bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring Atmospheric Aerosols by Twilight Photometry
Authors: Kumari B. Padma , Kulkarni S. H. , Jadhav D. B. , Londhe A. L. , Trimbake H. K. 
Published: February 2008

Abstract
The instrument twilight photometer was designed, developed, and installed at the Indian Institute of Tropical Meteorology (IITM), Pune, India (18°43′N, 73°51′E), to monitor the vertical distribution of atmospheric aerosols. The instrument, based on passive remote sensing technique, is simple and inexpensive. It is operated only during twilights, and the method of retrieval of aerosol profile is based on a simple twilight technique. It functions at a single wavelength (660 nm), and a photomultiplier tube is used as a detector. The amplifier, an important component of the system, was designed and developed by connecting 10 single integrated-circuit (IC) amplifiers in parallel so that the noise at the output is drastically reduced and the sensitivity of the system has been increased. As a result, the vertical profiles are retrieved to a maximum of 120 km. A brief description of the basic principle of twilight technique, the experimental setup, and the method of retrieval of aerosol profiles using the above photometer are detailed in this paper.
Characteristics of High-Resolution Versions of the Met Office Unified Model for Forecasting Convection over the United Kingdom
Authors: Lean Humphrey W. , Clark Peter A. , Dixon Mark , Roberts Nigel M. , Fitch Anna , Forbes Richard , Halliwell Carol 
Published: February 2008

Abstract
With many operational centers moving toward order 1-km-gridlength models for routine weather forecasting, this paper presents a systematic investigation of the properties of high-resolution versions of the Met Office Unified Model for short-range forecasting of convective rainfall events. The authors describe a suite of configurations of the Met Office Unified Model running with grid lengths of 12, 4, and 1 km and analyze results from these models for a number of convective cases from the summers of 2003, 2004, and 2005. The analysis includes subjective evaluation of the rainfall fields and comparisons of rainfall amounts, initiation, cell statistics, and a scale-selective verification technique. It is shown that the 4- and 1-km-gridlength models often give more realistic-looking precipitation fields because convection is represented explicitly rather than parameterized. However, the 4-km model representation suffers from large convective cells and delayed initiation because the grid length is too long to correctly reproduce the convection explicitly. These problems are not as evident in the 1-km model, although it does suffer from too numerous small cells in some situations. Both the 4- and 1-km models suffer from poor representation at the start of the forecast in the period when the high-resolution detail is spinning up from the lower-resolution (12 km) starting data used. A scale-selective precipitation verification technique implies that for later times in the forecasts (after the spinup period) the 1-km model performs better than the 12- and 4-km models for lower rainfall thresholds. For higher thresholds the 4-km model scores almost as well as the 1-km model, and both do better than the 12-km model.
Unilateral and Mild Bilateral Hearing Loss in Children: Past and Current Perspectives
Authors: Tharpe Anne Marie 
Published: February 2008

Since the early 1980s, audiologists have become increasingly aware of the potential effect of even mild degrees of hearing loss on the psychoeducational and psychosocial outcomes of children. This review describes some of the key research findings during the past several decades that have led us to our current thinking about unilateral and mild bilateral hearing loss in children. The first section addresses unilateral hearing loss. This is followed by a review of the literature on mild bilateral hearing loss. Specifically, the issues addressed include the significance of permanent mild degrees of hearing loss on children's psychoeducational and psychosocial development and the speech, language, and auditory characteristics of children with mild degrees of hearing loss. Finally, some recommendations regarding the direction of future research are offered. This review is followed by 2 articles summarizing the proceedings of a 2005 workshop convened by the Centers for Disease Control and Prevention (CDC), Early Hearing Detection and Intervention (EHDI) program, and the Marion Downs Hearing Center to address concerns about the underidentification of—and professionals' apparent lack of awareness of—permanent unilateral and minimal to mild hearing loss in children. 56 , 57
Factor H dysfunction in patients with atypical hemolytic uremic syndrome contributes to complement deposition on platelets and their activation
Authors: Ståhl Anne-lie , Vaziri-Sani Fariba , Heinen Stefan , Kristoffersson Ann-Charlotte , Gydell Karl-Henrik , Raafat Reem , Gutierrez Alberto , Beringer Ortraud , Zipfel Peter F. , Karpman Diana 
Published: February 2008

