bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Hair Follicle Bulge: A Niche for Adult Stem Cells
Authors: Pasolli Hilda Amalia 
Published: July 2011

AbstractAdult stem cells (SCs) are essential for tissue homeostasis and wound repair. They have the ability to both self-renew and differentiate into multiple cell types. They often reside in specialized microenvironments or niches that preserve their proliferative and tissue regenerative capacity. The murine hair follicle (HF) has a specialized and permanent compartment—the bulge, which safely lodges SCs and provides the necessary molecular cues to regulate their function. The HF undergoes cyclic periods of destruction, regeneration, and rest, making it an excellent system to study SC biology.
SAT-based termination analysis using monotonicity constraints over the integers
Authors: CODISH MICHAEL , GONOPOLSKIY IGOR , BEN-AMRAM AMIR M. , FUHS CARSTEN , GIESL JÜRGEN 
Published: July 2011

AbstractWe describe an algorithm for proving termination of programs abstracted to systems of monotonicity constraints in the integer domain. Monotonicity constraints are a nontrivial extension of the well-known size-change termination method. While deciding termination for systems of monotonicity constraints is PSPACE complete, we focus on a well-defined and significant subset, which we call MCNP (for “monotonicity constraints in NP”), designed to be amenable to a SAT-based solution. Our technique is based on the search for a special type of ranking function defined in terms of bounded differences between multisets of integer values. We describe the application of our approach as the back end for the termination analysis of Java Bytecode. At the front end, systems of monotonicity constraints are obtained by abstracting information, using two different termination analyzers:AProVEandCOSTA. Preliminary results reveal that our approach provides a good trade-off between precision and cost of analysis.
Normative design using inductive learning
Authors: CORAPI DOMENICO , RUSSO ALESSANDRA , DE VOS MARINA , PADGET JULIAN , SATOH KEN 
Published: July 2011

AbstractIn this paper we propose a use-case-driven iterative design methodology for normative frameworks, also called virtual institutions, which are used to govern open systems. Our computational model represents the normative framework as a logic program under answer set semantics (ASP). By means of an inductive logic programming approach, implemented using ASP, it is possible to synthesise new rules and revise the existing ones. The learning mechanism is guided by the designer who describes the desired properties of the framework through use cases, comprising (i) event traces that capture possible scenarios, and (ii) a state that describes the desired outcome. The learning process then proposes additional rules, or changes to current rules, to satisfy the constraints expressed in the use cases. Thus, the contribution of this paper is a process for the elaboration and revision of a normative framework by means of a semi-automatic and iterative process driven from specifications of (un)desirable behaviour. The process integrates a novel and general methodology for theory revision based on ASP.
Simple Neurite Tracer: open source software for reconstruction, visualization and analysis of neuronal processes
Authors: Longair Mark H. , Baker Dean A. , Armstrong J. Douglas 
Published: July 2011

Abstract
Motivation: Advances in techniques to sparsely label neurons unlock the potential to reconstruct connectivity from 3D image stacks acquired by light microscopy. We present an application for semi-automated tracing of neurons to quickly annotate noisy datasets and construct complex neuronal topologies, which we call the Simple Neurite Tracer.
Availability: Simple Neurite Tracer is open source software, licensed under the GNU General Public Licence (GPL) and based on the public domain image processing software ImageJ. The software and further documentation are available via http://fiji.sc/Simple_Neurite_Tracer as part of the package Fiji, and can be used on Windows, Mac OS and Linux. Documentation and introductory screencasts are available at the same URL.
Contact: longair@ini.phys.ethz.ch; longair@ini.phys.ethz.ch
StochKit2: software for discrete stochastic simulation of biochemical systems with events
Authors: Sanft Kevin R. , Wu Sheng , Roh Min , Fu Jin , Lim Rone Kwei , Petzold Linda R. 
Published: July 2011

