross-presentation as well as the CD4+ T cell response by dendritic cells. Furthermore, we observed that the internalized ORP150-peptide complex, but not OVA protein, which was not cross-presented, was sorted to the Rab5+, EEA1+ static early endosome, followed by translocation to a recycling endosome, where the ORP150-chaperoned peptide was processed and bound to MHC class I molecules. Moreover, we observed that immunization of mice with ORP150-peptide complexes elicited strong peptide-specific CTLs and antitumor effects in vivo. Our data indicate that targeting of the Ag to a “static” early endosme by ORP150 is required for the efficient cross-presentation.
Encephalitogenicity of Complete Freund’s Adjuvant Relative to CpG Is Linked to Induction of Th17 Cells
Authors: Tigno-Aranjuez Justine T. , Jaini Ritika , Tuohy Vincent K. , Lehmann Paul V. , Tary-Lehmann Magdalena 
Published: October 2009

Abstract
For decades, CFA has been the classic adjuvant for the induction of experimental autoimmune encephalomyelitis (EAE). Its encephalitogenic activity has been originally linked to the induction of Th1 responses. CpG, which is also a potent Th1 inducer, has been suggested by some studies to be comparably encephalitogenic. In this study, using the SJL proteolipid protein (PLP) 139–151 peptide EAE model, we show that active immunizations using CFA but not CpG 1826/IFA as an adjuvant induced disease. Passive induction of EAE resulted in severe disease when cells were transferred from PLP in CFA-primed mice but resulted in only a mild, transient disease when cells originated from PLP in CpG 1826/IFA-primed mice. In accordance with these findings, immunizations using CFA but not CpG 1826/IFA as an adjuvant elicited a delayed-type hypersensitivity response. ELISPOT analysis revealed that CFA promoted the differentiation of much higher levels of PLP-specific, IL-17-secreting cells compared with CpG 1826/IFA. Both adjuvants induced comparable frequencies of PLP-specific, IFN-γ-secreting cells and also induced Ag-specific proliferation to the same extent. The severity of EAE in PLP in CFA-immunized mice was reduced when IL-17 was neutralized in vivo, demonstrating the crucial role of this cytokine in disease induction. The data show that immunizations using the autoantigen in CpG 1826/IFA result in very low frequencies of Ag-specific IL-17 cells, suggesting a lower risk of Th17-mediated pathology when using this adjuvant.
Src Homology 2-Domain Containing Leukocyte-Specific Phosphoprotein of 76 kDa Is Mandatory for TCR-Mediated Inside-Out Signaling, but Dispensable for CXCR4-Mediated LFA-1 Activation, Adhesion, and Migration of T Cells
Authors: Horn Jessica , Wang Xiaoqian , Reichardt Peter , Stradal Theresia E. , Warnecke Nicole , Simeoni Luca , Gunzer Matthias , Yablonski Deborah , Schraven Burkhart , Kliche Stefanie 
Published: October 2009

Abstract
Engagement of the TCR or of chemokine receptors such as CXCR4 induces adhesion and migration of T cells via so-called inside-out signaling pathways. The molecular processes underlying inside-out signaling events are as yet not completely understood. In this study, we show that TCR- and CXCR4-mediated activation of integrins critically depends on the membrane recruitment of the adhesion- and degranulation-promoting adapter protein (ADAP)/Src kinase-associated phosphoprotein of 55 kDa (SKAP55)/Rap1-interacting adapter protein (RIAM)/Rap1 module. We further demonstrate that the Src homology 2 domain containing leukocyte-specific phosphoprotein of 76 kDa (SLP76) is crucial for TCR-mediated inside-out signaling and T cell/APC interaction. Besides facilitating membrane recruitment of ADAP, SKAP55, and RIAM, SLP76 regulates TCR-mediated inside-out signaling by controlling the activation of Rap1 as well as Rac-mediated actin polymerization. Surprisingly, however, SLP76 is not mandatory for CXCR4-mediated inside-out signaling. Indeed, both CXCR4-induced T cell adhesion and migration are not affected by loss of SLP76. Moreover, after CXCR4 stimulation, the ADAP/SKAP55/RIAM/Rap1 module is recruited to the plasma membrane independently of SLP76. Collectively, our data indicate a differential requirement for SLP76 in TCR- vs CXCR4-mediated inside-out signaling pathways regulating T cell adhesion and migration.
Transgenic Expression of Hsc70 in Pancreatic Islets Enhances Autoimmune Diabetes in Response to β Cell Damage
Authors: Alam Masih-ul , Harken Julie A. , Knorn Anna-Maria , Elford Alisha R. , Wigmore Kip , Ohashi Pamela S. , Millar Douglas G. 
Published: October 2009

