bluuebunny/crossref_metadata_2025 huggingface dataset:
Diminished Type III Collagen Promotes Myofibroblast Differentiation and Increases Scar Deposition in Cutaneous Wound Healing
Authors: Volk Susan W. , Wang Yanjian , Mauldin Elizabeth A. , Liechty Kenneth W. , Adams Sherrill L.
Published: January 2011

The repair of cutaneous wounds in the postnatal animal is associated with the development of scar tissue. Directing cell activities to efficiently heal wounds while minimizing the development of scar tissue is a major goal of wound management and the focus of intensive research efforts. Type III collagen (Col3), expressed in early granulation tissue, has been proposed to play a prominent role in cutaneous wound repair, although little is known about its role in this process. To establish the role of Col3 in cutaneous wound repair, we examined the healing of excisional wounds in a previously described murine model of Col3 deficiency. Col3 deficiency (Col3+/–) in aged mice resulted in accelerated wound closure with increased wound contraction. In addition, Col3-deficient mice had increased myofibroblast density in the wound granulation tissue as evidenced by an increased expression of the myofibroblast marker, α-smooth muscle actin. In vitro, dermal fibroblasts obtained from Col3-deficient embryos (Col3+/– and –/–) were more efficient at collagen gel contraction and also displayed increased myofibroblast differentiation compared to those harvested from wild-type (Col3+/+) embryos. Finally, wounds from Col3-deficient mice also had significantly more scar tissue area on day 21 postwounding compared to wild-type mice. The effect of Col3 expression on myofibroblast differentiation and scar formation in this model suggests a previously undefined role for this ECM protein in tissue regeneration and repair.
DLX3 Homeodomain Mutations Cause Tricho-Dento-Osseous Syndrome with Novel Phenotypes
Authors: Nieminen Pekka , Lukinmaa Pirjo-Liisa , Alapulli Heikki , Methuen Mirja , Suojärvi Timo , Kivirikko Sirpa , Peltola Jaakko , Asikainen Mikko , Alaluusua Satu
Published: January 2011

Tricho-dento-osseous syndrome (TDO) is a rare type of dominantly inherited ectodermal dysplasia so far described only in a few families and associated with 3 known mutations in the DLX3 homeobox gene. Here, we describe two families of Finnish origin that segregate features of TDO in several generations. The affected family members have sparse or curly/kinky hair at birth, markedly delayed or advanced dental maturity, defective tooth enamel and dentin, taurodontic molars, multiple dental abscesses and filling of tooth pulps with amorphous denticle-like material as well as an increased density and/or thickness of craniofacial bones. The disease is especially accentuated in one of the families in which the patients develop only lanugo-type hair and the dental abnormalities are severe. After mutational analysis of DLX3, we identified 2 missense mutations affecting the conserved homeodomain. We suggest that TDO is essentially caused by loss of function and haploinsufficiency of DLX3.
RNA Interference in Mammalian Cell Systems
Authors: Lochmatter Didier , Mullis Primus-E.
Published: January 2011

In the last decade, few areas of biology have been transformed as thoroughly as RNA molecular biology. Without any doubt, one of the most significant advances has been the discovery of small (20–30 nucleotide) noncoding RNAs that regulate genes and genomes. The effects of small RNAs on gene expression and control are generally inhibitory, and the corresponding regulatory mechanisms are therefore collectively subsumed under the heading of RNA silencing and/or RNA interference. Two primary categories of these small RNAs – short interfering RNAs (siRNAs) and microRNAs (miRNAs) – act in both somatic and germline lineages of eukaryotic species to regulate endogenous genes and to defend the genome from invasive nucleic acids. Recent advances have revealed unexpected diversity in their biogenesis pathways and the regulatory mechanisms that they access. Our understanding of siRNA and miRNA-based regulation has direct implications for fundamental biology as well as disease aetiology and treatment as it is discussed in this review on ‘new techniques in molecular biology’.
The QT Variability Index and Cardiac Autonomic Modulation: Perspectives from Apparently Healthy Men with Spinal Cord Injury
Authors: La Fountaine Michael F. , Wecht Jill M. , Rosado-Rivera Dwindally , Cirnigliaro Christopher M. , Spungen Ann M. , Bauman William A.
Published: January 2011

Objective: To describe the effect of spinal cord injury (SCI) on the QT variability index (QTVI). Methods: Digital electrocardiograms from 113 age-matched men (40 with tetraplegia, 26 with high paraplegia, 17 low paraplegia and 31 controls) were analyzed. RR interval, heart rate (HR) variability [total power (TPRR), low frequency (LFRR) and high frequency (HFRR)], QT interval duration, Bazett HR-corrected QT (QTc), QT interval variance (QTVN) and QTVI were compared. Results: Significant group main effects were present for RR, QTc, TPRR and LFRR, but not QT duration, QTVN or HFRR. Post hoc comparisons revealed the following: (1) longer RR in controls versus subjects with high paraplegia and low paraplegia, and in subjects with tetraplegia versus high paraplegia and low paraplegia; (2) QTc was longer in subjects with low paraplegia versus controls and shorter in subjects with tetraplegia versus high paraplegia, and (3) TPRR and LFRR were different in controls and subjects with high paraplegia compared to those with low paraplegia. QTVI was significantly elevated in all SCI groups compared to controls. Significant negative correlations between QTVI and HFRR were observed in all SCI groups, and TPRR and LFRR in subjects with tetraplegia and high paraplegia only. Age was negatively correlated in controls. Conclusions: QTVI is negatively affected in otherwise healthy SCI men compared to age-matched controls. This observation appears to reflect the attenuation of vagal modulation, sympathetic impairment above the sixth thoracic vertebra and/or a heightened degree of cardiovascular disease risk.
Analysis of the Time Course of the Effect of Subthalamic Nucleus Stimulation upon Hand Function in Parkinson’s Patients
Authors: Waldau Ben , Clayton Daniel A. , Gasperson Lynne B. , Turner Dennis A.
Published: January 2011

