bluuebunny/crossref_metadata_2025_split huggingface dataset:
Human Side Population Keratinocytes Exhibit Long-Term Proliferative Potential and a Specific Gene Expression Profile and Can Form a Pluristratified Epidermis
Authors: Larderet Gaëlle , Fortunel Nicolas O. , Vaigot Pierre , Cegalerba Marine , Maltère Peggy , Zobiri Olivia , Gidrol Xavier , Waksman Gilles , Martin Michèle T. 
Published: November 2005

Abstract
The aim of the present study was to characterize human side population (SP) epidermal keratinocytes isolated from primary cell cultures. For that purpose, keratinocytes were isolated from normal adult breast skin samples and the Hoechst 33342 exclusion assay described for hematopoietic cells was adapted to keratinocytes. Three types of keratinocytes were studied: the SP, the main population (MP), and the unsorted initial population. SP keratinocytes represented 0.16% of the total population. In short-term cultures, they exhibited an increased colony-forming efficiency and produced more actively growing colonies than did unsorted and MP keratinocytes. In long-term cultures, SP cells exhibited an extensive expansion potential, performing a mean of 44 population doublings for up to 12 successive passages after cell sorting. Moreover, even in long-term cultures, SP keratinocytes were able to form a pluristratified epidermis when seeded on a dermal substrate. Unsorted and MP keratinocytes promoted a reduced expansion: mean values of 14 population doublings for five passages and 12 population doublings for four successive passages, respectively. To further characterize SP cells, cDNA microarrays were used to identify their molecular signature. Transcriptome profiling showed that 41 genes were differentially expressed in SP (vs. MP) cells, with 37 upregulated genes and only four downregulated genes in SP cells. The majority of these genes were functionally related to the regulation of transcription and cell signaling. In conclusion, SP human keratinocytes isolated from primary cultures exhibited both short- and long-term high proliferative potential, formed a pluristratified epidermis, and were characterized by a specific gene expression profile.
Basic Fibroblast Growth Factor Support of Human Embryonic Stem Cell Self-Renewal
Authors: Levenstein Mark E. , Ludwig Tenneille E. , Xu Ren-He , Llanas Rachel A. , VanDenHeuvel-Kramer Kaitlyn , Manning Daisy , Thomson James A. 
Published: November 2005

Abstract
Human embryonic stem (ES) cells have most commonly been cultured in the presence of basic fibroblast growth factor (FGF2) either on fibroblast feeder layers or in fibroblast-conditioned medium. It has recently been reported that elevated concentrations of FGF2 permit the culture of human ES cells in the absence of fibroblasts or fibroblast-conditioned medium. Herein we compare the ability of unconditioned medium (UM) supplemented with 4, 24, 40, 80, 100, and 250 ng/ml FGF2 to sustain low-density human ES cell cultures through multiple passages. In these stringent culture conditions, 4, 24, and 40 ng/ml FGF2 failed to sustain human ES cells through three passages, but 100 ng/ml sustained human ES cells with an effectiveness comparable to conditioned medium (CM). Two human ES cell lines (H1 and H9) were maintained for up to 164 population doublings (7 and 4 months) in UM supplemented with 100 ng/ml FGF2. After prolonged culture, the cells formed teratomas when injected into severe combined immunodeficient beige mice and expressed markers characteristic of undifferentiated human ES cells. We also demonstrate that FGF2 is degraded more rapidly in UM than in CM, partly explaining the need for higher concentrations of FGF2 in UM. These results further facilitate the large-scale, routine culture of human ES cells and suggest that fibroblasts and fibro-blast-conditioned medium sustain human ES cells in part by stabilizing FGF signaling above a critical threshold.
Transcriptional Profiling of Mammary Gland Side Population Cells
Authors: Behbod Fariba , Xian Wa , Shaw Chad A. , Hilsenbeck Susan G. , Tsimelzon Anna , Rosen Jeffrey M. 
Published: November 2005

