bluuebunny/crossref_metadata_2025_split huggingface dataset:
Extraction of Total Protein from Arabidopsis
Authors: Larkin Rob 
Published: January 2007

INTRODUCTIONThe functions of most Arabidopsis genes cannot be understood simply by studying the expression patterns of their mRNAs. The level of a protein may not be closely correlated with the level of the corresponding mRNA, or a protein may need to be modified to be active. Furthermore, the function of proteins often depends on specific subcellular localization, so knowledge of this can exclude some hypotheses about possible function. The simplest way to analyze proteins is in unfractionated extracts. However, it is often desirable to fractionate proteins, e.g, by size. This procedure extracts total protein from Arabidopsis samples. Typical yields are ~2-3 mg/ml (using rosette leaves) or 6-8 mg/ml (using young seedlings).
Protein Coimmunoprecipitation in Arabidopsis
Authors: Serino Giovanna , Deng Xing-Wang 
Published: January 2007

INTRODUCTIONCoimmunoprecipitation is one of the most useful techniques for revealing protein-protein interactions. Briefly, it can be divided into three steps: (1) preparation of cell extracts without disruption of protein interactions; (2) formation of the antibody-antigen complexes; and (3) affinity purification of the protein complexes and subsequent detection. Good negative controls to verify the specificity of the coimmunoprecipitation procedure are (1) performing the same immunoprecipitation experiment using beads coupled to the preimmune serum and (2) probing the Western blot with antibodies against protein known not to interact with the coimmunoprecipitated proteins under physiological conditions.
Does mini‐incision donor nephrectomy improve quality of life in living kidney donors?
Authors: Schnitzbauer Andreas A. , Hornung Matthias , Seidel Ulrike , Krüger Bernd , Krämer Bernhard K. , Schlitt Hans J. , Obed Aiman 
Published: January 2007

Abstract: Background:  Living kidney donation helps to avoid or reduce the time period of dialysis and on waiting lists in patients requiring a new organ. Mini‐incision donor nephrectomy (MIDN) shows to result in better clinical outcome in comparison with traditional open donor nephrectomy (ODN). This study was performed to evaluate the impact of different surgical procedures on the quality of life (QoL) in patients that underwent donor nephrectomy.Methods:  The aim of the study was to detect differences in QoL assessed with the Short Form‐36 Version 2 (SF‐36v2) questionnaire between MIDN (n = 34) and ODN (n = 36). Furthermore, the development of QoL from prior to surgery until one yr afterwards, as well as outcomes of QoL in comparison with norm‐based scores was investigated.Results:  Sixty‐one of 70 patients, which is 87% (MIDN: 86%, ODN: 88%) resent a whole set questionnaires. QoL was similar at all time‐points (prior to surgery, one wk, three months and one yr) in both groups. A tendency of better QoL in MIDN (Bodily Pain) after one wk was detectable (p = 0.075). Physical Component Summaries (PCS) significantly decreased from prior to surgery until one wk after surgery (p = 0.001) and improved significantly until three months (MIDN: p = 0.006, ODN: p = 0.001) and also until one yr after surgery (p = 0.002). Mental Component Summaries (MCS) were stable throughout the whole investigated time period. In comparison with norm‐based scores, MIDN (p = 0.005) and ODN (p = 0.001) showed significantly higher PCS prior to, lower scores one wk after (p = 0.001), similar scores three months after and better scores (MIDN: p = 0.023, ODN: 0.015) one yr after surgery. Mental Component Scores were similar in both prior to and one wk after surgery. After three months and one yr scores were significantly better in MIDN (three months: p = 0.049, one yr: p = 0.037) and ODN (three months: 0.020, one yr: 0.073).Conclusion:  Quality of life after living donor nephrectomy is not influenced by the surgical technique. Nevertheless the standardized instrument of the SF‐36v2 Health Survey is a useful, practicable and universally interpretable tool to gain and estimate recovery from surgical procedures in the perioperative period and its development thereafter.
Nateglinide improves postprandial hyperglycemia and insulin secretion in renal transplant recipients
Authors: Voytovich Monica Hagen , Haukereid Cecilie , Hjelmesæth Jøran , Hartmann Anders , Løvik Astrid , Jenssen Trond 
Published: January 2007