Abstract
Summary: StochKit2 is the first major upgrade of the popular StochKit stochastic simulation software package. StochKit2 provides highly efficient implementations of several variants of Gillespie's stochastic simulation algorithm (SSA), and tau-leaping with automatic step size selection. StochKit2 features include automatic selection of the optimal SSA method based on model properties, event handling, and automatic parallelism on multicore architectures. The underlying structure of the code has been completely updated to provide a flexible framework for extending its functionality.
Availability: StochKit2 runs on Linux/Unix, Mac OS X and Windows. It is freely available under GPL version 3 and can be downloaded from http://sourceforge.net/projects/stochkit/.
Contact: petzold@engineering.ucsb.edu
Small Heat Shock Protein Hsp17.8 Functions as an AKR2A Cofactor in the Targeting of Chloroplast Outer Membrane Proteins in Arabidopsis
Authors: Kim Dae Heon , Xu Zheng-Yi , Na Yun Jeong , Yoo Yun-Joo , Lee Junho , Sohn Eun-Ju , Hwang Inhwan 
Published: July 2011

AbstractPlastid proteins that are encoded by the nuclear genome and synthesized in the cytosol undergo posttranslational targeting to plastids. Ankyrin repeat protein 2A (AKR2A) and AKR2B were recently shown to be involved in the targeting of proteins to the plastid outer envelope. However, it remains unknown whether other factors are involved in this process. In this study, we investigated a factor involved in AKR2A-mediated protein targeting to chloroplasts in Arabidopsis (Arabidopsis thaliana). Hsp17.8, a member of the class I (CI) cytosolic small heat shock proteins (sHsps), was identified in interactions with AKR2A. The interaction between Hsp17.8 and AKR2A was further confirmed by coimmunoprecipitation experiments. The carboxyl-terminal ankyrin repeat domain of AKR2A was responsible for AKR2A binding to Hsp17.8. Other CI cytosolic sHsps also interact with AKR2A to varying degrees. Additionally, Hsp17.8 binds to chloroplasts in vitro and enhances AKR2A binding to chloroplasts. HSP17.8 was expressed under normal growth conditions, and its expression increased after heat shock. Hsp17.8 exists as a dimer under normal physiological conditions, and it is converted to high oligomeric complexes, ranging from 240 kD to greater than 480 kD, after heat shock. High levels of Hsp17.8 together with AKR2A resulted in increased plastid targeting of Outer Envelope Protein7 (OEP7), a plastid outer envelope protein expressed as a green fluorescent protein fusion protein. In contrast, artificial microRNA suppression of HSP17.8 and closely related CI cytosolic sHSPs in protoplasts resulted in a reduction of OEP7:green fluorescent protein targeting to plastids. Based on these data, we propose that Hsp17.8 functions as an AKR2A cofactor in targeting membrane proteins to plastid outer membranes under normal physiological conditions.
Analysis of polymorphism and transcription of the effector gene Avr1b in Phytophthora sojae isolates from China virulent to Rps1b
Authors: CUI LINKAI , YIN WEIXIAO , DONG SUOMENG , WANG YUANCHAO 
Published: July 2011

SUMMARYThe effector gene Avr1b‐1 of Phytophthora sojae determines the efficacy of the resistance gene Rps1b in soybean. The sequences of the Avr1b‐1 locus in 34 Chinese isolates of P. sojae were obtained and analysed by polymerase chain reaction (PCR) and inverse PCR. Four different alleles and a complete deletion mutation of the Avr1b‐1 gene were identified. Molecular analysis of the deletion breakpoints in the Avr1b‐1 locus revealed that an 8‐kb DNA sequence containing Avr1b‐1 was deleted and a 12.7‐kb DNA sequence was inserted at the same locus. A truncated transposase gene was found and five transposable elements were predicted in the inserted sequence, suggesting that the deletion of Avr1b‐1 might be attributed to transposon movement. The transcription of Avr1b‐1 was analysed in virulent isolates containing four alleles of Avr1b‐1 by real‐time reverse transcription‐PCR. In all virulent isolates, only those isolates containing the second allele transcripted Avr1b‐1.
Roles of the immune system in skin cancer
Authors: Rangwala S. , Tsai K.Y. 
Published: July 2011

