bluuebunny/crossref_metadata_2025_split huggingface dataset:
IGFBP-4 tumor and serum levels are increased across all stages of epithelial ovarian cancer
Authors: Mosig Rebecca A , Lobl Mollie , Senturk Emir , Shah Hardik , Cohen Samantha , Chudin Eugene , Fruscio Robert , Marchini Sergio , D'Incalci Maurizio , Sachidanandam Ravi , Dottino Peter , Martignetti John A 
Published: January 2012

Abstract

Background
We sought to identify candidate serum biomarkers for the detection and surveillance of EOC. Based on RNA-Seq transcriptome analysis of patient-derived tumors, highly expressed secreted proteins were identified using a bioinformatic approach.

Methods
RNA-Seq was used to quantify papillary serous ovarian cancer transcriptomes. Paired end sequencing of 22 flash frozen tumors was performed. Sequence alignments were processed with the program ELAND, expression levels with ERANGE and then bioinformatically screened for secreted protein signatures. Serum samples from women with benign and malignant pelvic masses and serial samples from women during chemotherapy regimens were measured for IGFBP-4 by ELISA. Student's t Test, ANOVA, and ROC curves were used for statistical analysis.

Results
Insulin-like growth factor binding protein (IGFBP-4) was consistently present in the top 7.5% of all expressed genes in all tumor samples. We then screened serum samples to determine if increased tumor expression correlated with serum expression. In an initial discovery set of 21 samples, IGFBP-4 levels were found to be elevated in patients, including those with early stage disease and normal CA125 levels. In a larger and independent validation set (82 controls, 78 cases), IGFBP-4 levels were significantly increased (p < 5 × 10-5). IGFBP-4 levels were ~3× greater in women with malignant pelvic masses compared to women with benign masses. ROC sensitivity was 73% at 93% specificity (AUC 0.816). In women receiving chemotherapy, average IGFBP-4 levels were below the ROC-determined threshold and lower in NED patients compared to AWD patients.

Conclusions
This study, the first to our knowledge to use RNA-Seq for biomarker discovery, identified IGFBP-4 as overexpressed in ovarian cancer patients. Beyond this, these studies identified two additional intriguing findings. First, IGFBP-4 can be elevated in early stage disease without elevated CA125. Second, IGFBP-4 levels are significantly elevated with malignant versus benign disease. These findings provide the rationale for future validation studies.
Ten-week lifestyle changing program reduces several indicators for metabolic syndrome in overweight adults
Authors: Mecca Marita S , Moreto Fernando , Burini Franz HP , Dalanesi Reinaldo C , McLellan Kátia CP , Burini Roberto C 
Published: January 2012

Abstract
We aim to investigate the effectiveness of a 10-week lifestyle intervention focusing on physical activity and high fiber intake for reducing indicators for metabolic syndrome in overweight-obese individuals. A prospective study of 50 overweight (OW) adults (22 in the general educational group - G1; 28 in the high fiber nutrition group - G2) was performed. Both groups were offered dietary counseling and supervised exercise. Clinical, anthropometric, dietary and plasma biochemical tests were performed at baseline - time 0 (T0) and after 10 weeks - time 1 (T1). Both groups improved their dietary quality, but only G2 presented higher intake of fruit and vegetables (servings/day), higher plasma β-carotene levels and a 24% reduction of MetS incidence. Additionally G2 showed greater reductions in body fat (4%), and waist circumference (7%), obesity class III (2%) and obesity class II (14%) rate. Lifestyle intervention, including a high dietary fiber intake, improved healthy eating index and decreased body fat composition and plasma lipid concentrations leading to MetS incidence reduction.
SWI/SNF-mediated chromatin remodeling induces Z-DNA formation on a nucleosome
Authors: Mulholland Niveen , Xu Yan , Sugiyama Hiroshi , Zhao Keji 
Published: January 2012

Abstract

Background
Z-DNA is a higher-energy, left-handed form of the double helix. A primary function of Z-DNA formation is to facilitate transcriptional initiation and activation. Sequences favoring Z-DNA formation are frequently located in promoter regions and Z-DNA is stabilized by torsional strain resulting from negative supercoiling, such as that generated by an actively transcribing polymerase or by a nucleosome remodeling event. We previously have shown that activation of the CSF1 gene by a chromatin remodeling event in the promoter results in Z-DNA formation at TG repeats within the promoter.

