bluuebunny/crossref_metadata_2025_split huggingface dataset:
Primary local orbital amyloidosis: biochemical identification of the immunoglobulin light chain κIII subtype in a small formalin fixed, paraffin wax embedded tissue sample
Authors: Kaplan B , Martin B M , Cohen H I , Manaster J , Kassif Y , Rehany U , Livneh A 
Published: April 2005

Background:Amyloidosis refers to a heterogeneous group of disorders associated with the deposition of chemically distinct amyloid fibril proteins. Precise determination of chemical amyloid type has diagnostic, therapeutic, and prognostic relevance. Although immunohistochemical techniques are used routinely to determine the amyloid type, the results can be negative or inconclusive, so that biochemical characterisation is often required. The development and application of new biochemical microtechniques suitable for examination of extremely small tissue samples is essential for precise identification of the deposited amyloid proteins.Aims:To investigate biochemically the amyloid proteins present in a formalin fixed paraffin wax embedded orbital tissue from a patient with localised orbital amyloidosis in whom immunohistochemistry was not helpful in the determination of amyloid type.Methods:Extraction of amyloid proteins from fixed tissue and their identification was carried out by a recently developed microtechnique. An extremely small tissue sample was dewaxed and extracted with formic acid. The extracted material was analysed using electrophoresis, western blotting, and amino acid sequencing.Results:Biochemical examination of the extracted proteins showed the presence of immunoglobulin (Ig) derived amyloid proteins, which were composed of the N-terminal fragments of the Ig light chain κIII subtype (AL-κIII) (16, 8, and 3 kDa).Conclusions:This is the first chemically proved AL case reported in association with primary localised orbital amyloidosis. The biochemical microtechnique used was useful in achieving a precise diagnosis of amyloid disease, in a case where the results of routine immunohistochemical examination of amyloid were inconclusive.
Equity in the Courts of Merchants
Authors: Donahue Charles 
Published: April 2005

AbstractThis paper had its origins in a study of Benvenuto Stracca's De mercatura. The purpose of the study was to determine whether there was anything in that work that supported the notion that there was a system of customary mercantile law in operation in Italy in Stracca's time. The answer to that question proved to be a rather resounding 'no', and the arguments that lead to that conclusion will be published elsewhere. In the process of examining Stracca's sources, much information appeared about how the jurists of the fourteenth, fifteenth and early sixteenth centuries did deal with mercantile matters and, in particular, the way in which they manipulated the concept of equity to achieve what they deemed to be just results in such cases. Limitations of space allowed consideration of only a couple of procedural examples intheprevious paper. The story, it seemed to me, deserved consideration in its own right. What follows, then, is a fuller consideration of the use of equity by the commentators in their handling of mercantile cases, beginning, as the previous paper did, with Stracca's general remarks on the topic.
Diagnosis of Frontal Instabilities over the Southern Ocean
Authors: Patoux Jérôme , Hakim Gregory J. , Brown Robert A. 
Published: April 2005

The development of three fronts over the Southern Ocean is described using SeaWinds-on-QuikSCAT scatterometer surface winds and an attribution technique to partition the wind field in three components: nondivergent and irrotational components at the scale of the front, and the remaining harmonic component (or environmental flow) induced by the synoptic-scale flow. The front and the environment in which the front is embedded are analyzed separately. A frontal wave is shown to develop out of the first front when the large-scale alongfront stretching decreases, the environmental flow becomes frontolytic, and a connection with the upper levels is established. In the second case, the stretching remains relatively strong and no frontal wave develops. The third front exhibits a developing wave but is not in a favorable configuration with the upper levels; the frontal wave does not deepen significantly.
Numerical Study of a Typhoon with a Large Eye: Model Simulation and Verification
Authors: Zhang Qing-Hong , Chen Shou-Jun , Kuo Ying-Hwa , Lau Kai-Hon , Anthes Richard A. 
Published: April 2005

