bluuebunny/crossref_metadata_2025_split huggingface dataset:
Length‐dependent DNA separations using multiple end‐attached peptide nucleic acid amphiphiles in micellar electrokinetic chromatography
Authors: Savard Jeffrey M. , Grosser Shane T. , Schneider James W. 
Published: June 2008

AbstractEnd‐labeled free‐solution electrophoresis (ELFSE) is an alternative approach to gel‐based methods for size‐based electrophoretic separation of DNA. In ELFSE, an electrically neutral “drag‐tag” is appended to DNA to add significant hydrodynamic drag, thereby breaking its constant charge‐to‐friction ratio. Current drag‐tag architecture relies on covalent attachment of polymers to each DNA molecule. We have recently proposed the use of micellar drag‐tags in conjunction with sequence‐specific hybridization of peptide nucleic acid amphiphiles (PNAAs). This work investigates the effect of multiple PNAA attachment on DNA resolution using MEKC. Simultaneous PNAA hybridization allows for the separation of long DNA targets, up to 1012 bases, using micellar drag‐tags. Each PNAA handle independently interacts with the micellar phase, reducing the overall mobility of this complex relative to individual PNAA binding. The sequence‐ and size‐based dependence of this separation technique is maintained with multiple PNAA binding over a range of DNA sizes. Results are accurately described by ELFSE theory, yielding α = 54 for single‐micelle tagging and α = 142 for dual‐micelle tagging. This method is the first example of a non‐covalent drag‐tag used to separate DNA of 1000 bases based on both size and sequence.
Microfluidic differential resistive pulse sensors
Authors: Wu Xudong , Kang Yuejun , Wang Yao‐Nan , Xu Dongyan , Li Deyu , Li Dongqing 
Published: June 2008

AbstractThis study demonstrates an on‐chip resistive pulse‐sensing scheme with a design of symmetric mirror channels, which significantly reduces the noise and achieves better signal‐to‐noise ratio. Polystyrene particles of different sizes have been detected with the developed sensing scheme and a record low volume ratio of the particle to the sensing channel, or 0.0004%, has been detected with particles of 520 nm in diameter in a sensing aperture of 50×16×20 μm3. This volume ratio is about ten times lower than the lowest volume ratio reported in the literature including that specified for commercial Coulter counters.
Proteomic analysis of Helicobacter pylori cellular proteins fractionated by ammonium sulfate precipitation
Authors: Park Jeong‐Won , Lee Seung‐Gyu , Song Jae‐Young , Joo Jung‐Soo , Chung Mi‐Ja , Kim Sam‐Cheol , Youn Hee‐Shang , Kang Hyung‐Lyun , Baik Seung‐Chul , Lee Woo‐Kon , Cho Myung‐Je , Rhee Kwang‐Ho 
Published: June 2008

AbstractAmong 1590 ORFs in the Helicobacter pylori genome, >250 have been identified as authentic genes by proteomic analysis. Low‐abundance proteins need to be enriched to a minimal amount for MALDI‐TOF analysis and salt precipitation has generally been used for protein enrichment. Here, a whole‐cell extract of H. pylori strain 26695 was subjected to protein fractionation with stepwise concentrations of ammonium sulfate and the proteins were displayed by 2‐DE. The protein spots were quantified using PDQUEST software and identified by peptide fingerprinting. The 2‐DE profiles and intensities of individual protein spots differed among the protein fractions. Out of the 98 identified proteins, 61 were found in the stepwise ammonium sulfate fractions but not in the whole‐cell extract. Out of these, 37 proteins, including KdsA, were found exclusively in a single fraction. In contrast, GroEL, UreA, UreB, TrxA, NapA, and FldA were ubiquitously present in all fractions. Iron‐containing proteins such as NapA, SodB, CeuE, and Pfr were found predominantly in the 100% saturated ammonium sulfate precipitate. Additionally, 29 proteins were newly identified in this study. These data will facilitate the preparation of significant H. pylori proteins, as well as provide information about low‐abundance proteins.
Predicting changes in the health‐related quality of life of Chinese depressed older people
Authors: Chan Sally , Chiu Helen , Chien Wai‐tong , Goggins William , Thompson David , Lam Linda , Hong Benny 
Published: June 2008