Abstract
Similar to the bone marrow, the mammary gland contains a distinct population of Hoechst-effluxing side population cells, mammary gland side population cells (MG-SPs). To better characterize MG-SPs, their microarray gene profiles were compared to the remaining cells, which retain Hoechst dye (mammary gland non-side population cells [MG-NSPs]). For analysis, Gene Ontology (GO) that describes genes in terms of biological processes and Ontology Traverser (OT) that performs enrichment analysis were used. OT showed that MG-SP-specific genes were enriched in the GO categories of cell cycle regulation and checkpoints, multidrug-resistant transporters, organogenesis, and vasculogenesis. The MG-NSP-upregulated genes were enriched in the GO category of cellular organization and biogenesis, which includes basal epithelial markers, p63, smooth muscle actin, myosin, α6 integrin, cytokeratin (CK) 14, and luminal markers CK8 and CD24. Additional studies showed that a higher percentage of MG-SPs exist in the G1 phase of the cell cycle compared with the MG-NSPs. G1 cell cycle block of MG-SPs may be explained by higher expression of cell cycle-negative regulatory genes such as transforming growth factor-β2, insulin-like growth factor binding protein-5, P18INK4C, and wingless-5a (Wnt-5a). Accordingly, a smaller percentage of MG-SPs expressed nuclear β-catenin, possibly as a consequence of the higher expression of Wnt-5a. In conclusion, microarray gene profiling suggests that MG-SPs are a lineage-deficient mammary gland subpopulation expressing key genes involved in cell cycle regulation, development, and angiogenesis.
Integrins in Slow-Cycling Corneal Epithelial Cells at the Limbus in the Mouse
Authors: Pajoohesh-Ganji Ahdeah , Pal-Ghosh Sonali , Simmens Samuel J. , Stepp Mary Ann 
Published: November 2005

Abstract
Adult corneal epithelial stem cells (CESCs) have been shown to reside at the periphery of the cornea at a site called the corneoscleral junction or limbus. Although studies have shown that these cells are slow cycling, their molecular characteristics are not well understood. Using a whole-mount procedure, we show that whereas α9-integrin is present in a subset of the basal cells at the corneal limbus and absent in the central cornea, β1-, β4-, α3-, and α6-integrins are more highly expressed overall in central corneal basal cells. To characterize CESCs based on their slow-cycling nature, we simultaneously evaluated 5-bromo-2-deoxyuridine (BrdU) label-retaining cells (LRCs) and integrin expression (α9, β1, and β4) in a total of 1,889 cells at the limbus of adult mice that had been injected as neonates with BrdU. Whereas the LRCs were usually observed adjacent to α9-integrin-positive cells, most LRCs were α9-integrin–negative and expressed high levels of β1- and β4-integrin. In addition, we observed more BrdU-positive LRCs at the superior and inferior quadrants of adult mouse corneas than at the nasal and temporal quadrants, and determined that 0.94 to 3.6% of the limbal basal cells were slow cycling. We conclude from these data that the slow-cycling LRCs in the adult mouse cornea are enriched in cells that express high levels of β1- and β4-integrin and little α9-integrin.
In Vivo Formation of Unstable Heterokaryons after Liver Damage and Hematopoietic Stem Cell/Progenitor Transplantation
Authors: Kashofer Karl , Siapati Elena K. , Bonnet Dominique 
Published: November 2005

Abstract
Following reports of lineage plasticity in human hematopoietic stem cells (HSCs), we investigated the potential of human cord blood HSC-enriched cells to create hepatocytes in hosts after inducing liver damage. Carbon tetrachloride induces severe liver damage and subsequent repair via mitosis of resident hepatocytes. It additionally leads to a threefold increase in homing of human mononuclear cells to bone marrow and liver and subsequently to a substantial enhancement of bone marrow engraftment. Eight weeks after liver damage and infusion of an enhanced green fluorescent protein (eGFP) lentivirus-transduced human HSC-enriched cell population, we observed eGFP-positive cells with clear hepatocyte morphology in the livers of animals. These eGFP-positive cells co-expressed human albumin, and reverse-transcription polymerase chain reaction (PCR) analysis demonstrated the presence of human albumin and α-anti-trypsin mRNA. However, two antibodies against human mitochondria and human nuclei failed to mark eGFP-positive hepatocyte-like cells but did give clear staining of donor-derived hematopoietic cells. Subsequent fluorescent in situ hybridization (FISH) analysis revealed the presence of mouse Y chromosome in eGFP-positive hepatocyte-like cells. To resolve this discrepancy, we performed single-cell PCR analysis of microdissected eGFP-positive hepatocyte-like cells and found that they contained mostly mouse and little human genomic material. FISH analysis highlighting the centromeres of all human chromosomes revealed only few human chromosomes in these cells. From these results, we conclude that similar to their murine counterparts, human hematopoietic cells have the potential to fuse with resident host hepatocytes. Because no selective pressure is applied to retain the human genomic material, it is gradually lost over time, leading to a variable phenotype of the chimeric cells and making their detection difficult.
Description of Unexplained Chest Pain and Its Influence on Daily Life In Men and Women
Authors: Janson Fagring Annika , Gaston-Johansson Fannie , Danielson Ella 
Published: November 2005