Background: Deep brain stimulation (DBS) of the subthalamic nucleus (STN) as treatment for Parkinson’s disease has been in use for more than a decade, yet the immediate effect of stimulation upon movement parameters is not well characterized. Objective: The goal of the current study is the identification of the best time point to test hand function after programming DBS devices. Methods: Reaction time, movement time and velocity were measured at multiple time points with a movement-sensitive glove after the deep brain stimulator had been turned on or off, during ‘off medication’ conditions. Results: Velocity, movement time and reaction time worsened significantly in the first 20 min after the deep brain stimulator had been turned off. A ‘plateau effect’ after 20 min was not observed. Initiation of stimulation led to immediate significant increases in movement time and velocity and to a lesser degree a decrease in reaction time. Patients performed more inconsistently over time after onset of stimulation compared to stimulation withdrawal. Intraoperative testing showed an immediate improvement in velocity after placement of the STN deep brain stimulator. Conclusion: Movement time and velocity already reach their peak changes within 20 min after the deep brain stimulator has been reprogrammed, and therefore, this time point may be used to test the maximal clinical effect of stimulation.
Noninvasive Estimation of the Rate of Relaxation by the Analysis of Intraventricular Pressure Gradients
Authors: Yotti Raquel , Bermejo Javier , Benito Yolanda , Antoranz J. Carlos , Desco M. Mar , Rodríguez-Pérez Daniel , Cortina Cristina , Mombiela Teresa , Barrio Alicia , Elízaga Jaime , Fernández-Avilés Francisco
Published: January 2011

Background—

During late ejection, myocardial relaxation causes systolic flow to decelerate and stop, and this phenomenon is coupled with the generation of a pressure gradient inside the left ventricle (LV). We hypothesized that the peak reverse ejection intraventricular pressure difference (REIVPD) between the LV apex and the outflow tract could be a useful method to improve the assessment of LV relaxation using Doppler echocardiography.

Methods and Results—

Three sets of animal experiments and 1 clinical study were designed. In 6 pigs, a close relationship between REIVPD and the intensity of the relaxation wave (
R
rm
=0.89) was demonstrated using wave intensity analysis of high-fidelity pressure-volume-velocity data. In 19 animals, REIVPD sensitively detected modifications of the lusotropic state and closely correlated with the time constant of LV relaxation (τ) within animals (
R
rm
=−0.93). Load-dependence analysis in 5 pigs showed that REIVPD remained stable up to values of 35% to 40% acute preload reduction. Clinical validation was tested in 50 patients (23 with normal systolic function) undergoing simultaneous Doppler echocardiography and high-fidelity LV pressure measurements on the same beat. REIVPD and tissue Doppler mitral annulus velocity (e′) were independently related to τ, but the REIVPD · e′ product correlated better with τ than either variable separately (bootstrap-corrected correlation coefficients:
R
=−0.84 versus −0.71, and −0.70, respectively,
P
<0.05). Area under the receiver operating characteristic curve to predict impaired relaxation (τ>50 ms) for e′ · REIVPD was 0.96 (95% confidence interval, 0.85 to 0.99).

Conclusions—

The Doppler-derived REIVPD provides a sensitive, reliable, reproducible, and relatively load-independent index of the rate of LV relaxation. Combined with tissue Doppler measurements of longitudinal function, this method improves noninvasive assessment of LV relaxation in the clinical setting.
Classifiers Are Functional
Authors: Gebhardt Lewis
Published: January 2011

Wu and Bodomo (2009) dispute Cheng and Sybesma's (1999, 2005) analysis of Chinese numeral classifiers as being able to function as definite articles. While I agree with Wu and Bodomo's overall conclusion, here I focus on parts of their argument that do not stand up to scrutiny and distract from their main point. In particular, I argue that Wu and Bodomo's conclusion that numeral classifiers are lexical items is incorrect. Also, I question their apparent conclusion that the availability of numeral classifiers in a language indicates that that language's nouns are inherently mass.
Long Hair as a Glory and as a Covering Removing an Ambiguity from 1 Cor 11:15
Authors: Massey Preston T.
Published: January 2011

This study addresses the issue of v. 15 in 1 Cor 11:2-16 from the perspective of a veiling custom. If veiling is in view (the position adopted here), then how does one confront the difficulty of reconciling the overall context with the exceptional statement in v. 15 that long hair for a woman is a glory. If, as the text argues, long hair is to be taken as a “glory,” by what logic could a woman understand that she should place a veil upon her head? This article provides a way out of the dilemma by showing how a veil can serve the double function of reflecting the hair’s beauty while at the same time preserving a symbol of female modesty.
Degrees of Anthropocentrism in Accounts of Wildlife-Vehicle Collisions
Authors: Kuha Mai
Published: January 2011