Abstract: Background: Postprandial hyperglycemia (PPHG) frequently occurs among renal transplant recipients (RTR). Reduced early insulin response (EIR) after a meal leads to impaired suppression of endogenous glucose production and subsequently PPHG, which is a risk factor for cardiovascular disease. Nateglinide is a rapid acting insulin secretagogue inducing an EIR after a meal. Our main objective was to investigate the safety and effect of nateglinide treatment on postprandial plasma glucose excursions and insulin secretion in RTR with PPHG.Patients and methods: A total of 14 Caucasian RTR with new‐onset diabetes mellitus (NODM; n = 6) or impaired glucose tolerance (IGT; n = 8) were included. The insulin response and glucose excursions were measured for 240 min after a standardized liquid meal at baseline and after two‐wk treatment with nateglinide.Results: Treatment with nateglinide was followed by a significant decrease in mean two‐h plasma glucose from 10.5 mmol/L (3.1) to 7.6 mmol/L (2.1; p < 0.001) and a decline in total postprandial area under the curve (AUC) of glucose concentration (p < 0.001). Both estimated EIR and the late insulin response increased significantly (p = 0.008 and p = 0.003, respectively). No serious adverse event was observed during the study period.Conclusions: Treating RTR with nateglinide for two‐wk significantly improved PPHG, increased the insulin response following a standardized meal and was well tolerated.
Mitogenic bovine whey extract modulates matrix metalloproteinase‐2, ‐9, and tissue inhibitor of matrix metalloproteinase‐2 levels in chronic leg ulcers
Authors: Varelias Antiopi , Cowin Allison J. , Adams Damian , Harries Richard H. C. , Cooter Rodney D. , Belford David A. , Fitridge Robert A. , Rayner, PhD Timothy E. 
Published: January 2007

ABSTRACTMatrix metalloproteinases (MMPs) and their tissue inhibitors play important roles in the wound‐healing process. An imbalance in the expression of these molecules is thought to contribute to the failure of chronic ulcers to heal. We investigated whether a mitogenic bovine whey extract enriched with growth factors modulated the expression and activity of MMP‐2 and ‐9, and the tissue inhibitor of MMP‐2 (TIMP‐2) in chronic leg ulcers. Wound fluids and biopsies were collected from chronic leg ulcer patients whose ulcers were treated topically for 4 weeks with placebo or mitogenic bovine whey extract at concentrations of 2.5, 10, and 20 mg/mL. The levels of MMP‐2 and ‐9 in wound fluid samples was assessed by gelatin zymography and showed a decrease in active MMP‐2 in the 2.5 and 10.0 mg/mL mitogenic bovine whey extract‐treated ulcers compared with placebo (p<0.05). Immunohistochemical analysis of ulcer biopsies for MMP‐2, ‐9, and TIMP‐2 expression showed a reduction in the number of MMP‐2–positive dermal fibroblasts in the mitogenic bovine whey extract‐treated ulcers compared with pretreatment biopsies (p<0.05) that persisted over the course of the study. In contrast, a transient increase in the number of MMP‐9– and TIMP‐2–positive cells was observed in mitogenic bovine whey extract treated ulcer biopsies compared with pretreatment levels (p<0.05). These results show that topical application of mitogenic bovine whey extract was able to modulate the expression of MMP‐2, ‐9, and TIMP‐2 in chronic leg ulcers and that its constituent growth factors may have the potential to redress the proteolytic imbalance observed in nonhealing chronic ulcers.
Therapeutic Use of Citrulline in Cardiovascular Disease
Authors: Romero Maritza J. , Platt Daniel H. , Caldwell Ruth B. , Caldwell R. William 
Published: January 2007