Results
We show that remodeling of a mononucleosome by the human SWI/SNF complex results in Z-DNA formation when the DNA within the mononucleosome contains Z-DNA favoring sequence. Nuclease accessibility patterns of nucleosome core particle consisting of Z-DNA are quite different from counterpart nucleosomes containing classic B-DNA. Z-nucleosomes represent a novel mononucleosome structure.

Conclusions
We present evidence that Z-DNA can form on nucleosomes though previous observations indicate the occlusion of nucleosome formation from Z-DNA.
Serum COMP-C3b complexes in rheumatic diseases and relation to anti-TNF-α treatment
Authors: Happonen Kaisa E , Saxne Tore , Geborek Pierre , Andersson Maria , Bengtsson Anders A , Hesselstrand Roger , Heinegård Dick , Blom Anna M 
Published: January 2012

Abstract
Introduction
Cartilage oligomeric matrix protein (COMP) is found at elevated concentrations in sera of patients with joint diseases such as rheumatoid arthritis (RA) and osteoarthritis (OA). We recently showed that COMP activates complement via the alternative pathway and that COMP-C3b complexes are present in sera of RA patients, but not in healthy controls. We now set out to elaborate on the information provided by this marker in a variety of diseases and larger patient cohorts.

Methods
COMP-C3b levels in sera were measured by using an enzyme-linked immunosorbent assay (ELISA) capturing COMP and detecting C3b. Serum COMP was measured by using ELISA.

Results
COMP-C3b levels were significantly elevated in patients with RA as well as in systemic lupus erythematosus (SLE), compared with healthy controls. SLE patients with arthritis had significantly higher COMP-C3b levels than did those without. COMP-C3b was furthermore elevated in patients with ankylosing spondylitis (AS), psoriatic arthritis (PsA), reactive arthritis, systemic sclerosis, and OA. COMP-C3b did not correlate with COMP in any of the patient groups. COMP-C3b correlated with disease activity in RA, but not in other diseases. COMP-C3b levels in RA patients decreased on treatment with tumor necrosis factor (TNF)-α inhibitors, whereas the levels increased in patients with AS or PsA. The changes of COMP-C3b did not parallel the changes of C-reactive protein (CRP).

Conclusions
COMP-C3b levels are elevated in several rheumatologic diseases and correlate with inflammatory measures in RA. COMP-C3b levels in RA decrease during TNF-α inhibition differently from those of CRP, suggesting that formation of COMP-C3b relates to disease features not reflected by general inflammation measures.
Microenvironmental regulation of inducible nitric oxide synthase expression and nitric oxide production in mouse bone marrow-derived mast cells
Authors: Moon Tae Chul , Yoshimura Tsuyoshi , Parsons Thomas , Befus A Dean 
Published: January 2012

ABSTRACTIn addition to its well-known role in relaxation of vascular smooth muscle, NO modulates immune responses in a concentration- and location-specific manner. For MC, it is well accepted that exogenous NO regulates their function. However, there are inconsistencies in the literature of whether MC express NOS and make NO. MC progenitors mature in peripheral tissues, but the factors that influence MC maturation and their specific phenotype, such as whether they express NOS, are not well understood. To study microenvironmental conditions that could be “permissive” for NOS expression, we cultured BMMC in various conditions—BMMCIL-3, BMMCSCF/IL-3, or BMMCSCF/IL-4—for &gt;3 weeks and examined NOS expression. We detected Nos2 mRNA in BMMCSCF/IL-4 but not BMMCIL-3 or BMMCSCF/IL-3. After stimulation with IFN-γ and/or LPS, NOS2 expression and NO production were detected in BMMCSCF/IL-4 but rarely detected in BMMC cultured with other conditions. Confocal microscopic analysis showed that NOS2 expression induced by IFN-γ colocalized in CD117+ BMMC. NO production, after activation with IFN-γ and LPS in BMMCSCF/IL-4, was abrogated by pretreatment with the NOS2-specific inhibitor. In addition to NOS2 expression, BMMCSCF/IL-4 were distinguished from BMMCIL-3 in heparin and MMCP expression. Thus, MC progenitors that develop in SCF + IL-4 can be induced to express NOS2 after receiving appropriate signals, such as IFN-γ, and subsequently produce NO. Microenvironmental conditions during their development can influence whether MC are capable of NOS expression and of NO production.
Four-Color Alternating-Laser Excitation Single-Molecule Fluorescence Spectroscopy for Next-Generation Biodetection Assays
Authors: Yim Seok W , Kim Taiho , Laurence Ted A , Partono Steve , Kim Dongsik , Kim Younggyu , Weiss Shimon , Reitmair Armin 
Published: January 2012