Background: Patients with unexplained chest pain have seldom organic pathology. Although both physical and psychological factors have been studied and suggested as causes of chest pain. Aim: The aim was to describe the experience of unexplained chest pain and its influence on daily life situation in men and women. Methods: Nine women and eleven men with unexplained chest pain, aged 31–62 years were interviewed. A qualitative descriptive design was used. The interviews were analyzed by content analysis focusing on experience by gender. Results: The results embraced two domains descriptions and consequences of chest pain and daily life situation. Words like pressure, cramp, strong, or burning were used in the descriptions of the chest pain experienced with more similarities than variations between men and women. Physical, psychological and social consequences due to chest pain influenced daily life. The men specifically reported having a ‘fast tempo’ in their lives, with stress at work being seen as a feature experienced by both men and women. Conclusions: This study shows that men and women had more similarities than variations in descriptions of chest pain. Their unexplained chest pain influenced their functions in daily life that led to, especially for the men, few contacts outside the family and therefore a weak social network.
The response of Atlantic cod (Gadus morhua) to future climate change
Authors: Drinkwater Kenneth F. 
Published: November 2005

Abstract
Future CO2-induced climate change scenarios from Global Circulation Models (GCMs) indicate increasing air temperatures, with the greatest warming in the Arctic and Subarctic. Changes to the wind fields and precipitation patterns are also suggested. These will lead to changes in the hydrographic properties of the ocean, as well as the vertical stratification and circulation patterns. Of particular note is the expected increase in ocean temperature. Based upon the observed responses of cod to temperature variability, the expected responses of cod stocks throughout the North Atlantic to the future temperature scenarios are reviewed and discussed here. Stocks in the Celtic and Irish Seas are expected to disappear under predicted temperature changes by the year 2100, while those in the southern North Sea and Georges Bank will decline. Cod will likely spread northwards along the coasts of Greenland and Labrador, occupy larger areas of the Barents Sea, and may even extend onto some of the continental shelves of the Arctic Ocean. In addition, spawning sites will be established further north than currently. It is likely that spring migrations will occur earlier, and fall returns will be later. There is the distinct possibility that, where seasonal sea ice disappears altogether, cod will cease their migration. Individual growth rates for many of the cod stocks will increase, leading to an overall increase in the total production of Atlantic cod in the North Atlantic. These responses of cod to future climate changes are highly uncertain, however, as they will also depend on the changes to climate and oceanographic variables besides temperature, such as plankton production, the prey and predator fields, and industrial fishing.
The effect of abiotic and biotic factors on the importance of macroplankton in the diet of Northeast Arctic cod in recent years
Authors: Orlova E.L. , Dolgov A.V. , Rudneva G.B. , Nesterova V.N. 
Published: November 2005

AbstractUsing cod feeding data, this paper considers the distribution and abundance of macroplankton from different ecological groups (euphausiids and hyperiids) and the variability in their consumption by cod over a period of years during which different water mass temperatures were observed. These years were also characterized by variable abundance of capelin, cod's main food source. Differences in intensity and duration of cod consumption of euphausiids and hyperiids species are shown, depending on their abundance, temperature conditions, cod distribution, and the supply of capelin for cod. This paper discusses the energetics of consuming different types of prey and the role euphausiids play in the energy balance of cod. The low fat content of cod is sometimes associated with feeding on postspawning euphausiids in summer and autumn.
Antiviral prodrugs – the development of successful prodrug strategies for antiviral chemotherapy
Authors: De Clercq Erik , Field Hugh J 
Published: November 2005