AbstractObjectiveTo identify predictors of change in Health Related Quality of Life (HRQoL) among community dwelling Chinese older people with depression.MethodsA community based prospective, longitudinal study was conducted in a regional psychiatric outpatient department. A convenience sample of 31 older people who were newly diagnosed with depression was recruited. Assessments were conducted at the first session of psychiatric consultation and again after 12 months. Measures included subjective perception of HRQoL, level of depression, number of medical conditions, activities of daily living, functional abilities, and social support.ResultsThe majority of participants had significant improvement in their HRQoL, level of depression, and general health conditions at 12‐month follow‐up. The ability of instrumental activity of daily living skills was a predictor of baseline HRQoL and changes in 12‐month follow‐up. Level of depression was also a predictor of changes in HRQoL over the 12‐months period.ConclusionsTreatment and interventions of depression were effective in improvement participants' mental condition and their perceived HRQoL. Interventions to promote older people's level of depression and their instrumental activity of daily living abilities could help to improve their perceived HRQoL. This study provides insight for healthcare professionals in planning innovative services to meet their health needs. Copyright © 2008 John Wiley & Sons, Ltd.
Family history of prostate cancer and prostate cancer risk in the Alpha‐Tocopherol, Beta‐Carotene Cancer Prevention (ATBC) Study
Authors: Ahn Jiyoung , Moslehi Roxana , Weinstein Stephanie J. , Snyder Kirk , Virtamo Jarmo , Albanes Demetrius 
Published: June 2008

AbstractProstate cancer family history has been associated with increased risk of the malignancy. Most prior studies have been retrospective and subject to recall bias, however, and data evaluating interactions with other important risk factors are limited. We examined the relationship between a family history of prostate cancer and prostate cancer risk in relation to body size, micronutrients and other exposures in the Alpha‐Tocopherol, Beta‐Carotene Cancer Prevention (ATBC) Study cohort of Finnish male smokers. Family history of cancer information was self‐reported once during the study in 1991, and anthropometry was measured by trained personnel. Among 19,652 men with complete data, 1,111 incident cases were identified during up to 12.3 years of follow‐up. A first‐degree family history of prostate cancer was associated with an overall relative risk (RR) of 1.91 (95% CI = 1.49–2.47) and a RR of 4.16 (95% CI = 2.67–6.49) for advanced disease (stage ≥ 3), adjusted for age and trial intervention. Our data also suggest that to some degree, height, body mass index, and serum α‐tocopherol and β‐carotene modify the family history and prostate cancer association, although the interactions were not statistically significant. Supplementation with vitamin E or β‐carotene did not modify the family history‐prostate cancer association. This study provides additional evidence that family history is a significant risk factor for prostate cancer. Published 2008 Wiley‐Liss, Inc.
p73 isoforms affect VEGF, VEGF165b and PEDF expression in human colorectal tumors: VEGF165b downregulation as a marker of poor prognosis
Authors: Díaz Raquel , Peña Cristina , Silva Javier , Lorenzo Yolanda , García Vanesa , García José M. , Sánchez Antonio , Espinosa Pablo , Yuste Rosario , Bonilla Félix , Domínguez Gemma 
Published: June 2008

AbstractThe secreted mitogen vascular endothelial growth factor, VEGF, plays a pivotal role in angiogenesis. Hypoxia, inactivation of p53 and oncogenic K‐Ras induce VEGF expression. Other factors such as p73 may also affect VEGF levels. Curiously, p73 may also regulate angiogenesis by affecting the expression of the pigment epithelium‐derived factor, PEDF. Additionally, VEGF might harbor additional functions through the activation of E2F transcription factors. Recently, a new VEGF variant formed by alternative splicing, VEGF165b, has been described as exerting anti‐angiogenic activity. We study here whether p73 isoforms levels ‐TAp73 and ΔTAp73‐ and p53 and K‐Ras status affect the expression of the above‐mentioned angiogenesis‐related genes (through the correlation between their expressions), the prognostic value of VEGF165b and PEDF and the correlation between VEGF and E2F‐1 levels. Tumor and normal tissue of 112 colorectal cancer patients was analyzed to evaluate: (i) levels of TAp73, ΔTAp73, VEGF, VEGF165b, PEDF and E2F‐1 by quantitative real‐time RT‐PCR, (ii) p53 status by immunohistochemistry and (iii) mutations in the first exon of K‐Ras by PCR‐SSCP. Tumor characteristics were examined in each patient. Associations were observed between: (i) specific p73 isoforms and VEGF and VEGF165b expression; (ii) ΔEx2p73 variant and downregulation of PEDF; (iii) VEGF and PEDF expression; (iv) inactive p53 and VEGF165b levels; (v) oncogenic K‐Ras and PEDF downregulation; (vi) E2F‐1 and VEGF expressions; (vii) VEGF165b downregulation and poor prognosis parameters of tumors. We conclude that the levels of p73 isoforms could affect the expression of VEGF, VEGF165b and PEDF. This scenario becomes complicated because a feedback between VEGF and PEDF may exist. VEGF may activate the E2F‐1 factor. Mutations in K‐Ras could negatively regulate PEDF expression. p53 inactivation might result in compensatory mechanisms such as over‐expression of VEGF165b. Our data support the role of VEGF165b as a tumor suppressor factor in colorectal carcinogenesis and its possible prognosis value. © 2008 Wiley‐Liss, Inc.
Genistein selectively potentiates arsenic trioxide‐induced apoptosis in human leukemia cells via reactive oxygen species generation and activation of reactive oxygen species‐inducible protein kinases (p38‐MAPK, AMPK)
Authors: Sánchez Yolanda , Amrán Donna , Fernández Carlos , de Blas Elena , Aller Patricio 
Published: June 2008