ABSTRACTL‐citrulline is the natural precursor of L‐arginine, substrate for nitric oxide synthase (NOS) in the production of NO. Supplemental administration L‐arginine has been shown to be effective in improving NO production and cardiovascular function in cardiovascular diseases associated with endothelial dysfunction, such as hypertension, heart failure, atherosclerosis, diabetic vascular disease and ischemia‐reperfusion injury, but the beneficial actions do not endure with chronic therapy. Substantial intestinal and hepatic metabolism of L‐arginine to ornithine and urea by arginase makes oral delivery very ineffective. Additionally, all of these disease states as well as supplemental L‐arginine enhance arginase expression and activity, thus reducing the effectiveness of L‐arginine therapy. In contrast, L‐citrulline is not metabolized in the intestine or liver and does not induce tissue arginase, but rather inhibits its activity. L‐citrulline entering the kidney, vascular endothelium and other tissues can be readily converted to L‐arginine, thus raising plasma and tissue levels of L‐arginine and enhancing NO production. Supplemental L‐citrulline has promise as a therapeutic adjunct in disease states associated with L‐arginine deficiencies.
Inertial Motions during the Transient Adjustment of a Density Anomaly in the Equatorial Ocean with Application to the Western Pacific Warm Pool
Authors: Le Sommer J. , Scherer E. , Zeitlin V. 
Published: January 2007

Abstract
This paper is focused on the spontaneous transient adjustment of a buoyant lens of water with uniform density, initially at rest in the vicinity of the equator. For parameters typical of the western Pacific warm pool, the adjustment is shown to generate finite-amplitude wave motions with period ∼8 days, which are not covered by the standard theory of linear equatorial waves. This mechanism may be at the origin of inertial motions at the early stages of ENSO events in the western Pacific Ocean. The lens adjustment is studied within the 11/2-layer reduced-gravity approximation on the equatorial β plane, using the high-resolution finite-volume numerical methods that are specially designed to handle outcropping isopycnals. Under the reduced-gravity approximation, a buoyant region of light water with outcropping boundaries in the vicinity of the equator is described by two parameters: the meridional-to-zonal scale aspect ratio δ and the ratio γ of the Coriolis force to the pressure force on its meridional boundary. For realistic parameters (δ ∼ 10−1; γ ∼ 1), the lens, initially at rest, spreads eastward in accord with nonrotating gravity current dynamics, whereas its westward extrusion is arrested so that the western edge splits into two anticyclonic vortices. Meanwhile finite-amplitude westward-propagating inertial wave motions develop at the interface between the spreading current and the ambient fluid. The inertial wave structure is shown to be consistent with the structure of stable wave modes predicted by linear analysis of small amplitude perturbations superimposed on a zonally symmetric equatorial current with outcropping isopycnals. A Wentzel–Kramers–Brillouin–Jeffreys ray-tracing analysis indicates that the inertial wave is emitted during the early stage of the gravity current evolution and then dispersed on the spreading current.
Algorithms for Density, Potential Temperature, Conservative Temperature, and the Freezing Temperature of Seawater
Authors: Jackett David R. , McDougall Trevor J. , Feistel Rainer , Wright Daniel G. , Griffies Stephen M. 
Published: January 2007

Abstract
Algorithms are presented for density, potential temperature, conservative temperature, and the freezing temperature of seawater. The algorithms for potential temperature and density (in terms of potential temperature) are updates to routines recently published by McDougall et al., while the algorithms involving conservative temperature and the freezing temperatures of seawater are new. The McDougall et al. algorithms were based on the thermodynamic potential of Feistel and Hagen; the algorithms in this study are all based on the “new extended Gibbs thermodynamic potential of seawater” of Feistel. The algorithm for the computation of density in terms of salinity, pressure, and conservative temperature produces errors in density and in the corresponding thermal expansion coefficient of the same order as errors for the density equation using potential temperature, both being twice as accurate as the International Equation of State when compared with Feistel’s new equation of state. An inverse function relating potential temperature to conservative temperature is also provided. The difference between practical salinity and absolute salinity is discussed, and it is shown that the present practice of essentially ignoring the difference between these two different salinities is unlikely to cause significant errors in ocean models.
Incremental Analysis Update Implementation into a Sequential Ocean Data Assimilation System
Authors: Ourmières Y. , Brankart J-M. , Berline L. , Brasseur P. , Verron J. 
Published: January 2007