AbstractAtypical hemolytic uremic syndrome (aHUS) may be associated with mutations in the C-terminal of factor H (FH). FH binds to platelets via the C-terminal as previously shown using a construct consisting of short consensus repeats (SCRs) 15 to 20. A total of 4 FH mutations, in SCR15 (C870R) and SCR20 (V1168E, E1198K, and E1198Stop) in patients with aHUS, were studied regarding their ability to allow complement activation on platelet surfaces. Purified FH-E1198Stop mutant exhibited reduced binding to normal washed platelets compared with normal FH, detected by flow cytometry. Washed platelets taken from the 4 patients with aHUS during remission exhibited C3 and C9 deposition, as well as CD40-ligand (CD40L) expression indicating platelet activation. Combining patient serum/plasma with normal washed platelets led to C3 and C9 deposition, CD40L and CD62P expression, aggregate formation, and generation of tissue factor-expressing microparticles. Complement deposition and platelet activation were reduced when normal FH was preincubated with platelets and were minimal when using normal serum. The purified FH-E1198Stop mutant added to FH-deficient plasma (complemented with C3) allowed considerable C3 deposition on washed platelets, in comparison to normal FH. In summary, mutated FH enables complement activation on the surface of platelets and their activation, which may contribute to the development of thrombocytopenia in aHUS.
Simultaneous targeting of Aurora kinases and Bcr-Abl kinase by the small molecule inhibitor PHA-739358 is effective against imatinib-resistant BCR-ABL mutations including T315I
Authors: Gontarewicz Artur , Balabanov Stefan , Keller Gunhild , Colombo Riccardo , Graziano Alessio , Pesenti Enrico , Benten Daniel , Bokemeyer Carsten , Fiedler Walter , Moll Jürgen , Brümmendorf Tim H. 
Published: February 2008

Abstract
The emergence of resistance to imatinib (IM) mediated by mutations in the BCR-ABL domain has become a major challenge in the treatment of chronic myeloid leukemia (CML). Here, we report on studies performed with a novel small molecule inhibitor, PHA-739358, which selectively targets Bcr-Abl and Aurora kinases A to C. PHA-739358 exhibits strong antiproliferative and proapoptotic activity against a broad panel of human BCR-ABL–positive and –negative cell lines and against murine BaF3 cells ectopically expressing wild-type (wt) or IM-resistant BCR-ABL mutants, including T315I. Pharmacologic synergism of IM and PHA-739358 was observed in leukemia cell lines with subtotal resistance to IM. Treatment with PHA-739358 significantly decreased phosphorylation of histone H3, a marker of Aurora B activity and of CrkL, a downstream target of Bcr-Abl, suggesting that PHA-739358 acts via combined inhibition of Bcr-Abl and Aurora kinases. Moreover, strong antiproliferative effects of PHA-739358 were observed in CD34+ cells derived from untreated CML patients and from IM-resistant individuals in chronic phase or blast crisis, including those harboring the T315I mutation. Thus, PHA-739358 represents a promising new strategy for treatment of IM-resistant BCR-ABL-positive leukemias, including those harboring the T315I mutation. Clinical trials investigating this compound in IM-resistant CML have recently been initiated.
The combination of granulocyte colony-stimulating factor and stem cell factor significantly increases the number of bone marrow–derived endothelial cells in brains of mice following cerebral ischemia
Authors: Toth Zsuzsanna E. , Leker Ronen R. , Shahar Tal , Pastorino Sandra , Szalayova Ildiko , Asemenew Brook , Key Sharon , Parmelee Alissa , Mayer Balazs , Nemeth Krisztian , Bratincsák Andras , Mezey Éva 
Published: February 2008