An investigation of language use in news stories about collisions involving vehicles and nonhuman animals in the wild reveals that reports of bird-airplane collisions tend to focus on the safety of the humans involved, even to the point of constructing the bird as a projectile, rather than a victim. Reports of land vehicles and boats colliding with larger nonhuman animals tend to demonstrate a greater concern for nonhuman participants, attributing greater responsibility to humans for the collisions, although they are more dangerous to humans. Although similar patterns are found in news reports in several languages and in several English-speaking countries, anthropocentrism alone does not fully explain the patterns in journalists’ choice of expressions and structures in these news stories.
The Shared Meal—a Therapeutical Device The Function and Meaning of Hos 6:6 in Matt 9:10-13
Authors: Ottenheijm Eric
Published: January 2011

In Matt 9:10-13, the disciples of Jesus are asked why their master eats with tax-collectors and sinners. Both the question and the threefold answer are analysed in this study. Wisdom traditions prescribe Torah teachers not to engage with blatant sinners. This approach becomes contested in the first century C.E., as is clear from Pharisaic disputes on sinners and tax-collectors. In his answer, Jesus characterises himself as the divine doctor, who stirs the capacity to repentance by his sheer presence. The quote of Hosea functions as a legal justification of this strategy. Hos 6:6 points to the concept of good works, benevolent actions that save even blatant sinners.
Gang Membership and Race as Risk Factors for Juvenile Arrest
Authors: Tapia Michael
Published: January 2011

This study addresses the link between gang membership and arrest frequency, exploring the Gang × Race interaction on those arrests. The focus on youth’s earliest point of contact with the juvenile justice system corresponds to the latest priority of the federal initiative on Disproportionate Minority Contact (DMC). Using Poisson regression to analyze longitudinal data on a representative sample of U.S. teens, results support both main effects and interaction hypotheses. Gang membership, racial minority status, and their interaction each increase the risk of arrest, controlling for other demographic and legal items. Results suggest that bias against these groups is most pronounced with less serious crimes. Main effects for Black youth are stronger than for Hispanic youth, underscoring the importance of conducting tests for each minority group separately. Interactions for Black and Hispanic gang youth are equally robust, suggesting they warrant similar priority in policy initiatives to reduce DMC.
Role of Technology in Supporting Quality Control and Treatment Fidelity in a Family Caregiver Clinical Trial
Authors: Farran Carol J. , Etkin Caryn D. , McCann Judith J. , Paun Olimpia , Eisenstein Amy R. , Wilbur JoEllen
Published: January 2011

This article describes how a family caregiver lifestyle physical activity clinical trial uses research technology to enhance quality control and treatment fidelity. This trial uses a range of Internet, Blaise® Windows-based software and Echo Server technologies to support quality control issues, such as data collection, data entry, and study management advocated by the clinical trials literature, and to ensure treatment fidelity concerning intervention implementation (i.e., design, training, delivery, receipt, and enactment) as proposed by the National Institutes of Health Behavior Change Consortium. All research staff are trained to use these technologies. Strengths of this technological approach to support quality control and treatment fidelity include the comprehensive plan, involvement of all staff, and ability to maintain accurate and timely data. Limitations include the upfront time and costs for developing and testing these technological methods, and having support staff readily available to address technological issues if they occur.
Comparison of Brain PrPd Distribution in Ovine BSE and Scrapie
Authors: Lezmi S. , Seuberlich T. , Oevermann A. , Baron T. , Bencsik A.
Published: January 2011

Scrapie and bovine spongiform encephalopathy (BSE) are both prion diseases affecting ruminants, and these diseases do not share the same public health concerns. Surveillance of the BSE agent in small ruminants has been a great challenge, and the recent identification of diverse prion diseases in ruminants has led to the development of new methods for strain typing. In our study, using immunohistochemistry (IHC), we assessed the distribution of PrPd in the brains of 2 experimentally BSE-infected sheep with the ARQ/ARQ genotype. Distribution of PrPd in the brain, from the spinal cord to the frontal cortex, was remarkably similar in the 2 sheep despite different inoculation routes and incubation periods. Comparatively, overall PrPd brain distribution, evaluated by IHC, in 19 scrapie cases with the ARQ/ARQ, ARQ/VRQ, and VRQ/VRQ genotypes, in some cases showed similarities to the experimentally BSE-infected sheep. There was no exclusive neuroanatomical site with a characteristic and specific PrPd type of accumulation induced by the BSE agent. However, a detailed analysis of the topography, types, and intensity of PrPd deposits in the frontal cortex, striatum, piriform cortex, hippocampus, mesencephalon, and cerebellum allowed the BSE-affected sheep group to be distinguished from the 19 scrapie cases analyzed in our study. These results strengthen and emphasize the potential interest of PrPd brain mapping to help in identifying prion strains in small ruminants.
Identification of Cancer Stem Cells Derived From a Canine Lung Adenocarcinoma Cell Line
Authors: Nemoto Y. , Maruo T. , Sato T. , Deguchi T. , Ito T. , Sugiyama H. , Ishikawa T. , Madarame H. , Watanabe T. , Shida T. , Sahara H.
Published: January 2011