Abstract
This study deals with the enhancement of a sequential assimilation method applied to an ocean general circulation model (OGCM). A major drawback of sequential assimilation methods is the time discontinuity of the solution resulting from intermittent corrections of the model state. The data analysis step can induce shocks in the model restart phase, causing spurious high-frequency oscillations and data rejection. A method called Incremental Analysis Update (IAU) is now recognized to efficiently tackle these problems.
In the present work, an IAU-type method is implemented into an intermittent data assimilation system using a low-rank Kalman filter [Singular Evolutive Extended Kalman (SEEK)] in the case of an OGCM with a 1/3° North Atlantic grid. A 1-yr (1993) experiment has been conducted for different setups in order to evaluate the impact of the IAU scheme. Results from all of the different tests are compared with a specific interest in high-frequency output behaviors and solution consistency. The improvements brought up by the IAU implementation, such as the disappearance of spurious high-frequency oscillations and the time continuity of the solution, are shown. An overall assessment of the impact of this new approach on the assimilated runs is discussed. Advantages and drawbacks of the IAU method are pointed out.
Remote Sensing of Ocean Waves by Polarimetric SAR
Authors: He Yijun , Shen Hui , Perrie William 
Published: January 2007

AbstractA new method to measure ocean wave slope spectra using fully polarimetric synthetic aperture radar (POLSAR) data was developed without the need for a complex hydrodynamic modulation transform function. There is no explicit use of a hydrodynamic modulation transfer function. This function is not clearly known and is based on hydrodynamic assumptions. The method is different from those developed by Schuler and colleagues or Pottier but complements their methods. The results estimated from NASA Jet Propulsion Laboratory (JPL) Airborne Synthetic Aperture Radar (AIRSAR) C-band polarimetric SAR data show that the ocean wavelength, wave direction, and significant wave height are in agreement with buoy measurements. The proposed method can be employed by future satellite missions such as RADARSAT-2.
An Approach for Retrieving Marine Boundary Layer Refractivity from GPS Occultation Data in the Presence of Superrefraction
Authors: Xie Feiqin , Syndergaard Stig , Kursinski E. Robert , Herman Benjamin M. 
Published: January 2007

Abstract
The global positioning system (GPS) radio occultation (RO) technique has demonstrated the ability to precisely probe earth’s atmosphere globally with high vertical resolution. However, the lowermost troposphere still presents some challenges for the technique. Over moist marine areas, especially in subtropical regions, a very large negative moisture gradient often exists across the thermal inversion capping the marine boundary layer (MBL), which frequently causes superrefraction (SR), or ducting. In the presence of SR, the reconstruction of refractivity from RO data becomes an ill-posed inverse problem. This study shows that one given RO bending angle profile is consistent with a continuum (an infinite number) of refractivity profiles. The standard Abel retrieval gives the minimum refractivity solution of the continuum and thus produces the largest negative bias, consistent with a negative bias often present in the retrieved refractivity profiles in the moist lower troposphere. By applying a simple linear parameterization of the refractivity structure within and just below the SR layer, an analytical relation between the Abel-retrieved refractivity and a continuum of solutions is derived. Combining the Abel retrieval and the analytical relation with some physical constraints, a novel approach is developed to reconstruct the vertical refractivity structure within and below the SR layer. Numerical simulation studies in this paper have demonstrated the great potential of the reconstruction method to provide a much-improved retrieval in the presence of SR, and the method should greatly enhance the ability to measure the MBL structure globally using the GPS RO technique.
Internalization of novel non-viral vector TAT-streptavidin into human cells
Authors: Rinne Johanna , Albarran Brian , Jylhävä Juulia , Ihalainen Teemu O , Kankaanpää Pasi , Hytönen Vesa P , Stayton Patrick S , Kulomaa Markku S , Vihinen-Ranta Maija 
Published: January 2007

Abstract

Background
The cell-penetrating peptide derived from the Human immunodeficiency virus-1 transactivator protein Tat possesses the capacity to promote the effective uptake of various cargo molecules across the plasma membrane in vitro and in vivo. The objective of this study was to characterize the uptake and delivery mechanisms of a novel streptavidin fusion construct, TAT47–57-streptavidin (TAT-SA, 60 kD). SA represents a potentially useful TAT-fusion partner due to its ability to perform as a versatile intracellular delivery vector for a wide array of biotinylated molecules or cargoes.