Abstract

BACKGROUND
Single-molecule detection (SMD) technologies are well suited for clinical diagnostic applications by offering the prospect of minimizing precious patient sample requirements while maximizing clinical information content. Not yet available, however, is a universal SMD-based platform technology that permits multiplexed detection of both nucleic acid and protein targets and that is suitable for automation and integration into the clinical laboratory work flow.

METHODS
We have used a sensitive, specific, quantitative, and cost-effective homogeneous SMD method that has high single-well multiplexing potential and uses alternating-laser excitation (ALEX) fluorescence-aided molecule sorting extended to 4 colors (4c-ALEX). Recognition molecules are tagged with different-color fluorescence dyes, and coincident confocal detection of ≥2 colors constitutes a positive target-detection event. The virtual exclusion of the majority of sources of background noise eliminates washing steps. Sorting molecules with multidimensional probe stoichiometries (S) and single-molecule fluorescence resonance energy transfer efficiencies (E) allows differentiation of numerous targets simultaneously.

RESULTS
We show detection, differentiation, and quantification—in a single well—of (a) 25 different fluorescently labeled DNAs; (b) 8 bacterial genetic markers, including 3 antibiotic drug–resistance determinants found in 11 septicemia-causing Staphylococcus and Enterococcus strains; and (c) 6 tumor markers present in blood.

CONCLUSIONS
The results demonstrate assay utility for clinical molecular diagnostic applications by means of multiplexed detection of nucleic acids and proteins and suggest potential uses for early diagnosis of cancer and infectious and other diseases, as well as for personalized medicine. Future integration of additional technology components to minimize preanalytical sample manipulation while maximizing throughput should allow development of a user-friendly (“sample in, answer out”) point-of-care platform for next-generation medical diagnostic tests that offer considerable savings in costs and patient sample.
Microwave-Induced Heating of HMX for Decomposition Kinetic Analysis
Authors: Duque Amanda L. , Perry W. Lee 
Published: January 2012

ABSTRACTWe use microwave (MW) absorption to induce rapid, uniform heating of the secondary high explosive octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) for decomposition analysis in a fast kinetic regime (10-2 s). Because HMX alone is MW inactive, composites comprised of an HMX-polymeric binder system doped with a small mass fraction (<1 wt%) multiwalled carbon nanotubes or graphite, were fabricated. The dielectric properties were measured (real and imaginary permittivity between 1 – 18 GHz), which is necessary for describing the expected MW-materials interaction and predicted heating response. The real component of the relative dielectric permittivity ranged from 3 – 4 while the imaginary component was 0.01 – 0.07, depending on the amount of carbon dopant added. Dynamic temperature measurements of a similar explosive composite under MW exposure were accomplished using fiber-optic temperature measurement techniques, and can be reproducibly correlated to the amount of MW energy absorbed in the sample.
Immediate Loading of Dental Implants Placed in Severely Resorbed Edentulous Maxillae Reconstructed With Le Fort I Osteotomy and Interpositional Bone Grafting
Authors: Pieri Francesco , Lizio Giuseppe , Bianchi Alberto , Corinaldesi Giuseppe , Marchetti Claudio 
Published: January 2012

Background: Reconstruction and rehabilitation of atrophic maxillae with bone grafts is a lengthy and demanding procedure. This study reports the immediate loading of 50 implants placed on six extremely atrophied edentulous maxillae reconstructed with Le Fort I osteotomy and iliac bone grafting.Methods: Six patients, aged 49 to 68 years, with severely atrophied maxillae were treated with Le Fort I osteotomy and iliac bone grafting to allow for implant‐borne prosthetic rehabilitation. Four to 5 months thereafter, 50 implants (seven to 10 per patient) were placed in reconstructed maxillae and immediately functionally loaded with a screw‐retained definitive prosthesis. The patients were followed by clinical and radiographic examinations for 24 months after prosthetic loading.Results: The grafting procedure and healing period before implant placement were uneventful in all patients. Two implants were lost within 2 months after prosthesis insertion in two patients, with an overall survival rate of 96%. The prostheses success rate was 100%. At the end of the follow‐up period, all remaining implants appeared clinically healthy; crestal bone loss was >1.7 mm for six implants, resulting in a cumulative success rate of 84%.Conclusion: Immediate loading of implants placed after Le Fort I osteotomy and interpositional iliac bone grafting could be considered a viable protocol to rehabilitate extremely atrophied edentulous maxillae, considerably reducing the treatment time.
Cupping and definability in the local structure of the enumeration degrees
Authors: Ganchev Hristo , Soskova Mariya I. 
Published: January 2012