Typhoon Winnie (1997) was the fourth supertyphoon in the western North Pacific in 1997. In its mature stage, an outer eyewall, consisting of deep convection with a diameter of 370 km, was observed by satellite and radar. Within this unusually large outer eyewall existed an inner eyewall, which consisted of a ring of shallow clouds with a diameter of ∼50 km. In this study, Typhoon Winnie is simulated using a nested-grid version of the fifth-generation Pennsylvania State University–National Center for Atmospheric Research (PSU–NCAR) Mesoscale Model (MM5) with an inner grid length of 9 km. The model reproduces an outer cloud eyewall with a diameter of ∼350 km. The simulated radar reflectivity and hourly precipitation are verified with satellite microwave, infrared, and cloud brightness temperature images. Analysis of the model results indicates that the large outer eyewall in many ways possesses the structure of a typical hurricane eyewall. This includes strong tangential winds and radial inflow outside the eyewall as well as an extremely large horizontal wind shear right at the eyewall. The outer eyewall is characterized with a ring of high vorticity (RHV). This RHV is closely related to a ring of high convergence (RHC). This RHC is caused by organized convective systems along the eyewall. The eye simulated by Winnie is characterized by a broad region of warm, dry slowly sinking air. The factors determining the diameter of eyes in tropical cyclones are discussed by considering the scale of the environmental angular momentum and the maximum kinetic energy achieved by parcels of air originating in the environment and reaching the radius of maximum wind. It is hypothesized that the formation of a large eye is favored by large circulations in which parcels of air are drawn in toward the center of the storm from great distances, and trajectories of air in Winnie that support this hypothesis are shown.
Influence of a Hailstreak on Boundary Layer Evolution
Authors: Segele Zewdu T. , Stensrud David J. , Ratcliffe Ian C. , Henebry Geoffrey M. 
Published: April 2005

Severe thunderstorms developed on 20 June 1997 and produced heavy precipitation, damaging winds, and large hail over two swaths in southeastern South Dakota. Calculations of fractional vegetation coverage (scaled from 0 to 1) based upon composite satellite data indicate that, within the hailstreak region, vegetation coverage decreased from 0.50 to near 0.25 owing to the damaging effects of hail on the growing vegetation. The northern edge of the larger hailstreak was located a few kilometers south of Chamberlain, South Dakota, a National Weather Service surface observation site. Hourly observations from Chamberlain and several nearby surface sites in South Dakota are averaged over 7 days both before and after this hail event. These observations illustrate that the late-afternoon (nighttime) temperatures are 2°C higher (2°C lower) near the hailstreak after the event than before the event. Similarly, daily average dewpoint temperatures after the event are 2.6°C lower near the hailstreak. These changes are consistent with the influences of a recently devegetated zone on changes to the surface energy budget. To explore how these hailstreaks further affected the evolution of the planetary boundary layer in this region, two model simulations are performed using the fifth-generation Pennsylvania State University–National Center for Atmospheric Research (PSU–NCAR) Mesoscale Model (MM5). In the control run, climatology is used for the land surface characteristics, and hence the simulation is independent of the hailstreaks. In the hailstreak simulation (HSS), the fractional vegetation coverage and soil moisture in the hailstreak regions are modified to reflect the likely conditions within the hailstreaks. Two different days are simulated: one with low surface wind speeds and one with stronger surface wind speeds. For the low surface wind speed case, the HSS simulation produces a sea-breeze-like circulation in the boundary layer by midmorning. For the stronger surface wind speed case, this sea-breeze-like circulation does not develop in the HSS, but the simulated low-level temperatures are modified over a larger area. These results suggest that to capture and reasonably simulate the evolution of boundary layer structures, there is a need for routine daily updates of land surface information. Hailstreaks also are important to consider in the future as the focus for observational studies on nonclassical mesoscale circulations.
Stem cell factor promotes mast cell survival via inactivation of FOXO3a-mediated transcriptional induction and MEK-regulated phosphorylation of the proapoptotic protein Bim
Authors: Möller Christine , Alfredsson Jessica , Engström Maria , Wootz Hanna , Xiang Zou , Lennartsson Johan , Jönsson Jan-Ingvar , Nilsson Gunnar 
Published: April 2005