Abstract
Granulocyte colony-stimulating factor (G-CSF) induces proliferation of bone marrow–derived cells. G-CSF is neuroprotective after experimental brain injury, but the mechanisms involved remain unclear. Stem cell factor (SCF) is a cytokine important for the survival and differentiation of hematopoietic stem cells. Its receptor (c-kit or CD117) is present in some endothelial cells. We aimed to determine whether the combination of G-CSF/SCF induces angiogenesis in the central nervous system by promoting entry of endothelial precursors into the injured brain and causing them to proliferate there. We induced permanent middle cerebral artery occlusion in female mice that previously underwent sex-mismatched bone marrow transplantation from enhanced green fluorescent protein (EGFP)–expressing mice. G-CSF/SCF treatment reduced infarct volumes by more than 50% and resulted in a 1.5-fold increase in vessel formation in mice with stroke, a large percentage of which contain endothelial cells of bone marrow origin. Most cells entering the brain maintained their bone marrow identity and did not transdifferentiate into neural cells. G-CSF/SCF treatment also led to a 2-fold increase in the number of newborn cells in the ischemic hemisphere. These findings suggest that G-CSF/SCF treatment might help recovery through induction of bone marrow–derived angiogenesis, thus improving neuronal survival and functional outcome.
Regenerative repair after endoluminal injury in mice with specific antagonism of protease activated receptors on CD34+ vascular progenitors
Authors: Chen Daxin , Abrahams Joel M. , Smith Leanne M. , McVey John H. , Lechler Robert I. , Dorling Anthony 
Published: February 2008

Abstract
Tissue factor (TF) and thrombin are involved in intimal hyperplasia (IH) and remodelling following vascular injury. Because many neointimal smooth muscle cells (VSMCs) derive from circulating vascular progenitors (VPs), we investigated how thrombin influences VP phenotype and function. Following wire-induced carotid artery injury in mice, the majority of circulating VPs expressed TF, were capable of initiating clotting in vitro, and had protease-activated receptors (PAR)–1, –2, and –4. Thrombin, through PAR-1, inhibited apoptosis and caused proliferation, resulting in the outgrowth of VP coexpressing markers of activated endothelial cells and VSMCs, even in the presence of growth factors. These mixed-phenotype VPs circulated as a minority population after injury and shared a similar phenotype with many neointimal cells. Labeled CD34+ cells, injected up to 2 weeks after injury, could be detected in the injured vessel wall, suggesting that continued recruitment may contribute to progressive IH. Finally, CD34+ cells incubated with thrombin prior to injection promoted florid neointimal lesions, whereas those incubated with PAR antagonists inhibited IH and promoted regenerative repair characterized by the development of a quiescent endothelium. We conclude that IH after vascular injury is due to the direct actions of thrombin on mobilized VPs.
Microarray data mining using landmark gene-guided clustering
Authors: Chopra Pankaj , Kang Jaewoo , Yang Jiong , Cho HyungJun , Kim Heenam Stanley , Lee Min-Goo 
Published: February 2008

Abstract

Background
Clustering is a popular data exploration technique widely used in microarray data analysis. Most conventional clustering algorithms, however, generate only one set of clusters independent of the biological context of the analysis. This is often inadequate to explore data from different biological perspectives and gain new insights. We propose a new clustering model that can generate multiple versions of different clusters from a single dataset, each of which highlights a different aspect of the given dataset.

Results
By applying our SigCalc algorithm to three yeast Saccharomyces cerevisiae datasets we show two results. First, we show that different sets of clusters can be generated from the same dataset using different sets of landmark genes. Each set of clusters groups genes differently and reveals new biological associations between genes that were not apparent from clustering the original microarray expression data. Second, we show that many of these new found biological associations are common across datasets. These results also provide strong evidence of a link between the choice of landmark genes and the new biological associations found in gene clusters.

Conclusion
We have used the SigCalc algorithm to project the microarray data onto a completely new subspace whose co-ordinates are genes (called landmark genes), known to belong to a Biological Process. The projected space is not a true vector space in mathematical terms. However, we use the term subspace to refer to one of virtually infinite numbers of projected spaces that our proposed method can produce. By changing the biological process and thus the landmark genes, we can change this subspace. We have shown how clustering on this subspace reveals new, biologically meaningful clusters which were not evident in the clusters generated by conventional methods. The R scripts (source code) are freely available under the GPL license. The source code is available [see Additional File 1] as additional material, and the latest version can be obtained at http://www4.ncsu.edu/~pchopra/landmarks.html. The code is under active development to incorporate new clustering methods and analysis.
The Sterolgene v0 cDNA microarray: a systemic approach to studies of cholesterol homeostasis and drug metabolism
Authors: Režen Tadeja , Juvan Peter , Fon Tacer Klementina , Kuzman Drago , Roth Adrian , Pompon Denis , Aggerbeck Lawrence P , Meyer Urs A , Rozman Damjana 
Published: February 2008

Abstract

Background
Cholesterol homeostasis and xenobiotic metabolism are complex biological processes, which are difficult to study with traditional methods. Deciphering complex regulation and response of these two processes to different factors is crucial also for understanding of disease development. Systems biology tools as are microarrays can importantly contribute to this knowledge and can also discover novel interactions between the two processes.