AbstractThe observation that genistein may behave as a pro‐oxidant agent lead us to examine the capacity of this isoflavone to modulate the toxicity of the oxidation‐sensitive anti‐leukemic agent arsenic trioxide (ATO), and for comparison other anti‐tumor drugs. Co‐treatment with genistein increased ATO‐provoked apoptosis and activated apoptosis regulatory events (Bcl‐XL down‐regulation, cytochrome c and Omi/HtrA2 release from mitochondria, XIAP decrease and caspase‐8/Bid and caspase‐3 activation) in U937 promonocytes and other human leukemia cell lines (HL60, THP‐1, Jurkat, RPMI‐8866), but not in phytohemagglutinin‐stimulated non‐tumor peripheral blood lymphocytes (PBLs). Genistein, alone and with ATO, stimulated reactive oxygen species generation, and apoptosis was attenuated by N‐acetyl‐L‐cysteine and butylated hydroxyanisole. Addition of low H2O2 concentrations mimicked the capacity of genistein to increase ATO‐provoked apoptosis in leukemia cells, but not in PBLs. By contrast, co‐treatment with genistein or H2O2 failed to potentiate the toxicity of DNA‐targeting agent cisplatin, the proteasome inhibitor MG‐132 and the histone deacetylase inhibitor MS‐275. Within the here used time‐period (14 hr) genistein, alone or with ATO, did not significantly affect Akt phosphorylation and NF‐κB binding activity, nor decreased intracellular GSH content. However, it elicited N‐acetyl‐L‐cysteine‐inhibitable phosphorylation of p38‐MAPK and AMPK, and apoptosis was attenuated by pharmacologic inhibitors against these kinases. The pro‐oxidant capacity of genistein might be exploited to improve the efficacy of ATO as anti‐leukemic agent, and perhaps the efficacy of other oxidation‐based therapeutic approaches. © 2008 Wiley‐Liss, Inc.
Structure and Spatial‐Temporal Dynamics of Chironomidae Fauna (Diptera) in Upland and Lowland Fluvial Habitats of the Chocancharava River Basin (Argentina)
Authors: Principe Romina E. , Boccolini Maricel F. , Corigliano Maria C. 
Published: June 2008

AbstractStructure of benthic Chironomidae assemblages and their spatial‐temporal dynamic were analyzed in upland and lowland habitats from the Chocancharava River basin (Córdoba, Argentina). Sampling was performed in three tributary streams and in three lowland reaches of the river during high and low rainfall periods. Characteristic taxa of upland and lowland reaches and of the different habitats in these reaches were identified using the IndVal method. Chironomidae assemblages were different between upland and lowland reaches and among habitats in each reach, as assessed by Multiresponse Permutation Procedure and Canonical Correspondence Analyses. Substrate type and current velocity were the major explanatory variables structuring the assemblages in upland reaches whereas in lowland reaches current velocity and aquatic vegetation were the most important variables. The highest richness was found in the most complex habitat units in both upland and lowland stretches as assessed by Analyses of Variance. Chironomidae larvae responded to longitudinal changes of hydraulic variables and to local variations of fluvial habitats at different reaches. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Influence of Emergent and Submerged Macrophytes on the Structure of Planktonic Ciliate Communities in Shallow Freshwater Lakes (Eastern Poland)
Authors: Mieczan Tomasz 
Published: June 2008