AbstractMast cells are found in tissues throughout the body where they play important roles in the regulation of inflammatory responses. One characteristic feature of mast cells is their longevity. Although it is well established that mast cell survival is dependent on stem cell factor (SCF), it has not been described how this process is regulated. Herein, we report that SCF promotes mast cell survival through inactivation of the Forkhead transcription factor FOXO3a (forkhead box, class O3A) and down-regulation and phosphorylation of its target Bim (Bcl-2 [B-cell lymphoma-2] interacting modulator of cell death), a Bcl-2 homology 3 (BH3)–only proapoptotic protein. SCF induced a rapid and transient phosphorylation of Akt (protein kinase B) and FOXO3a. SCF treatment prevented up-regulation of Bim protein expression and led to increased Bim phosphorylation. Bim phosphorylation was inhibited by PD98059 and LY294002 treatment, suggesting the involvement of mitogen-activated protein kinase kinase/mitogen-activated protein kinase (MEK/MAPK) and phosphatidylinositol 3 (PI3)–kinase pathways in this process. Overexpression of phosphorylation-deficient FOXO3a caused an up-regulation of Bim and induced mast cell apoptosis even in the presence of SCF. Mast cell apoptosis induced by the phosphorylation-deficient FOXO3a was attenuated in bim–/– mast cells. Because apoptosis is abnormally reduced in bim–/– mast cells, these data provide evidence that Akt-mediated inhibition of FOXO3a and its transcription target Bim provides an important mechanism by which SCF acts to prevent apoptosis in mast cells.
Quadratic regression analysis for gene discovery and pattern recognition for non-cyclic short time-course microarray experiments
Authors: Liu Hua , Tarima Sergey , Borders Aaron S , Getchell Thomas V , Getchell Marilyn L , Stromberg Arnold J 
Published: April 2005

Abstract
Background
Cluster analyses are used to analyze microarray time-course data for gene discovery and pattern recognition. However, in general, these methods do not take advantage of the fact that time is a continuous variable, and existing clustering methods often group biologically unrelated genes together.

Results
We propose a quadratic regression method for identification of differentially expressed genes and classification of genes based on their temporal expression profiles for non-cyclic short time-course microarray data. This method treats time as a continuous variable, therefore preserves actual time information. We applied this method to a microarray time-course study of gene expression at short time intervals following deafferentation of olfactory receptor neurons. Nine regression patterns have been identified and shown to fit gene expression profiles better than k-means clusters. EASE analysis identified over-represented functional groups in each regression pattern and each k-means cluster, which further demonstrated that the regression method provided more biologically meaningful classifications of gene expression profiles than the k-means clustering method. Comparison with Peddada et al.'s order-restricted inference method showed that our method provides a different perspective on the temporal gene profiles. Reliability study indicates that regression patterns have the highest reliabilities.

Conclusion
Our results demonstrate that the proposed quadratic regression method improves gene discovery and pattern recognition for non-cyclic short time-course microarray data. With a freely accessible Excel macro, investigators can readily apply this method to their microarray data.
Detection of target DNA using fluorescent cationic polymer and peptide nucleic acid probes on solid support
Authors: Raymond Frédéric R , Ho Hoang-Anh , Peytavi Régis , Bissonnette Luc , Boissinot Maurice , Picard François J , Leclerc Mario , Bergeron Michel G 
Published: April 2005

Abstract
Background
Nucleic acids detection using microarrays requires labelling of target nucleic acids with fluorophores or other reporter molecules prior to hybridization.

Results
Using surface-bound peptide nucleic acids (PNA) probes and soluble fluorescent cationic polythiophenes, we show a simple and sensitive electrostatic approach to detect and identify unlabelled target nucleic acid on microarray.