Accumulating evidence supporting the cancer stem cell (CSC) hypothesis is based on the finding that tumors contain a small population of self-renewing cells that generate differentiated progeny and thereby contribute to tumor heterogeneity. CSCs are reported to exist in several human cancers, yet only a few reports demonstrate the existence of CSCs in primary lung cancer in dogs. In this study, the authors established a cancer cell line derived from a canine primary lung adenocarcinoma and identified a side population (SP) of cells that displayed drug-resistant features. To confirm the characteristics of these SP cells, the authors investigated the tumorigenicity of the cells in vivo by using a nude mouse xenograft model. Only 100 SP cells were able to give rise to new tumors, giving a 10-fold enrichment over the main population (MP) of cells, suggesting that these cells have the cancer-initiating ability of CSCs. Further studies characterizing CSCs in canine lung adenocarcinoma might contribute to the elucidation of the mechanisms of tumorigenesis and to the establishment of novel therapeutic strategies.
Specifying the Attentional Selection That Moderates the Fearlessness of Psychopathic Offenders
Authors: Baskin-Sommers Arielle R. , Curtin John J. , Newman Joseph P.
Published: January 2011

Our previous research demonstrated that psychopathy-related fear deficits involve abnormalities in attention that undermine sensitivity to peripheral information. In the present study, we specified this attention-mediated abnormality in a new sample of 87 prisoners assessed with Hare’s Psychopathy Checklist-Revised (Hare, 2003). We measured fear-potentiated startle (FPS) under four conditions that crossed attentional focus (threat vs. alternative) with early versus late presentation of threat cues. The psychopathic deficit in FPS was apparent only in the early-alternative-focus condition, in which threat cues were presented after the alternative goal-directed focus was established. Furthermore, psychopathy interacted with working memory capacity in the late-alternative-focus condition, which suggests that individuals high in psychopathy and working memory capacity were able to maintain a set-related alternative focus that reduced FPS. The results not only provide new evidence that attention moderates the fearlessness of psychopathic individuals, but also implicate an early attention bottleneck as a proximal mechanism for deficient response modulation in psychopathy.
Recovering From Conflict in Romantic Relationships
Authors: Salvatore Jessica E. , Kuo Sally I-Chun , Steele Ryan D. , Simpson Jeffry A. , Collins W. Andrew
Published: January 2011

This study adopted a developmental perspective on recovery from conflict in romantic relationships. Participants were 73 young adults (target participants), studied since birth, and their romantic partners. A novel observational coding scheme was used to evaluate each participant’s degree of conflict recovery, operationalized as the extent to which the participant disengaged from conflict during a 4-min “cool-down” task immediately following a 10-min conflict discussion. Conflict recovery was systematically associated with developmental and dyadic processes. Targets who were rated as securely attached more times in infancy recovered from conflict better, as did their romantic partners. Concurrently, having a romantic partner who displayed better recovery predicted more positive relationship emotions and greater relationship satisfaction. Prospectively, target participants’ early attachment security and their partners’ degree of conflict recovery interacted to predict relationship stability 2 years later, such that having a partner who recovered from conflict better buffered targets with insecure histories.
Creating Social Opportunities for Students With Autism Spectrum Disorder in Inclusive Settings
Authors: Hart Juliet E. , Whalon Kelly J.
Published: January 2011

Increasing numbers of students with autism spectrum disorder (ASD) are being included in general education settings. Learners with ASD can benefit from the general education curriculum, with some achieving at a high academic level. Yet, social communication and behavioral difficulties can present challenges to their successful inclusion. Instructional priorities for children with ASD include social communication interventions that teach children how to spontaneously initiate functional communication in academic and social contexts. This article describes evidence-based strategies that will help educators create opportunities for social interaction for students with ASD in the context of naturally occurring classroom activities and routines.
Mothers’ Involvement in Early Intervention for Children With Hearing Loss
Authors: Ingber Sara , Al-Yagon Michal , Dromi Esther
Published: January 2011

This study examined the contribution of a model of maternal characteristics in explaining mothers’ involvement in the early intervention of their 1- to 7-year-old children with hearing loss. The model of maternal factors affecting mothers’ involvement in intervention comprised (a) four personal characteristics conceived as exogenous variables (anxiety, curiosity, anger, and motivation) and (b) two maternal context-based perceptions conceived as mediating variables (pessimism about their children’s potentials and informal social support). The sample included 114 mother—child dyads (67 boys, 47 girls) who attended the Kesher early intervention program in Israel. Path analysis indicated a high fit between the theoretical model and the empirical findings. Discussion focused on understanding the unique value of mothers’ characteristics for their involvement in their children’s early intervention programs.
A Primer on Disseminating Applied Quantitative Research
Authors: Bell Bethany A. , DiStefano Christine , Morgan Grant B.
Published: January 2011