AbstractInflammation following tissue damage promotes lymphocyte recruitment, tissue remodeling, and wound healing while maintaining self tolerance. Endogenous signals associated with tissue damage and cell death have been proposed to initiate and instruct immune responses following injury. In this study, we have examined the effects of elevated levels of a candidate endogenous danger signal, heat shock cognate protein 70 (hsc70), on stimulation of inflammation and autoimmunity following cell damage. We find that damage to pancreatic β cells expressing additional cytosolic hsc70 leads to an increased incidence of diabetes in a transgenic mouse model. Steady-state levels of activated APC and T cell populations in the draining lymph node were enhanced, which further increased following streptozotocin-induced β cell death. In addition, proinflammatory serum cytokines, and lymphocyte recruitment were increased in hsc70 transgenic mice. Islet Ag-specific T cells underwent a greater extent of proliferation in the lymph nodes of mice expressing hsc70 following β cell damage, suggesting elevated Ag presentation following release of Ag in the presence of hsc70. These findings suggest that an elevated content of hsc70 in cells undergoing necrotic or apoptotic cell death can increase the extent of sterile inflammation and increase the susceptibility to autoimmunity.
Demonstration of entrapment in a totally occluded popliteal artery-a case report
Authors: Gupta A K 
Published: October 2009

AbstractA case of intermittent claudication in a young male patient with short segment occlusion of popliteal artery is presented. Entrapment of the artery was recognised during attempted angioplasty by demonstration of extrinsic impression on the inflated balloon during forced plantar flexion. The importance of identifying this condition for definitive surgical management is stressed.
Tolosa hunt syndrome: A case report
Authors: Khera P S , Singh S , Chowdhury V , Dixit R 
Published: October 2009

AbstractTolosa-Hunt syndrome (THS) is a painful ophthalmoplegia caused by nonspecific inflammation of the cavernous sinus or superior orbital fissure. We present a case of THS disease evaluated on a 1.5 Tesla MR scanner.
Tumor markers in clinical practice: General principles and guidelines
Authors: Sharma S 
Published: October 2009

AbstractTumor markers are assuming a growing role in all aspects of cancer care, starting from screening to follow-up after treatment, and their judicious application in clinical practice needs a thorough understanding of the basics of pathophysiology, techniques of identification or testing, reasons for out-of-range levels of tumor markers, as well as the knowledge of evidence of their role in any given malignancy. These are, at the most, just an adjunct to diagnosis, and establishing a diagnosis on the basis of tumor markers alone (especially a single result) is fraught with associated pitfalls because of the problem of nonspecificity. In reality an ideal tumor marker does not exist. Detection can be done either in tissue or in body fluids like ascitic or pleural fluid or serum. Clinical uses can be broadly classified into 4 groups: screening and early detection, diagnostic confirmation, prognosis and prediction of therapeutic response and monitoring disease and recurrence. In addition to variable sensitivity and specificity, the prevalence of a particular malignancy may be a major determinant in the application of a particular test as a screening tool. Serum levels, in certain situations, can be used in staging, prognostication or prediction of response to therapy. Monitoring disease is, perhaps, the most common clinical use of serum tumor markers. Rising trend in serum levels may detect recurrence of disease well before any clinical or radiological evidence of disease is apparent ("biochemical recurrence"). Sampling should ideally be repeated after 5-6 half-lives of the marker in question (or the marker with the longest half-life if multiple markers are being considered); but if found elevated, the next sampling after 2-4 weeks, for additional evidence, may be justified.
Adrenocortical carcinoma with skeletal metastases in a postmenopausal woman
Authors: Mitra Shila , Roy Suparna Ghosh , Sur Prabir Kumar 
Published: October 2009

AbstractAdrenocortical cancer is a very rare tumor with a poor prognosis. About half of them are hormone-secreting tumors. In most cases, hormonal investigations reveal an excess secretion of steroids, mostly cortisol and androgens. A 54-year-old lady presented with history of pain in left shoulder and leg for 6 months and features of virilization. CT-guided fine-needle aspiration cytology of an abdominal mass revealed the presence of a carcinoma of the left adrenal cortex. A whole-body radionuclide bone scan revealed increased uptake in the left clavicle and left femur. The patient has received palliative radiotherapy for the skeletal lesions and 3 cycles of palliative chemotherapy at present.
Primary transitional cell carcinoma of the Fallopian tube in a premenopausal woman: A case report and review of literature
Authors: Babu Manoj R , Haji Altaf Gauhar , Chitrathara K , Vijaykumar D K , Samanta Jayeeta , Hiran K H 
Published: October 2009

AbstractTransitional carcinomas are extremely rare in the fallopian tube. A 41-year-old premenopausal lady presented with colicky abdominal pain and was found to have a left-sided pelvic mass on examination. In view of the elevated CA-125 and imaging findings suggestive of ovarian mass, she underwent staging laparotomy. Pathological examination confirmed a primary transitional cell carcinoma of the left fallopian tube. Review of available literature suggested that the primary transitional cell carcinoma is probably less aggressive compared to classical adenocarcinoma of the fallopian tube, and it has to be distinguished from the recently recognized entity, parafallopian tube transitional cell carcinoma.
Thymic seminoma
Authors: Kannan J , Karkuzhali P , Lakshminarasimhan S 
Published: October 2009

AbstractThymic seminoma is a rare clinical entity. We report a case of an 18-year-old male patient who presented with chest pain, dyspnea, dysphagia of 1-month duration. Contrast-enhanced computer tomogram of chest showed an anterior mediastinal mass. He was subjected to thoracotomy and excision of the mass. Histopathology examination revealed seminoma of thymus. He failed to follow up for a period of 8 months post-surgery as he was asymptomatic. He then presented with a recurrence of the tumor locally, along with metastases to the lung, para-aortic and peri-aortic lymph nodes. He was kept on cisplatin, bleomycin and etoposide.