Results
We have developed a low density Sterolgene v0 cDNA microarray dedicated to studies of cholesterol homeostasis and drug metabolism in the mouse. To illustrate its performance, we have analyzed mouse liver samples from studies focused on regulation of cholesterol homeostasis and drug metabolism by diet, drugs and inflammation. We observed down-regulation of cholesterol biosynthesis during fasting and high-cholesterol diet and subsequent up-regulation by inflammation. Drug metabolism was down-regulated by fasting and inflammation, but up-regulated by phenobarbital treatment and high-cholesterol diet. Additionally, the performance of the Sterolgene v0 was compared to the two commercial high density microarray platforms: the Agilent cDNA (G4104A) and the Affymetrix MOE430A GeneChip. We hybridized identical RNA samples to the commercial microarrays and showed that the performance of Sterolgene is comparable to commercial arrays in terms of detection of changes in cholesterol homeostasis and drug metabolism.

Conclusion
Using the Sterolgene v0 microarray we were able to detect important changes in cholesterol homeostasis and drug metabolism caused by diet, drugs and inflammation. Together with its next generations the Sterolgene microarrays represent original and dedicated tools enabling focused and cost effective studies of cholesterol homeostasis and drug metabolism. These microarrays have the potential of being further developed into screening or diagnostic tools.
Effect of thyroid hormone concentration on the transcriptional response underlying induced metamorphosis in the Mexican axolotl (Ambystoma)
Authors: Page Robert B , Voss Stephen R , Samuels Amy K , Smith Jeramiah J , Putta Srikrishna , Beachy Christopher K 
Published: February 2008

AbstractBackgroundThyroid hormones (TH) induce gene expression programs that orchestrate amphibian metamorphosis. In contrast to anurans, many salamanders do not undergo metamorphosis in nature. However, they can be induced to undergo metamorphosis via exposure to thyroxine (T4). We induced metamorphosis in juvenile Mexican axolotls (Ambystoma mexicanum) using 5 and 50 nM T4, collected epidermal tissue from the head at four time points (Days 0, 2, 12, 28), and used microarray analysis to quantify mRNA abundances.ResultsIndividuals reared in the higher T4concentration initiated morphological and transcriptional changes earlier and completed metamorphosis by Day 28. In contrast, initiation of metamorphosis was delayed in the lower T4concentration and none of the individuals completed metamorphosis by Day 28. We identified 402 genes that were statistically differentially expressed by ≥ two-fold between T4treatments at one or more non-Day 0 sampling times. To complement this analysis, we used linear and quadratic regression to identify 542 and 709 genes that were differentially expressed by ≥ two-fold in the 5 and 50 nM T4treatments, respectively.ConclusionWe found that T4concentration affected the timing of gene expression and the shape of temporal gene expression profiles. However, essentially all of the identified genes were similarly affected by 5 and 50 nM T4. We discuss genes and biological processes that appear to be common to salamander and anuran metamorphosis, and also highlight clear transcriptional differences. Our results show that gene expression in axolotls is diverse and precise, and that axolotls provide new insights about amphibian metamorphosis.
Intragraft gene expression profile associated with the induction of tolerance
Authors: Doki Tomoko , Mello Michael , Mock Dennis , Evans Jacqueline M , Kearns-Jonker Mary 
Published: February 2008