Conclusion
This simple methodology opens exciting possibilities for applied genetic analysis for the diagnosis of infections, identification of genetic mutations, and forensic inquiries. This electrostatic strategy could also be used with other nucleic acid detection methods such as electrochemistry, silver staining, metallization, quantum dots, or electrochemical dyes.
Characterization of histopathology and gene-expression profiles of synovitis in early rheumatoid arthritis using targeted biopsy specimens
Authors: Tsubaki Takahito , Arita Norimasa , Kawakami Takuma , Shiratsuchi Takayuki , Yamamoto Haruyasu , Takubo Nobuo , Yamada Kazuhito , Nakata Sanpei , Yamamoto Sumiki , Nose Masato 
Published: April 2005

AbstractThe disease category of early rheumatoid arthritis (RA) has been limited with respect to clinical criteria. Pathological manifestations of synovitis in patients whose disease is clinically classified as early RA seem to be heterogeneous, with regular variations. To clarify the relation between the molecular and histopathological features of the synovitis, we analyzed gene-expression profiles in the synovial lining tissues to correlate them with histopathological features. Synovial tissues were obtained from knee joints of 12 patients with early RA by targeted biopsy under arthroscopy. Surgical specimens of long-standing RA (from four patients) were examined as positive controls. Each histopathological parameter characteristic of rheumatoid synovitis in synovial tissues was scored under light microscopy. Total RNAs from synovial lining tissues were obtained from the specimens selected by laser capture microdissection and the mRNAs were amplified by bacteriophage T7 RNA polymerase. Their cDNAs were analyzed in a cDNA microarray with 23,040 cDNAs, and the levels of gene expression in multilayered lining tissues, compared with those of normal-like lining tissues in specimens from the same person, were determined to estimate gene-expression profiles characteristic of the synovial proliferative lesions in each case. Based on cluster analysis of all cases, gene-expression profiles in the lesions in early RA fell into two groups. The groups had different expression levels of genes critical for proliferative inflammation, including those encoding cytokines, adhesion molecules, and extracellular matrices. One group resembled synovitis in long-standing RA and had high scores for some histopathological features – involving accumulations of lymphocytes and plasma cells – but not for other features. Possible differences in the histopathogenesis and prognosis of synovitis between the two groups are discussed in relation to the candidate genes and histopathology.
Effects of milk fermented by Lactobacillus helveticusR389 on a murine breast cancer model
Authors: de Moreno de LeBlanc Alejandra , Matar Chantal , LeBlanc Nicole , Perdigón Gabriela 
Published: April 2005

Abstract
Introduction
Antitumour activity is one of the health-promoting effects attributed to the lactic acid bacteria and their products of fermentation. Previous studies in mice demonstrated that bioactive compounds released in milk fermented by Lactobacillus helveticus R389 contribute to its immunoenhancing and antitumour properties. The aim of the present work was to study the effects of the consumption of milk fermented by L. helveticus R389 or its proteolytic-deficient variant, L. helveticus L89, on a murine hormone-dependent breast cancer model.

Methods
Mice were fed with milk fermented by L. helveticus R389 or L. helveticus L89, during 2 or 7 days. The tumour control group received no special feeding. At the end of the feeding period, the mice were challenged by a subcutaneous injection of tumour cells in the mammary gland. Four days post-injection, the mice received fermented milk on a cyclical basis. The rate of tumour development and the cytokines in serum, mammary gland tissue and tumour-isolated cells were monitored. Bcl-2-positive cells in mammary glands and cellular apoptosis in tumour tissue were also studied.

Results
Seven days of cyclical administration of milk fermented by either bacterial strain delayed or stopped the tumour development. Cytokines demonstrated that L. helveticus R389 modulated the immune response challenged by the tumour. IL-10 and IL-4 were increased in all the samples from this group. In comparison with the tumour control, all test groups showed a decrease of IL-6, a cytokine involved in oestrogen synthesis. Seven days of cyclical feeding with milk fermented by L. helveticus R389 produced an increase in the number of apoptotic cells, compared with all other groups.

Conclusion
This study demonstrated that 7 days of cyclical administration of milk fermented by both strains of L. helveticus diminishes tumour growth, stimulating an antitumour immune response. Compounds released during milk fermentation with L. helveticus R389 would be implicated in its immunoregulatory capacity on the immune response in mammary glands and tumour, which were correlated with the cytokines found at the systemic level. The milk fermented by L. helveticus R389 was able to modulate the relationship between immune and endocrine systems (by IL-6 diminution), which is very important in oestrogen-dependent tumour and induced cellular apoptosis.
Phase I and Pharmacokinetic Study of MS-275, a Histone Deacetylase Inhibitor, in Patients With Advanced and Refractory Solid Tumors or Lymphoma
Authors: Ryan Qin C. , Headlee Donna , Acharya Milin , Sparreboom Alex , Trepel Jane B. , Ye Joseph , Figg William D. , Hwang Kyunghwa , Chung Eun Joo , Murgo Anthony , Melillo Giovanni , Elsayed Yusri , Monga Manish , Kalnitskiy Mikhail , Zwiebel James , Sausville Edward A. 
Published: April 2005