Following the discovery of the first effective antiviral compound (idoxuridine) in 1959, nucleoside analogues, especially acyclovir (ACV) for the treatment of herpesvirus infections, have dominated antiviral therapy for several decades. However, ACV and similar acyclic nucleosides suffer from low aqueous solubility and low bioavailability following oral administration. Derivatives of acyclic nucleosides, typically esters, were developed to overcome this problem and valaciclovir, the valine ester of ACV, was among the first of a new series of compounds that were readily metabolized upon oral administration to produce the antiviral nucleosidein vivo, thus increasing the bioavailility by several fold. Concurrently, famciclovir was developed as an oral formulation of penciclovir. These antiviral ‘prodrugs’ thus established a principle that has led to many successful drugs including both nucleoside and nucleotide analogues for the control of several virus infections, notably those caused by herpes‐, retro‐ and hepatitisviruses. This review will chart the origins and development of the most important of the antiviral prodrugs to date.British Journal of Pharmacology(2006)147, 1–11. doi:10.1038/sj.bjp.0706446
4‐methyl benzylamine stimulates food consumption and counteracts the hypophagic effects of amphetamine acting on brainShaker‐likeKv1.1 channels
Authors: Pirisino Renato , Galeotti Nicoletta , Livi Silvia , Raimondi Laura , Ghelardini Carla 
Published: November 2005

4‐methyl benzylamine (4‐MBZ; 28 μg, 231 nmol) elicits a hyperphagic response in starved mice in contrast to the hypophagia induced by the parent compound benzylamine (BZ; 33 μg, 231 nmol) or by amphetamine (AMPH, 2 μg).In mice starved for only 4 h, and therefore with little stimulation to eat, the maximal increase in food consumption induced by intracerebroventricular (i.c.v.)‐injected 4‐MBZ was 190% over that of the controls (ED508.3±2.7 μg mouse−1; 68±22 nmol mouse−1), whereas after i.p. administration, these values were 160% and approximately 129 mg kg−1, respectively.The hyperphagic effect of 4‐MBZ was reduced by more than 60% in mice pretreated with antisense oligodeoxyribonucleotide (aODN1) previously found to selectively inhibit (over 50%) the expression ofShaker‐likeKv1.1 channels.In mice highly stimulated to eat after 12‐h fasting, 4‐MBZ (28 μg) significantly reduced (to about 70%) the hypophagic response by AMPH (2 μg) or BZ (33 μg). Conversely, these two compounds reduced (respectively, by 69 and 44%) the hyperphagic response of 4‐MBZ in 4‐h fasting mice.4‐MBZ (28 μg) also reduced the hypermotility and the stimulation of inspection activity elicited by AMPH in mice and the release of DA stimulated by AMPH (2 μg) from the nucleus accumbens of rats.We hypothesize that 4‐MBZ elicits hyperphagic effects probably by openingShaker‐likeKv1.1 subtypes in the brain, whereas AMPH and BZ are hypophagic by blocking these channels.British Journal of Pharmacology(2006)147, 218–224. doi:10.1038/sj.bjp.0706465
A Novel Approach for Nontargeted Data Analysis for Metabolomics. Large-Scale Profiling of Tomato Fruit Volatiles
Authors: Tikunov Yury , Lommen Arjen , de Vos C.H. Ric , Verhoeven Harrie A. , Bino Raoul J. , Hall Robert D. , Bovy Arnaud G. 
Published: November 2005

AbstractTo take full advantage of the power of functional genomics technologies and in particular those for metabolomics, both the analytical approach and the strategy chosen for data analysis need to be as unbiased and comprehensive as possible. Existing approaches to analyze metabolomic data still do not allow a fast and unbiased comparative analysis of the metabolic composition of the hundreds of genotypes that are often the target of modern investigations. We have now developed a novel strategy to analyze such metabolomic data. This approach consists of (1) full mass spectral alignment of gas chromatography (GC)-mass spectrometry (MS) metabolic profiles using the MetAlign software package, (2) followed by multivariate comparative analysis of metabolic phenotypes at the level of individual molecular fragments, and (3) multivariate mass spectral reconstruction, a method allowing metabolite discrimination, recognition, and identification. This approach has allowed a fast and unbiased comparative multivariate analysis of the volatile metabolite composition of ripe fruits of 94 tomato (Lycopersicon esculentum Mill.) genotypes, based on intensity patterns of &gt;20,000 individual molecular fragments throughout 198 GC-MS datasets. Variation in metabolite composition, both between- and within-fruit types, was found and the discriminative metabolites were revealed. In the entire genotype set, a total of 322 different compounds could be distinguished using multivariate mass spectral reconstruction. A hierarchical cluster analysis of these metabolites resulted in clustering of structurally related metabolites derived from the same biochemical precursors. The approach chosen will further enhance the comprehensiveness of GC-MS-based metabolomics approaches and will therefore prove a useful addition to nontargeted functional genomics research.
Evolutionary Expansion, Gene Structure, and Expression of the Rice Wall-Associated Kinase Gene Family
Authors: Zhang Shibo , Chen Calvin , Li Lei , Meng Ling , Singh Jaswinder , Jiang Ning , Deng Xing-Wang , He Zheng-Hui , Lemaux Peggy G. 
Published: November 2005