Abstract

Background
Xenotransplantation holds the promise of providing an unlimited supply of donor organs for terminal patients with organ failure. Pre-existing natural antibodies to the Galα1,3Galβ1,4GlcNac-R (αGal) carbohydrate xenoantigen, however, bind rapidly to the graft endothelium and initiate hyperacute rejection of wild type pig grafts in humans. Experimental procedures designed to prevent xenoantibody-mediated rejection have been tested in gal knockout mice. These mice produce anti-gal xenoantibodies and are widely used as small animal models for xenotransplantation research. In this model, chimerism for cells expressing the gal carbohydrate can be achieved by transplantation of mixed cells or by transduction of bone marrow cells with viral vectors expressing a functional α1,3 galactosyltransferase gene. Chimerism induces tolerance to heart grafts expressing αGal. The mechanisms by which tolerance is achieved include systemic changes such as clonal deletion and/or anergy. Intragraft changes that occur during the early stages of tolerance induction have not been characterized.

Results
Cytoprotective genes heme oxygenase-1 (HO-1), Bcl2, and A20 that have been reported to contribute to long-term graft survival in various models of accommodation were not expressed at high levels in tolerant heart grafts. Intragraft gene expression at both early (Day 10) and late (>2 month) time points after heart transplant were examined by real-time PCR and microarray analysis was used to identify changes associated with the induction of tolerance. Intragraft gene expression profiling using microarray analysis demonstrated that genes identified in the functional categories of stress and immunity and signal transduction were significantly up-regulated in early tolerant grafts compared with syngeneic control grafts. Biological process classification showed lower binomial p-values in the categories of "response to biotic stimulus, defense response, and immune response" suggesting that up-regulated genes identified in these grafts promote survival in the presence of an immune response. The expression of the incompatible carbohydrate antigen (αGal) was reduced by 2 months post-transplant when compared with the expression of this gene at Day 10 post-transplant. These results suggest that the gal carbohydrate antigen is downmodulated over time in grafts that demonstrate tolerance.

Conclusion
Our study suggests that tolerance is associated with intragraft gene expression changes that render the heart resistant to immune-mediated rejection. Genes associated with stress and immunity are up-regulated, however cytoprotective genes HO-1, Bcl2 and A20 were not up-regulated. The expression of the gal carbohydrate, the key target initiating an immune response in this model, is down-regulated in the post-transplant period.
Transitions into and out of daylight saving time compromise sleep and the rest-activity cycles
Authors: Lahti Tuuli A , Leppämäki Sami , Lönnqvist Jouko , Partonen Timo 
Published: February 2008

Abstract

Background
The aim of this study was to analyze the effects of transition out of and into daylight saving time on the rest-activity cycles and sleep. Rest-activity cycles of nine healthy participants aged 20 to 40 years were measured around transitions out of and into daylight saving time on fall 2005 and spring 2006 respectively. Rest-activity cycles were measured using wrist-worn accelerometers. The participants filled in the Morningness-Eveningness and Seasonal Pattern Assessment Questionnaires before starting the study and kept a sleep diary during the study.

Results
Fall transition was more disturbing for the more morning type and spring transition for the more evening type of persons. Individuals having a higher global seasonality score suffered more from the transitions.

Conclusion
Transitions out of and into daylight saving time enhanced night-time restlessness and thereby compromised the quality of sleep.
To know or not to know: archiving and the under-appreciated historical value of data
Authors: Covarrubias David , Van Emburgh Maurice , Naqvi Hassan R , Schmidt Christian , Mathur Shawn 
Published: February 2008

Abstract
Surplus goods, produced by a community, allow individuals to dedicate their efforts to abstract problems, while enjoying the benefits of support from the community. In return, the community benefits from the intellectual work, say, efficiently producing goods or profound medical aid. In further elevating quality of life, we need to understand nature and biology on the most detailed level. Inevitably, research costs are increasing along with the need for more scientists to specialize their efforts. As a result, a vast amount of data and information is generated that needs to be archived and made openly accessible with the permission to re-use and re-distribute. With economies undergoing crises and prosperity in an almost cyclic manner, it seems that funding for science and technology follows a similar pattern. Another aspect to the problem of the loss of data is the human propensity, at the level of each individual researcher, to passively discard data in the course of daily life and through a career. In a typical laboratory, significant amounts of information is still stored on disks in file cabinets or on isolated computers, and is lost when a research group disbands. Being conscientious to one's data, to see that it reaches a place in which it can persist beyond the lifespan of any one individual requires responsibility on the part of its creator.