Purpose The objective of this study was to define the maximum-tolerated dose (MTD), the recommended phase II dose, the dose-limiting toxicity, and determine the pharmacokinetic (PK) and pharmacodynamic profiles of MS-275. Patients and Methods Patients with advanced solid tumors or lymphoma were treated with MS-275 orally initially on a once daily × 28 every 6 weeks (daily) and later on once every-14-days (q14-day) schedules. The starting dose was 2 mg/m2 and the dose was escalated in three- to six-patient cohorts based on toxicity assessments. Results With the daily schedule, the MTD was exceeded at the first dose level. Preliminary PK analysis suggested the half-life of MS-275 in humans was 39 to 80 hours, substantially longer than predicted by preclinical studies. With the q14-day schedule, 28 patients were treated. The MTD was 10 mg/m2 and dose-limiting toxicities were nausea, vomiting, anorexia, and fatigue. Exposure to MS-275 was dose dependent, suggesting linear PK. Increased histone H3 acetylation in peripheral-blood mononuclear-cells was apparent at all dose levels by immunofluorescence analysis. Ten of 29 patients remained on treatment for ≥ 3 months. Conclusion The MS-275 oral formulation on the daily schedule was intolerable at a dose and schedule explored. The q14-day schedule is reasonably well tolerated. Histone deacetylase inhibition was observed in peripheral-blood mononuclear-cells. Based on PK data from the q14-day schedule, a more frequent dosing schedule, weekly × 4, repeated every 6 weeks is presently being evaluated.
The Initial Use of Free-running Electromyography to Detect Early Motor Tract Injury during Resection of Intramedullary Spinal Cord Lesions
Authors: Skinner Stanley A. , Nagib Mahmoud , Bergman Thomas A. , Maxwell Robert E. , Msangi Gaspar 
Published: April 2005

Abstract

OBJECTIVE:
The resection of intramedullary spinal cord lesions (ISCLs) can be complicated by neurological deficits. Neuromonitoring has been used to reduce intraoperative risk. We have used somatosensory evoked potentials (SEPs) and muscle-derived transcranial electrical motor evoked potentials (myogenic TCE-MEPs) to monitor ISCL removal. We report our retrospective experience with the addition of free-running electromyography (EMG).

METHODS:
Thirteen patients underwent 14 monitored ISCL excisions. Anesthesia was maintained with minimal inhalant to reduce motoneuron suppression and enhance the myogenic TCE-MEPs. Free-running EMG was examined in the four limbs for evidence of abnormal bursts, prolonged tonic discharge, or sudden electrical silence. Warning of an electromyographic abnormality or myogenic TCE-MEP loss prompted interventions, including blood pressure elevation, a pause in surgery, a wake-up test, or termination of surgery. Pre- and postoperative neurological examinations determined the incidence of new deficits.

RESULTS:
The combined use of free-running EMG and myogenic TCE-MEPs detected all eight patients with a new motor deficit after surgery; there was one false-positive report. In three of the eight true-positive cases, an electromyographic abnormality immediately anticipated loss of the myogenic TCE-MEPs. Two patients with abnormal EMGs but unchanged myogenic TCE-MEPs experienced mild postoperative worsening of motor deficits; myogenic TCE-MEPs alone would have generated false-negative reports in these cases.

CONCLUSION:
During resection of ISCLs, free-running EMG can supplement motor tract monitoring by TCE-MEPs. Segmental and suprasegmental elicitation of neurotonic discharges can be observed in four-limb EMG. Abnormal electromyographic bursts, tonic discharge, or abrupt electromyographic silence may anticipate myogenic TCE-MEP loss and predict a postoperative motor deficit.