SummaryOver the past several decades, there has been increasing interest in understanding the roles of the immune system in the development and progression of cancer. The importance of the immune system in human skin cancer has been long recognized based primarily upon the increased incidence of skin cancers in organ transplant recipients and mechanisms of ultraviolet (UV) radiation-mediated immunomodulation. In this review, we integrate multiple lines of evidence highlighting the roles of the immune system in skin cancer. First, we discuss the concepts of cancer immunosurveillance and immunoediting as they might relate to human skin cancers. We then describe the clinical and molecular mechanisms of skin cancer development and progression in the contexts of therapeutic immunosuppression in organ transplant recipients, viral oncogenesis, and UV radiation-induced immunomodulation with a primary focus on basal cell carcinoma and squamous cell carcinoma. The clinical evidence supporting expanding roles for immunotherapy is also described. Finally, we discuss recent research examining the functions of particular immune cell subsets in skin cancer and how they might contribute to both antitumour and protumour effects. A better understanding of the biological mechanisms of cancer immunosurveillance holds the promise of enabling better therapies.
Teledermatology applied following patient selection by general practitioners in daily practice improves efficiency and quality of care at lower cost
Authors: van der Heijden J.P. , de Keizer N.F. , Bos J.D. , Spuls P.I. , Witkamp L. 
Published: July 2011

Summary
Background Teledermatology, the application of telemedicine in the field of dermatology, has similar accuracy and reliability as physical dermatology. Teledermatology has been widely used in daily practice in the Netherlands since 2005 and is fully reimbursed.
Objectives This study prospectively investigated the effect of teledermatology on efficiency, quality and costs of care when integrated in daily practice and applied following patient selection by the general practitioner (GP).
Methods Teledermatology consultations between GP and regional dermatologist were performed in daily GP practice in the Netherlands. Efficiency of care was measured by the decrease in the number of physical referrals to the dermatologist. Quality of care was measured by the percentage of teleconsultations for second opinion, physical referrals resulting from these teleconsultations, the response time of the dermatologists and educational effect experienced by the GP. Costs of conventional healthcare without teledermatology were compared with costs with teledermatology.
Results One thousand, eight hundred and twenty GPs and 166 dermatologists performed teledermatology, and 37 207 teleconsultations performed from March 2007 to September 2010 were included. In the group of patients where the GP used teleconsultation to prevent a referral (n =26 596), 74% of physical referrals were prevented. In the group of patients where the GP used teleconsultation for a second opinion (n =10 611), 16% were physically referred after teleconsultation. The prevented referral rate in the total population was 68%. The mean response time of dermatologists was 4·6 h (median 2·0). GPs indicated that there was a beneficial educational effect in 85% of the teleconsultations. The estimated cost reduction was 18%.
Conclusions Teledermatology can lead to efficient care probably at lower cost. We are therefore of the opinion that teledermatology following GP selection should be considered as a possible pathway of referral to secondary care.
Brain-derived nerve factor and neurotrophins in androgenetic alopecia
Authors: Panchaprateep R. , Korkij W. , Asawanonda P. 
Published: July 2011

Summary
Background Several growth factors and cytokines have been shown to be involved in normal hair cycling as well as in androgenetic alopecia (AGA). However, the molecular cascades in AGA downstream from androgen receptor activation are far from being fully elucidated.
Objectives We sought to determine the difference in the protein expression of growth factors/cytokines in balding vs. nonbalding scalp specimens from the same individuals affected with AGA.
Methods Balding and nonbalding scalp specimens were collected from four men with pattern baldness. Dermal papilla (DP) cells were isolated and cultured. Quantifying the protein expression of growth factors and cytokines expressed by these cells was performed using Quantibody® Human Growth Factor Array-1 (RayBiotech, Inc., Norcross, GA, U.S.A.).
Results Brain-derived nerve factor (BDNF) protein expression was upregulated by approximately 12-fold in supernatants obtained from balding as compared with nonbalding DP cells (P &lt;0·001). Expression of neurotrophin-3 and of β-nerve growth factor was also upregulated. On the other hand, protein expression of insulin-like growth factor-1 and its binding proteins as well as of the vascular endothelial growth factor family were significantly downregulated in the balding scalp.
Conclusions Neurotrophic factors, especially BDNF, may be important in mediating the effects of androgens on hair follicles, serving as a negative regulatory control signal. Further studies may lead to novel pharmacological interventions in AGA.
Patterns of bone mineral acquisition in children with epidermolysis bullosa: a longitudinal study
Authors: Fu T. , Lingala B. , Kent K. , Bachrach L.K. , Bruckner A.L. 
Published: July 2011