Transparency and replication are essential features of scientific inquiry, yet scientific communications of applied quantitative research are often lacking in much-needed procedural information. In an effort to promote researchers dissemination of their quantitative studies in a cohesive, detailed, and informative manner, the authors delineate information concerning writing for publication in applied research journals. Specifically, they present 10 basic recommendations, ranging from how to construct well-written abstracts through outlining what to include in discussions. They emphasize information needed for the Method and Results sections, given that those two sections are where transparency and procedural and analytic details—considered necessary to replicate studies—are traditionally provided.
The Place of Planning in Sustainability Metrics for Public Works: Lessons From the Philadelphia Region
Authors: Dilworth Richardson , Stokes Robert , Weinberger Rachel , Spatari Sabrina
Published: January 2011

This article reports and analyzes survey and focus group data regarding baseline goals for public works administration, against which new metrics can be constructed that meaningfully reflect the ideals implied by the notion of sustainability, focusing in particular on four policy areas in the Philadelphia metropolitan region.We administered a survey to key informants, all of whom had also agreed to participate in focus groups.The major conclusion from the survey and focus group data is that land-use policies could most likely serve as a common matrix for sustainability baselines and measurements in water, energy, and transportation.
Using a Multiple Criteria Decision-Making Model to Streamline and Enhance NEPA and Public Participation Processes
Authors: Stich Bethany , Holland Joseph H.
Published: January 2011

The use of existing data from remote sensing technologies, Geographic Information Systems (GIS), and economic modeling can be integrated in a visual Multiple Criteria Decision Making (MCDM) tool that can aid in streamlining and enhancing the National Environmental Policy Act (NEPA) process and public participation. The interoperability of different data outputs provides researchers and practitioners the ability to produce high quality visualizations that can enhance the communication of proposed projects and the projected economic and social impacts on a community and surrounding area. User priority and value inputs combined with the high quality visualizations in a MCDM tool can provide multiple alignment alternatives for each transportation project participant. By providing additional and improved data through a new decision-making tool, ECO-PAL, researchers and practitioners will be able to enhance the efficiency and effectiveness of the efforts regarding NEPA development and make “every day count.”
Laparoscopy Entry in Patients With Previous Abdominal and Pelvic Surgery
Authors: Tinelli Andrea , Malvasi Antonio , Guido Marcello , Tsin Daniel Alberto , Hudelist Gernot , Stark Michael , Mettler Liselotte
Published: January 2011

Background: The background of this investigation is based on a common surgical problem: The access in laparoscopic surgery is more difficult in women with previous abdominopelvic surgery, since adhesions and viscera could be close to the point of trocar insertion. Purpose: The authors analyzed the safety and the efficacy of a modified direct optical entry (DOE) method versus the Hasson’s method by open laparoscopy (OL) in women with previous abdominopelvic surgery in a preliminary prospective case–control study. Materials and methods: A total of 168 women underwent laparoscopic surgery in university-affiliated hospitals: 86 were assigned to abdominal DOE (group A) and 82 to OL (group B). The main outcome measures were statistically compared: time required for entry into abdomen, blood loss, and occurrence of vascular and/or bowel injury. All patients had an intraperitoneal view of the primary port site during surgical procedure. Results: Statistical differences, in favor of the DOE group ( P < .01), were found in duration of entry and blood loss. The vascular and bowel injuries in OL versus DOE were not statistically different. Conclusions: Obtaining access to the peritoneal cavity in laparoscopic surgery is more difficult in patients with previous abdominopelvic surgery, since it can become a difficult, time-consuming, and occasionally hazardous procedure. The study results suggest that DOE is advantageous when compared with OL in terms of saving time enabling a safe and expeditious visually guided entry for laparoscopy.
AML1/ETO induces self-renewal in hematopoietic progenitor cells via the Groucho-related amino-terminal AES protein
Authors: Steffen Björn , Knop Markus , Bergholz Ulla , Vakhrusheva Olesya , Rode Miriam , Köhler Gabriele , Henrichs Marcel-Philipp , Bulk Etmar , Hehn Sina , Stehling Martin , Dugas Martin , Bäumer Nicole , Tschanter Petra , Brandts Christian , Koschmieder Steffen , Berdel Wolfgang E. , Serve Hubert , Stocking Carol , Müller-Tidow Carsten
Published: January 2011

The most frequent translocation t(8;21) in acute myeloid leukemia (AML) generates the chimeric AML1/ETO protein, which blocks differentiation and induces self-renewal in hematopoietic progenitor cells. The underlying mechanisms mediating AML1/ETO-induced self-renewal are largely unknown. Using expression microarray analysis, we identified the Groucho-related amino-terminal enhancer of split (AES) as a consistently up-regulated AML1/ETO target. Elevated levels of AES mRNA and protein were confirmed in AML1/ETO-expressing leukemia cells, as well as in other AML specimens. High expression of AES mRNA or protein was associated with improved survival of AML patients, even in the absence of t(8;21). On a functional level, knockdown of AES by RNAi in AML1/ETO-expressing cell lines inhibited colony formation. Similarly, self-renewal induced by AML1/ETO in primary murine progenitors was inhibited when AES was decreased or absent. High levels of AES expression enhanced formation of immature colonies, serial replating capacity of primary cells, and colony formation in colony-forming unit-spleen assays. These findings establish AES as a novel AML1/ETO-induced target gene that plays an important role in the self-renewal phenotype of t(8;21)-positive AML.
Strong CD28 costimulation suppresses induction of regulatory T cells from naive precursors through Lck signaling
Authors: Semple Kenrick , Nguyen Antony , Yu Yu , Wang Honglin , Anasetti Claudio , Yu Xue-Zhong
Published: January 2011