AbstractData from two shallow macrophyte‐dominated lakes (Eastern Poland) sampled with standardized methods, were evaluated in order to examine the effects of various stands of macrophytes in predicting protozooplankton community structure. Differences in macrophyte structure led to two distinct groups of habitats having different patterns of ciliate distribution. The first group consists of two vegetated habitats of sparse stem density and of the open water zone, and the second of submerged macrophyte species, which were more dense and complex. The number of significant correlations was different in the studied habitats. In central zones of macrophyte habitats the number of ciliates had the strongest correlation with concentrations of total organic carbon and Ptot. On the other side in the border zone a significant correlation between the number of ciliates and the chlorophyll a concentration was found. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Impacts of a Small Dam on Riverine Zooplankton
Authors: Zhou Shuchan , Tang Tao , Wu Naicheng , Fu Xiaocheng , Cai Qinghua 
Published: June 2008

AbstractIn order to explore the temporal impacts of a small dam on riverine zooplankton, monthly samples were conducted from November 2005 to June 2006 in a reach of Xiangxi River, China, which is affected by a small hydropower plant. A total of 56 taxa of zooplankton were recorded during the study and rotifers were the most abundant group, accounting for 97% of total taxa, while the others were copepod nauplii and copepod adults. This study indicated that: (1) the small dam in the Xiangxi River study area created distinct physical and ecological conditions relative to free‐flowing lotic reaches despite the constrained channel and small size of the dam; (2) the existence of the plant's small dam had a significant effect on the zooplankton community. In long periods of drought or dry seasons the effect of the dam on potamoplankton was more pronounced (e.g., November, February, March, and May). But the downfall or the connectivity of channel appeared to decrease the effect of small hydropower plants on riverine zooplankton (e.g., April). The present observation underscores the need for additional studies that provide more basic data on riverine zooplankton communities and quantify ecological responses to dam construction over longer time spans. (© 2008 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Synthesis of bioactive ceramic on the titanium substrate by micro‐arc oxidation
Authors: Zhao Zhongwei , Chen Xingyu , Chen Ailiang , Shen Meiling , Wen Shimei 
Published: June 2008

AbstractBioactive ceramic films on titanium substrate are prepared successfully by micro‐arc oxidation in electrolyte solution containing NaOH only. The coatings are prepared by micro‐arc oxidation at various applied current densities (200–400 mA/cm2) and in NaOH electrolyte with different concentrations. The XRD shows that they are composed of rutile, anatase, Na2Ti6O13, and Na2Ti4O9 phases. The composition and surface morphologies are strongly dependent on the applied current density and electrolyte concentration. For example, at high current density, the phase is mainly composed of rutile and Na2Ti6O13, and at high electrolyte concentration, it is Na2Ti6O13 phase. The morphologies of the samples vary with the increase of current and electrolyte concentration. The apatite‐inducing ability of bioactive ceramic films is evaluated in biological model fluids. After soaking in biological model fluids, the titania‐based coatings containing Na2Ti6O13 phase have excellent capability of inducing bone‐like apatite. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res, 2009
Decorin moieties tethered into PEG networks induce chondrogenesis of human mesenchymal stem cells
Authors: Salinas Chelsea N. , Anseth Kristi S. 
Published: June 2008

AbstractA versatile approach to fabricate PEG‐peptide copolymer gels was utilized to design niches to promote chondrogenic differentiation of human mesenchymal stem cells (hMSCs). The sequences RGD and KLER were chosen as motifs to modify PEG gels through a thiol‐acrylate polymerization. The KLER sequence, a binding site from decorin protein, is known to bind strongly to collagen type II and is responsible for matrix organization, while RGD promotes general survival of encapsulated cells. hMSCs were encapsulated at 2 × 106 cells/mL into 10 wt % PEG gels with 1 mM CRGDSG in the presence or absence of 5 mM CKLERG. A scrambled sequence served as a control. The gels were cultured in control and chondrogenic media, containing 5 ng/mL TGFβ1 over a 6‐week period. Cell/gel constructs were analyzed at various time points for glycosaminoglycan (GAG) content, type II collagen deposition, immunostaining, and gene analysis. After 14 days in chondrogenic cultures, cells in RGDS and KLER functionalized gels produced 2.5 times as much GAG/cell as those in gels containing only RGD. By day 28, hMSCs within the chondrogenic KLER gels produced 27‐fold higher hydroxyproline than that of day 0, whereas cells in chondrogenic culture with RGDS alone produced twofold of initial. Immunostained images indicated that col II was more predominant in the KLER‐derivatized gels than others, and enhanced chondrogenic differentiation in KLER containing gels was further supported by RT‐PCR analysis of type II collagen and aggrecan expression. Collectively, these results demonstrate how incorporation of matrix‐binding peptide interacts with hMSCs inducing chondrogenic differentiation and cartilage‐specific ECM deposition. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res, 2009
Development of a fibrin composite‐coated poly(ε‐caprolactone) scaffold for potential vascular tissue engineering applications
Authors: Pankajakshan Divya , Philipose Lizymol P , Palakkal Minshiya , Krishnan Kalliyana , Krishnan Lissy K. 
Published: June 2008