Summary
Background Reduced bone mass and fractures are known complications of generalized forms of epidermolysis bullosa (EB). However, the aetiology – inadequate bone acquisition, premature bone loss, or a combination – is unclear.
Objectives To determine patterns of bone mineral acquisition in children with EB and to identify clinical and laboratory correlates of change in areal bone mineral density (aBMD).
Methods Seventeen subjects ≥ 6 years of age with generalized EB were studied at two visits at least 12 months apart with clinical and laboratory evaluations and dual energy X-ray absorptiometry scans of the lumbar spine. Wilcoxon signed-rank tests were used to determine if changes from baseline to follow-up were significant. Wilcoxon rank-sum tests were used to compare subjects with gains in aBMD Z-score with those who experienced no change or decreases to determine if baseline laboratory or clinical characteristics differed between the two groups.
Results Subjects gained height and weight at follow-up, but there was no significant improvement in mean Z-scores for height, weight or body mass index. Laboratory values did not change significantly. Mean bone mineral content and aBMD of the lumbar spine increased significantly at follow-up, but mean aBMD Z-scores remained static. No differences in clinical characteristics or laboratory values were seen between subjects with increased aBMD Z-scores vs. those whose scores decreased or did not change.
Conclusions Low bone mass in children with generalized EB is due primarily to inadequate gains in aBMD. Interventions to improve overall health and to help build bone mass in this patient population are warranted.
Effect modification of immunoglobulin E‐mediated atopy and rhinitis by glutathione S‐transferase genotypes in passive smokers
Authors: Gerbase M. W. , Keidel D. , Imboden M. , Gemperli A. , Bircher A. , Schmid‐Grendelmeier P. , Bridevaux P.‐O. , Berger W. , Schindler C. , Rochat T. , Probst‐Hensch N. 
Published: July 2011

Summary
Background Experimental studies suggest that glutathione S‐transferase (GST) genotypes modify nasal allergen responses induced by secondhand smoke (SHS) exposure.
Objective We aimed to investigate whether GSTs affected systemic IgE and allergic rhinitis (AR) in SHS‐exposed individuals from a population‐based cohort.
Methods Analyses comprised 2309 never‐smokers from the Swiss study on air pollution and health in adults cohort, reporting SHS status at baseline and 11 years later. Outcomes were defined by total serum IgE⩾100 kU/L, specific serum IgE determined by Phadiatop® ⩾0.35 kU/L and self‐reported AR. GSTP1 Ile105Val, GSTM1 and GSTT1 gene deletion genotypes were identified at the follow‐up survey.
Results After adjustment for relevant covariates, the homozygous GSTP1 105‐Val genotype was negatively associated with high total IgE and high‐specific IgE by Phadiatop®, notably in subjects persistently exposed to SHS (OR: 0.20, 95% CI 0.05–0.75; P=0.02, for high total IgE and OR: 0.29, 95% CI 0.10–0.89; P=0.03, for high specific IgE by Phadiatop®). Carrying at least one copy of the GSTM1 gene (non‐null) showed a similar association for high specific IgE by Phadiatop® (OR: 0.41, 95% CI 0.22–0.76; P=0.004). No significant associations were found between GSTs and rhinitis.
Conclusion and Clinical Relevance In this large cohort, homozygosity for GSTP1 105‐Val or carrying the GSTM1 non‐null genotype decreased the risk of high total IgE or high specific IgE using Phadiatop® by nearly half in subjects exposed to SHS, as compared with subjects carrying opposite alleles. These findings underline the value of genetic susceptibility when evaluating the effects of environmental exposure on allergic illness. The potential long‐term effects of persistent SHS exposure in genetically vulnerable individuals may be of public health relevance.
Cite this as: M. W. Gerbase, D. Keidel, M. Imboden, A. Gemperli, A. Bircher, P. Schmid‐Grendelmeier, P.‐O. Bridevaux, W. Berger, C. Schindler, T. Rochat and N. Probst‐Hensch, Clinical & Experimental Allergy, 2011 (41) 1579–1586.
Negative regulation of inflammatory responses by immunoglobulin A receptor (FcαRI) inhibits the development of Toll-like receptor-9 signalling-accelerated glomerulonephritis
Authors: Watanabe T , Kanamaru Y , Liu C , Suzuki Y , Tada N , Okumura K , Horikoshi S , Tomino Y 
Published: July 2011