AbstractWe show that every splitting of in the local structure of the enumeration degrees, , contains at least one low-cuppable member. We apply this new structural property to show that the classes of all -pairs in , all downwards properly enumeration degrees and all upwards properly enumeration degrees are first order definable in .
Normal forms for elementary patterns
Authors: Carlson Timothy J. , Wilken Gunnar 
Published: January 2012

AbstractA notation for an ordinal using patterns of resemblance is based on choosing an isominimal set of ordinals containing the given ordinal. There are many choices for this set meaning that notations are far from unique. We establish that among all such isominimal sets there is one which is smallest under inclusion thus providing an appropriate notion of normal form notation in this context. In addition, we calculate the elements of this isominimal set using standard notations based on collapsing functions. This provides a capstone to the results in [2, 6, 8, 9, 7], using further refinement of ordinal arithmetic developed in [8] which then both allows for a simple characterization of normal forms for patterns of order one and will play a key role in the arithmetical analysis of pure patterns of order two, [5].
Auditor Rotation: The PCAOB Considers a New Direction
Authors: Roush Pamela B. , Church Bryan K. , Jenkins J. Gregory , McCracken Susan A. , Stanley Jonathan D. 
Published: January 2012

SUMMARY
The Public Company Accounting Oversight Board (PCAOB) recently undertook an exploration of the need for mandatory audit firm rotation with its issuance of the Concept Release on Auditor Independence and Auditor Rotation (PCAOB 2011a). The accumulation of evidence from PCAOB inspections of audit engagements over the last eight years has led the Board to consider additional steps to protect auditors' independence. We provide a brief synopsis of these matters based primarily on remarks by the PCAOB's chairman, James R. Doty (PCAOB 2011b, 2011c). In addition, we include relevant observations from prior academic studies and end with a call for the active participation of stakeholders in this important debate.
Long-term outcome of endovascular reconstruction with the Pipeline embolization device in the management of unruptured dissecting aneurysms of the intracranial vertebral artery
Authors: Yeung Tsz Wai , Lai Vincent , Lau Hin Yue , Poon Wai Lun , Tan Chong Boon , Wong Yiu Chung 
Published: January 2012

Object
Use of a flow-diverting device has shown promising short-term results in the management of vertebral artery (VA) dissecting aneurysms, but there is still uncertainty regarding its long-term efficacy and safety. The authors report their initial experience with respect to the potential utility and long-term clinical outcomes of using a flow-diverting device in the treatment of unruptured dissecting VA aneurysms.

Methods
The authors conducted a retrospective review of all cases of unruptured intracranial VA dissecting aneurysms treated at their institution (Tuen Mun Hospital) with a flow-diverting device. They describe the clinical presentations and angiographic features of the cases and report the clinical outcome (with modified Rankin Scale [mRS] scores) at most recent follow-up, as well as results of the latest angiographic assessment, with particular focus on in-stent patency and side-branch occlusion.

Results
A total of 4 aneurysms were successfully obliterated by using flow-diverting devices alone. Two devices were deployed in a telescoping fashion in each of 2 aneurysms, whereas only 1 device was inserted in each of the other 2 aneurysms. No periprocedural complication was encountered. No patient showed any angiographic evidence of recurrence, in-stent thrombosis, or side-branch occlusion in angiographic reassessment at a mean of 22 months after treatment (range 18–24 months). As of the most recent clinical follow-up (mean 30 months after treatment, range 24–37 months), all patients had favorable outcomes (mRS Score 0).