CD28 costimulation is required for the generation of naturally derived regulatory T cells (nTregs) in the thymus through lymphocyte-specific protein tyrosine kinase (Lck) signaling. However, it is not clear how CD28 costimulation regulates the generation of induced Tregs (iTregs) from naive CD4 T-cell precursors in the periphery. To address this question, we induced iTregs (CD25+Foxp3+) from naive CD4 T cells (CD25−Foxp3−) by T-cell receptor stimulation with additional transforming growth factorβ (TGFβ) in vitro, and found that the generation of iTregs was inversely related to the level of CD28 costimulation independently of IL-2. Using a series of transgenic mice on a CD28-deficient background that bears wild-type or mutated CD28 in its cytosolic tail that is incapable of binding to Lck, phosphoinositide 3-kinase (PI3K), or IL-2–inducible T-cell kinase (Itk), we found that CD28-mediated Lck signaling plays an essential role in the suppression of iTreg generation under strong CD28 costimulation. Furthermore, we demonstrate that T cells with the CD28 receptor incapable of activating Lck were prone to iTreg induction in vivo, which contributed to their reduced ability to cause graft-versus-host disease. These findings reveal a novel mechanistic insight into how CD28 costimulation negatively regulates the generation of iTregs, and provide a rationale for promoting T-cell immunity or tolerance by regulating Tregs through targeting CD28 signaling.
Blunted hepcidin response to inflammation in the absence of Hfe and transferrin receptor 2
Authors: Wallace Daniel F. , McDonald Cameron J. , Ostini Lesa , Subramaniam V. Nathan
Published: January 2011

The induction of the iron-regulatory peptide hepcidin by proinflammatory cytokines is thought to result in the withholding of iron from invading pathogens. Hfe and transferrin receptor 2 (Tfr2) are involved in the homeostatic regulation of hepcidin and their disruption causes hereditary hemochromatosis (HH). To determine whether either Hfe or Tfr2 is involved in the inflammatory pathway regulating hepcidin, we analyzed the effect of inflammation in 3 mouse models of HH. The inflammatory response and indicators of iron homeostasis were measured in wild-type, Hfe−/−, Tfr2−/−, and Hfe−/−/Tfr2−/− mice injected with lipopolysaccharide (LPS). The administration of LPS significantly reduced serum iron in wild-type and Hfe−/− mice, with smaller reductions in Tfr2−/− and Hfe−/−/Tfr2−/− mice. Low basal levels of hepcidin in the Hfe−/−/Tfr2−/− mice were increased in response to LPS, but remained significantly lower than in the other strains of mice. These results suggest that despite the absence of Hfe and Tfr2, hepcidin is responsive to inflammation; however, the low basal expression and subsequent low levels of circulating hepcidin are insufficient to reduce serum iron effectively. This suggests that in HH, the iron-withholding response to invading pathogens may be inadequate, and this is especially the case in the absence of both Hfe and Tfr2.
Recovery of infectious virus from full-length cowpox virus (CPXV) DNA cloned as a bacterial artificial chromosome (BAC)
Authors: Roth Swaantje J , Höper Dirk , Beer Martin , Feineis Silke , Tischer B Karsten , Osterrieder Nikolaus
Published: January 2011

Transmission from pet rats and cats to humans as well as severe infection in felids and other animal species have recently drawn increasing attention to cowpox virus (CPXV). We report the cloning of the entire genome of cowpox virus strain Brighton Red (BR) as a bacterial artificial chromosome (BAC) in Escherichia coli and the recovery of infectious virus from cloned DNA. Generation of a full-length CPXV DNA clone was achieved by first introducing a mini-F vector, which allows maintenance of large circular DNA in E. coli, into the thymidine kinase locus of CPXV by homologous recombination. Circular replication intermediates were then electroporated into E. coli DH10B cells. Upon successful establishment of the infectious BR clone, we modified the full-length clone such that recombination-mediated excision of bacterial sequences can occur upon transfection in eukaryotic cells. This self-excision of the bacterial replicon is made possible by a sequence duplication within mini-F sequences and allows recovery of recombinant virus progeny without remaining marker or vector sequences. The in vitro growth properties of viruses derived from both BAC clones were determined and found to be virtually indistinguishable from those of parental, wild-type BR. Finally, the complete genomic sequence of the infectious clone was determined and the cloned viral genome was shown to be identical to that of the parental virus. In summary, the generated infectious clone will greatly facilitate studies on individual genes and pathogenesis of CPXV. Moreover, the vector potential of CPXV can now be more systematically explored using this newly generated tool.
Analysis on the reconstruction accuracy of the Fitch method for inferring ancestral states
Authors: Yang Jialiang , Li Jun , Dong Liuhuan , Grünewald Stefan
Published: January 2011

Background

As one of the most widely used parsimony methods for ancestral reconstruction, the Fitch method minimizes the total number of hypothetical substitutions along all branches of a tree to explain the evolution of a character. Due to the extensive usage of this method, it has become a scientific endeavor in recent years to study the reconstruction accuracies of the Fitch method. However, most studies are restricted to 2-state evolutionary models and a study for higher-state models is needed since DNA sequences take the format of 4-state series and protein sequences even have 20 states.