AbstractPoor cell adhesion, cytotoxicity of degradation products and lack of biological signals for cell growth, survival, and tissue generation are the limitations in the use of a biodegradable polymer scaffold for vascular tissue engineering. We have fabricated a hybrid scaffold by integrating physicochemical characteristics of poly(ε‐caprolactone) (PCL) and biomimetic property of a composite of fibrin, fibronectin, gelatin, growth factors, and proteoglycans to improve EC growth on the scaffold. Solvent cast porous films of poly(ε‐caprolactone) was prepared using PEG as a porogen. Porosity varied between 5 and 200 μm, and FTIR spectroscopy confirmed structural aspects of PCL. Films kept in PBS for 60 days showed tensile strength and elongation matching native blood vessel. Slow degradation of the scaffold was demonstrated by gravimetric analysis and molecular weight determination. Human umbilical vein endothelial cell (HUVEC) adhesion and proliferation on bare films were minimal. FTIR spectroscopy and environmental scanning electron microscopy (ESEM) of PCL‐fibrin hybrid scaffold confirmed the presence of fibrin composite on PCL film. HUVEC was subsequently cultured on hybrid scaffold, and continuous EC lining was observed in 15 and 30 days of culture using ESEM. Results suggest that the new hybrid scaffold can be a suitable candidate for cardiovascular tissue engineering. © 2008 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 2008
Cdk9‐55: A new player in muscle regeneration
Authors: Giacinti Cristina , Musarò Antonio , De Falco Giulia , Jourdan Isabelle , Molinaro Mario , Bagella Luigi , Simone Cristiano , Giordano Antonio 
Published: June 2008

AbstractAdult skeletal muscle contains a specialized population of myogenic quiescent stem cells, termed satellite cells, which contribute to repair myofibers after injury. During muscle regeneration, satellite cells exit their normal quiescent state, proliferate, activating MyoD and Myf‐5 expression, and finally differentiate and fuse to reconstitute the injured muscle architecture. We have previously reported that cdk9 is required for myogenesis in vitro by activating MyoD‐dependent transcription. In myoblasts induced to differentiate, MyoD recruits cdk9 on the chromatin of muscle‐specific regulatory regions. This event correlates with chromatin‐modifying enzyme recruitment and phosphorylation of cdk9‐specific target residues at the carboxyl‐terminal domain of RNA polymerase II. Here we report that a second cdk9 isoform, termed cdk9‐55, plays a fundamental role in muscle regeneration and differentiation in vivo. This alternative form is specifically induced in injured myofibers and its activity is strictly required for the completion of muscle regeneration process. J. Cell. Physiol. 216: 576–582, 2008, © 2008 Wiley‐Liss, Inc.
Detailing the role of Bax translocation, cytochrome c release, and perinuclear clustering of the mitochondria in the killing of HeLa cells by TNF
Authors: Pucci Bruna , Bertani Francesca , Karpinich Natalie O. , Indelicato Manuela , Russo Matteo A. , Farber John L. , Tafani Marco 
Published: June 2008

AbstractInduction of cell death in HeLa cells with TNF and cycloheximide (CHX) required an adequate ATP supply and was accompanied by decrease in intracellular pH, translocation of Bax, perinuclear clustering of the mitochondria, and cytochrome c release. The chloride channel inhibitor furosemide prevented the intracellular acidification, the translocation of Bax and the cell death. Cyclosporin A (CyA) or bongkrekic acid (BK) inhibited the induction of the MPT, the release of cytochrome c and the cell death without affecting the perinuclear clustering of the mitochondria or the translocation of Bax. Energy depletion with the ATP synthase inhibitor oligomycin or the uncoupler FCCP in the presence of 2‐deoxy‐glucose prevented the perinuclear clustering of the mitochondria and the cell killing. However, mitochondrial translocation of Bax was still observed. By contrast, cytochrome c was released in the oligomycin‐treated cells but not in the same cells treated with FCCP. The data demonstrate that apoptosis in HeLa cells is ATP dependent and requires the translocation of Bax. The movement of Bax to the mitochondria occurs before and during the perinuclear clustering of these organelles and does not require the presence of ATP. The release of cytochrome c depends on the induction of the mitochondrial permeability transition but not ATP content. J. Cell. Physiol. 217: 442–449, 2008. © 2008 Wiley‐Liss, Inc.