Conclusions
Reconstruction using a flow-diverting device is an attractive alternative in definitive treatment of dissecting VA aneurysms, demonstrating favorable long-term clinical and angiographic outcomes and the ability to maintain parent artery and side-branch patency. It is particularly useful in cases with eloquent side-branch or dominant VA involvement.
Analysis of the uncinate processes of the cervical spine: an anatomical study
Authors: Tubbs R. Shane , Rompala Olivia J. , Verma Ketan , Mortazavi Martin M. , Benninger Brion , Loukas Marios , Chambers M. Rene 
Published: January 2012

Object
Although the uncovertebral region is neurosurgically relevant, relatively little is reported in the literature, specifically the neurosurgical literature, regarding its anatomy. Therefore, the present study aimed at further elucidation of this region's morphological features.

Methods
Morphometry was performed on the uncinate processes of 40 adult human skeletons. Additionally, range of motion testing was performed, with special attention given to the uncinate processes. Finally, these excrescences were classified based on their encroachment on the adjacent intervertebral foramen.

Results
The height of these processes was on average 4.8 mm, and there was an inverse relationship between height of the uncinate process and the size of the intervertebral foramen. Degeneration of the vertebral body (VB) did not correlate with whether the uncinate process effaced the intervertebral foramen. The taller uncinate processes tended to be located below C-3 vertebral levels, and their average anteroposterior length was 8 mm. The average thickness was found to be 4.9 mm for the base and 1.8 mm for the apex. There were no significant differences found between vertebral level and thickness of the uncinate process. Arthritic changes of the cervical VBs did not necessarily deform the uncinate processes. With axial rotation, the intervertebral discs were noted to be driven into the ipsilateral uncinate process. With lateral flexion, the ipsilateral uncinate processes aided the ipsilateral facet joints in maintaining the integrity of the ipsilateral intervertebral foramen.

Conclusions
A good appreciation for the anatomy of the uncinate processes is important to the neurosurgeon who operates on the spine. It is hoped that the data presented herein will decrease complications during surgical approaches to the cervical spine.
Vertical Circulation and Release of Kinetic Energy during the Development of Hurricane Hazel into an Extratropical Storm
Authors: Palmén E. 
Published: January 2012

The thermal structure of the atmosphere over the eastern and central parts of the U. S. on October 15, 1954, when the tropical hurricane “Hazel” entered the American continent and rapidly was transformed into an extratropical cyclone of great intensity, is analyzed by the aid of upper air charts and vertical cross sections. The field of divergence and vertical velocity is determined from the horizontal wind field at different levels for the synoptic time October 15, 1500 GCT, and the results are used for computing the precipitation in the region of strongest ascent of the warm and moist air of the tropical disturbance and for a determination of the release of kinetic energy in the whole region due to vertical solenoidal circulations associated with the general sinking of the cold polar air masses and the simultaneous ascent of the warm tropical air masses. The production of kinetic energy is also computed directly from the work done by the horizontal pressure forces in the same area. Both methods give a production of kinetic energy of about 19 × 1010 kilojoules or 19 × 1020 ergs per second over an area 366 × 104 km2 large. Only a small part of the energy released is again dissipated due to friction in the same area, whereas the essential part is exported outwards from the source region, thus furnishing the surrounding atmosphere with large amounts of kinetic energy.
In the last section some general conclusions are made concerning the budget of kinetic energy in the whole Northern Hemisphere, considering the net effect of the disturbances in the westerlies, the mean meridional circulations, the mean meridional flux of kinetic energy and the frictional dissipation.
Droplet Sampling in Cumulus Clouds
Authors: Durbin W. G. 
Published: January 2012

An analysis is made of 150 cloud droplet samples obtained by the impaction method in cumulus clouds varying in vertical depth from 750 to 7000 ft.
From a consideration of the spectra relating numbers of droplets with droplet diameter, a mode diameter of about 8 µ, is found. A secondary mode diameter of about 15 µ is in evidence in some clouds. In the main numbers of droplets are between 100 and 300 per cm3 but extreme values of about 20 and 1000 occur.
Spectra relating water content with droplet diameter show that in clouds between about 750 and 2500 ft thick the mode diameter is about 8 µ, whereas in clouds between about 4000 and 7000 ft thick the mode diameter is about 18 µ. The highest value of water content found is about 5 g m−3.
Evidence is found that mean volume diameter tends to increase with height above cloud base and that high values of water content are due to larger droplets rather than to greater numbers of droplets per cm3.
A droplet distribution formula given by Best is examined and the constants involved are found to depend on the largest size of droplet present.