Results
By confocal and immunoelectron microscopy the majority of internalized TAT-SA was shown to accumulate in perinuclear vesicles in both cancer and non-cancer cell lines. The uptake studies in living cells with various fluorescent endocytic markers and inhibiting agents suggested that TAT-SA is internalized into cells efficiently, using both clathrin-mediated endocytosis and lipid-raft-mediated macropinocytosis. When endosomal release of TAT-SA was enhanced through the incorporation of a biotinylated, pH-responsive polymer poly(propylacrylic acid) (PPAA), nuclear localization of TAT-SA and TAT-SA bound to biotin was markedly improved. Additionally, no significant cytotoxicity was detected in the TAT-SA constructs.

Conclusion
This study demonstrates that TAT-SA-PPAA is a potential non-viral vector to be utilized in protein therapeutics to deliver biotinylated molecules both into cytoplasm and nucleus of human cells.
Serial alterations in digital hemodynamics and endothelin-1 immunoreactivity, platelet-neutrophil aggregation, and concentrations of nitric oxide, insulin, and glucose in blood obtained from horses following carbohydrate overload
Authors: Eades Susan C. , Stokes Ashley M. , Johnson Philip J. , LeBlanc Casey J. , Ganjam Venkataseshu K. , Buff Preston R. , Moore Rustin M. 
Published: January 2007

Abstract
Objective—To quantify changes in endothelium-derived factors and relate those changes to various aspects of digital hemodynamics during the prodromal stages of carbohydrate overload (CHO)-induced laminitis in horses.
Animals—20 adult horses without abnormalities of the digit.
Procedures—Digital and jugular venous blood samples were collected at 1-hour intervals (for assessment of endothelin-1 [ET-1] immunoreactivity and measurement of glucose, insulin, and nitric oxide [NO] concentrations) or 4-hour intervals (CBC and platelet-neutrophil aggregate assessment) for 8 hours or 16 hours after induction of CHO-associated laminitis in horses treated with an ET-1 antagonist. Effects of treatment, collection site, and time and the random effects of horse on each variable were analyzed by use of a repeated-measures model. Where treatment and collection site had no significant effect, data were combined.
Results—Compared with baseline values, CHO resulted in changes in several variables, including a significant increase from baseline in digital blood ET-like immunoreactivity at 11 hours; digital blood ET-like immunoreactivity was significantly greater than that in jugular venous blood at 8, 9, 11, and 12 hours. Digital and jugular venous blood concentrations of glucose increased from baseline significantly at 3, 4, and 5 hours; insulin concentration increased significantly at 5 hours; and the number of platelet-neutrophil aggregates increased significantly at 12 hours.
Conclusions and Clinical Relevance—In horses, concurrent increases in venous blood ET-1 immunoreactivity, insulin and glucose concentrations, and platelet-neutrophil aggregates support a role of endothelial dysfunction in the pathogenesis of CHO-induced laminitis.
Use of three-dimensional computed tomography for diagnosis and treatment planning for open-mouth jaw locking in a cat
Authors: Beam Rebekah C. , Kunz David A. , Cook Cristi R. , Carson Robert L. , Briscoe Phillip , Cook James L. 
Published: January 2007

Abstract
Case Description—A 2.5-year-old spayed female Persian cat was evaluated for acute inability to close its mouth.
Clinical Findings—A wry-mouth malocclusion was evident, and the right side of the mandible was longer than the left side. The right mandibular tooth row appeared to be lowered. The lower jaw was persistently maintained in an open position. The presumptive diagnosis was open-mouth jaw locking. Diagnostic imaging with computed tomography and 3-dimensional reconstruction was performed for definitive diagnosis and to achieve a better understanding of the lesions. Imaging revealed locking of the right ramus of the mandible, which was displaced ventrolaterally, causing the coronoid process to impinge on the right zygomatic arch.
Treatment and Outcome—A bilateral partial ostectomy of the rostroventral margins of the zygomatic arches with an autogenous fat graft implantation was performed. The cat recovered without complications and by the following morning was bright, alert, and responsive and eating canned cat food comfortably. One year after surgery, the owner reported that the cat had continued to function well, was eating normally, and had not had any observed locking episodes since surgery.
Clinical Relevance—Unlike radiographic imaging, computed tomography may be used to create 3-dimensional reconstructions of structures in cases of suspected open-mouth jaw locking; improve evaluation of the lesions; and improve decision-making and client education for diagnosis, treatment options, and prognosis.