Results

In this paper, the ambiguous and unambiguous reconstruction accuracy of the Fitch method are studied for N-state evolutionary models. Given an arbitrary phylogenetic tree, a recurrence system is first presented to calculate iteratively the two accuracies. As complete binary tree and comb-shaped tree are the two extremal evolutionary tree topologies according to balance, we focus on the reconstruction accuracies on these two topologies and analyze their asymptotic properties. Then, 1000 Yule trees with 1024 leaves are generated and analyzed to simulate real evolutionary scenarios. It is known that more taxa not necessarily increase the reconstruction accuracies under 2-state models. The result under N-state models is also tested.

Conclusions

In a large tree with many leaves, the reconstruction accuracies of using all taxa are sometimes less than those of using a leaf subset under N-state models. For complete binary trees, there always exists an equilibrium interval [a, b] of conservation probability, in which the limiting ambiguous reconstruction accuracy equals to the probability of randomly picking a state. The value b decreases with the increase of the number of states, and it seems to converge. When the conservation probability is greater than b, the reconstruction accuracies of the Fitch method increase rapidly. The reconstruction accuracies on 1000 simulated Yule trees also exhibit similar behaviors. For comb-shaped trees, the limiting reconstruction accuracies of using all taxa are always less than or equal to those of using the nearest root-to-leaf path when the conservation probability is not less than

1
N

. As a result, more taxa are suggested for ancestral reconstruction when the tree topology is balanced and the sequences are highly similar, and a few taxa close to the root are recommended otherwise.
Context-dependent transcriptional regulations between signal transduction pathways
Authors: Hwang Sohyun , Kim Sangwoo , Shin Heesung , Lee Doheon
Published: January 2011

Background

Cells coordinate their metabolism, proliferation, and cellular communication according to environmental cues through signal transduction. Because signal transduction has a primary role in cellular processes, many experimental techniques and approaches have emerged to discover the molecular components and dynamics that are dependent on cellular contexts. However, omics approaches based on genome-wide expression analysis data comparing one differing condition (e.g. complex disease patients and normal subjects) did not investigate the dynamics and inter-pathway cross-communication that are dependent on cellular contexts. Therefore, we introduce a new computational omics approach for discovering signal transduction pathways regulated by transcription and transcriptional regulations between pathways in signaling networks that are dependent on cellular contexts, especially focusing on a transcription-mediated mechanism of inter-pathway cross-communication.

Results

Applied to dendritic cells treated with lipopolysaccharide, our analysis well depicted how dendritic cells respond to the treatment through transcriptional regulations between signal transduction pathways in dendritic cell maturation and T cell activation.

Conclusions

Our new approach helps to understand the underlying biological phenomenon of expression data (e.g. complex diseases such as cancer) by providing a graphical network which shows transcriptional regulations between signal transduction pathways. The software programs are available upon request.
NClassG+: A classifier for non-classically secreted Gram-positive bacterial proteins
Authors: Restrepo-Montoya Daniel , Pino Camilo , Nino Luis F , Patarroyo Manuel E , Patarroyo Manuel A
Published: January 2011

Background

Most predictive methods currently available for the identification of protein secretion mechanisms have focused on classically secreted proteins. In fact, only two methods have been reported for predicting non-classically secreted proteins of Gram-positive bacteria. This study describes the implementation of a sequence-based classifier, denoted as NClassG+, for identifying non-classically secreted Gram-positive bacterial proteins.

Results

Several feature-based classifiers were trained using different sequence transformation vectors (frequencies, dipeptides, physicochemical factors and PSSM) and Support Vector Machines (SVMs) with Linear, Polynomial and Gaussian kernel functions. Nestedk-fold cross-validation (CV) was applied to select the best models, using the inner CV loop to tune the model parameters and the outer CV group to compute the error. The parameters and Kernel functions and the combinations between all possible feature vectors were optimized using grid search.

Conclusions

The final model was tested against an independent set not previously seen by the model, obtaining better predictive performance compared to SecretomeP V2.0 and SecretPV2.0 for the identification of non-classically secreted proteins. NClassG+ is freely available on the web athttp://www.biolisi.unal.edu.co/web-servers/nclassgpositive/
Systematic error detection in experimental high-throughput screening
Authors: Dragiev Plamen , Nadon Robert , Makarenkov Vladimir
Published: January 2011

Background

High-throughput screening (HTS) is a key part of the drug discovery process during which thousands of chemical compounds are screened and their activity levels measured in order to identify potential drug candidates (i.e., hits). Many technical, procedural or environmental factors can cause systematic measurement error or inequalities in the conditions in which the measurements are taken. Such systematic error has the potential to critically affect the hit selection process. Several error correction methods and software have been developed to address this issue in the context of experimental HTS [1–7]. Despite their power to reduce the impact of systematic error when applied to error perturbed datasets, those methods also have one disadvantage - they introduce a bias when applied to data not containing any systematic error [6]. Hence, we need first to assess the presence of systematic error in a given HTS assay and then carry out systematic error correction method if and only if the presence of systematic error has been confirmed by statistical tests.