AbstractThe wall-associated kinase (WAK) gene family, one of the receptor-like kinase (RLK) gene families in plants, plays important roles in cell expansion, pathogen resistance, and heavy-metal stress tolerance in Arabidopsis (Arabidopsis thaliana). Through a reiterative database search and manual reannotation, we identified 125 OsWAK gene family members from rice (Oryza sativa) japonica cv Nipponbare; 37 (approximately 30%) OsWAKs were corrected/reannotated from earlier automated annotations. Of the 125 OsWAKs, 67 are receptor-like kinases, 28 receptor-like cytoplasmic kinases, 13 receptor-like proteins, 12 short genes, and five pseudogenes. The two-intron gene structure of the Arabidopsis WAK/WAK-Likes is generally conserved in OsWAKs; however, extra/missed introns were observed in some OsWAKs either in extracellular regions or in protein kinase domains. In addition to the 38 OsWAKs with full-length cDNA sequences and the 11 with rice expressed sequence tag sequences, gene expression analyses, using tiling-microarray analysis of the 20 OsWAKs on chromosome 10 and reverse transcription-PCR analysis for five OsWAKs, indicate that the majority of identified OsWAKs are likely expressed in rice. Phylogenetic analyses of OsWAKs, Arabidopsis WAK/WAK-Likes, and barley (Hordeum vulgare) HvWAKs show that the OsWAK gene family expanded in the rice genome due to lineage-specific expansion of the family in monocots. Localized gene duplications appear to be the primary genetic event in OsWAK gene family expansion and the 125 OsWAKs, present on all 12 chromosomes, are mostly clustered.
Are Poor Neighborhoods Resource Deprived? A Case Study of Childcare Centers in New York*
Authors: Small Mario Luis , Stark Laura 
Published: November 2005

Objective. Many social scientists believe poor mothers are better off in middle‐class than in poor neighborhoods, partly because the latter are deprived of important institutional resources. We test whether poor neighborhoods are more likely to lack one critical institutional resource, the childcare center.Methods. We use geocoded data on all licensed centers in the City of New York, address matched to Census tracts. We estimate logit models of presence of center in tract, testing for the linear and nonlinear effects of tract poverty level after controlling for residential instability, joblessness, ethnic makeup, and other demographic factors. We complement the analysis with documentary, interview, and ethnographic data on centers in one poor and one nonpoor neighborhood in the city.Results. We find (1) that the probability of presence of a childcare center does not decrease as poverty level increases; (2) the relationship depends strongly on funding source, with privately funded centers being less likely and publicly funded ones more likely to be present in poor neighborhoods; and (3) at least two factors affect why poor neighborhoods are more likely to have certain centers, the local state and the (often neglected) nonprofit infrastructure.Conclusions. The findings suggest that poor mothers are not necessarily better off in middle‐class neighborhoods in this respect. The market assumptions underlying the initial hypothesis should be modified. More empirical research on the effect of the nonprofit sector on the prevalence of neighborhood institutions is needed.
Child Poverty Among Racial Minorities and Immigrants: Explaining Trends and Differentials*
Authors: Lichter Daniel T. , Qian Zhenchao , Crowley Martha L. 
Published: November 2005

Objective. This article examines the effects of changing family structure (including cohabitation) and maternal employment during the 1990s on child poverty rates across America's diverse racial and ethnic groups. Unlike most previous studies focused on broad pan‐ethnic groups, our analyses examine children distinguished by race/ethnicity, immigrant generation, and national origin (e.g., Mexican, Japanese, Middle Eastern, among others).Methods. The analyses, using methods of demographic standardization, are based on data from the 1990 and 2000 Public Use Microdata Samples of the U.S. Decennial Censuses.Results. Child poverty rates declined broadly across population groups in the 1990s. Increasing maternal employment during the 1990s, rather than changing family structure, accounted for the largest share (nearly 40 percent) of the recent decline in child poverty rates. Changes in family structure played a minor role in reducing child poverty for most of the 25 groups considered in this article. Differences in family structure accounted for a large part of observed child poverty differences between minority groups.Conclusions. Rapid increases in maternal employment during the 1990s provided a hedge against rising child poverty and a route to economic self‐sufficiency for growing shares of single mothers and their children.