Results

We tested three statistical procedures to assess the presence of systematic error in experimental HTS data, including the χ2 goodness-of-fit test, Student's t-test and Kolmogorov-Smirnov test [8] preceded by the Discrete Fourier Transform (DFT) method [9]. We applied these procedures to raw HTS measurements, first, and to estimated hit distribution surfaces, second. The three competing tests were applied to analyse simulated datasets containing different types of systematic error, and to a real HTS dataset. Their accuracy was compared under various error conditions.

Conclusions

A successful assessment of the presence of systematic error in experimental HTS assays is possible when the appropriate statistical methodology is used. Namely, the t-test should be carried out by researchers to determine whether systematic error is present in their HTS data prior to applying any error correction method. This important step can significantly improve the quality of selected hits.
Drug-induced cell cycle modulation leading to cell-cycle arrest, nuclear mis-segregation, or endoreplication
Authors: Sakaue-Sawano Asako , Kobayashi Tamiyo , Ohtawa Kenji , Miyawaki Atsushi
Published: January 2011

Background

Cancer cell responses to chemotherapeutic agents vary, and this may reflect different defects in DNA repair, cell-cycle checkpoints, and apoptosis control. Cytometry analysis only quantifies dye-incorporation to examine DNA content and does not reflect the biological complexity of the cell cycle in drug discovery screens.

Results

Using population and time-lapse imaging analyses of cultured immortalized cells expressing a new version of the fluorescent cell-cycle indicator, Fucci (F luorescent U biquitination-based C ell C ycle I ndicator), we found great diversity in the cell-cycle alterations induced by two anticancer drugs. When treated with etoposide, an inhibitor of DNA topoisomerase II, HeLa and NMuMG cells halted at the G2/M checkpoint. HeLa cells remained there, but NMuMG cells then overrode the checkpoint and underwent nuclear mis-segregation or avoided the checkpoint and entered the endoreplication cycle in a drug concentration dependent manner. In contrast, an inhibitor of Cdk4 led to G1 arrest or endoreplication in NMuMG cells depending upon the initial cell-cycle phase of drug exposure.

Conclusions

Drug-induced cell cycle modulation varied not only between different cell types or following treatment with different drugs, but also between cells treated with different concentrations of the same drug or following drug addition during different phases of the cell cycle. By combining cytometry analysis with the Fucci probe, we have developed a novel assay that fully integrates the complexity of cell cycle regulation into drug discovery screens. This assay system will represent a powerful drug-discovery tool for the development of the next generation of anti-cancer therapies.
Sperm competition and the evolution of sperm design in mammals
Authors: Tourmente Maximiliano , Gomendio Montserrat , Roldan Eduardo RS
Published: January 2011

Background

The influence of sperm competition upon sperm size has been a controversial issue during the last 20 years which remains unresolved for mammals. The hypothesis that, when ejaculates compete with rival males, an increase in sperm size would make sperm more competitive because it would increase sperm swimming speed, has generated contradictory results from both theoretical and empirical studies. In addition, the debate has extended to which sperm components should increase in size: the midpiece to accommodate more mitochondria and produce more energy to fuel motility, or the principal piece to generate greater propulsion forces.

Results

In this study we examined the influence of sperm competition upon sperm design in mammals using a much larger data set (226 species) than in previous analyses, and we corrected for phylogenetic effects by using a more complete and resolved phylogeny, and more robust phylogenetic control methods. Our results show that, as sperm competition increases, all sperm components increase in an integrated manner and sperm heads become more elongated. The increase in sperm length was found to be associated with enhanced swimming velocity, an adaptive trait under sperm competition.

Conclusions

We conclude that sperm competition has played an important role in the evolution of sperm design in mammals, and discuss why previous studies have failed to detect it.
Evolution of ligand specificity in vertebrate corticosteroid receptors
Authors: Arterbery Adam S , Fergus Daniel J , Fogarty Elizabeth A , Mayberry John , Deitcher David L , Lee Kraus W , Bass Andrew H
Published: January 2011

Background

Corticosteroid receptors include mineralocorticoid (MR) and glucocorticoid (GR) receptors. Teleost fishes have a single MR and duplicate GRs that show variable sensitivities to mineralocorticoids and glucocorticoids. How these receptors compare functionally to tetrapod MR and GR, and the evolutionary significance of maintaining two GRs, remains unclear.

Results

We used up to seven steroids (including aldosterone, cortisol and 11-deoxycorticosterone [DOC]) to compare the ligand specificity of the ligand binding domains of corticosteroid receptors between a mammal (Mus musculus) and the midshipman fish (Porichthys notatus), a teleost model for steroid regulation of neural and behavioral plasticity. Variation in mineralocorticoid sensitivity was considered in a broader phylogenetic context by examining the aldosterone sensitivity of MR and GRs from the distantly related daffodil cichlid (Neolamprologus pulcher), another teleost model for neurobehavioral plasticity. Both teleost species had a single MR and duplicate GRs. All MRs were sensitive to DOC, consistent with the hypothesis that DOC was the initial ligand of the ancestral MR. Variation in GR steroid-specificity corresponds to nine identified amino acid residue substitutions rather than phylogenetic relationships based on receptor sequences.

Conclusion

The mineralocorticoid sensitivity of duplicate GRs in teleosts is highly labile in the context of their evolutionary phylogeny, a property that likely led to neo-functionalization and maintenance of two GRs.