SummaryMyeloid FcαRI, a receptor for immunoglobulin (Ig)A, mediates cell activation or inhibition depending on the type of ligand interaction, which can be either multivalent or monovalent. Anti-inflammatory signalling is triggered by monomeric targeting using anti-FcαRI Fab or IgA ligand binding, which inhibits immune and non-immune-mediated renal inflammation. The participation of Toll-like receptors (TLRs) in kidney pathology in experimental models and various forms of human glomerular nephritis has been discussed. However, little is known about negative regulation of innate-immune activation. In the present study, we generated new transgenic mice that express FcαRIR209L/FcRγ chimeric protein and showed that the monovalent targeting of FcαRI exhibited inhibitory effects in an in vivo model of TLR-9 signalling-accelerated nephritis. Mouse monoclonal anti-FcαRI MIP8a Fab improved urinary protein levels and reduced the number of macrophages and immunoglobulin deposition in the glomeruli. Monovalent targeting using MIP8a Fab attenuates the TLR-9 signalling pathway and is associated with phosphorylation of extracellular signal-related protein kinases [extracellular signal-regulated kinase (ERK), P38, c-Jun N-terminal kinase (JNK)] and the activation of nuclear factor (NF)-κB. The inhibitory mechanism involves recruitment of tyrosine phosphatase Src homology 2 domain-containing phosphatase-1 (SHP-1) to FcαRI. Furthermore, cell transfer studies with macrophages pretreated with MIP8a Fab showed that blockade of FcαRI signalling in macrophages prevents the development of TLR-9 signalling-accelerated nephritis. These results suggest a role of anti-FcαRI Fab as a negative regulator in controlling the magnitude of the innate immune response and a new type of anti-inflammatory drug for treatment of kidney disease.
The multi-hit hypothesis of primary biliary cirrhosis: polyinosinic-polycytidylic acid (poly I:C) and murine autoimmune cholangitis
Authors: Ambrosini Y M , Yang G-X , Zhang W , Tsuda M , Shu S , Tsuneyama K , Leung P S C , Ansari A A , Coppel R L , Gershwin M E 
Published: July 2011

Summary
A void in understanding primary biliary cirrhosis (PBC) is the absence of appropriate animal models. Our laboratory has studied a murine model of autoimmune cholangitis induced following immunization with 2-octynoic acid (2OA), an antigen identified following extensive quantitative structural activity relationship (QSAR) analysis, using human autoantibodies and three-dimensional analysis of the mitochondrial autoantigen, the E2 subunit of the pyruvate dehydrogenase complex (PDC-E2). Mice immunized with 2OA coupled to bovine serum albumin (BSA) develop anti-mitochondrial antibodies (AMAs) of the identical specificity as humans with PBC, and in addition develop inflammatory portal cell infiltrates in liver. However, the natural history of disease is less severe than in humans and does not include fibrosis. Data from human and autoimmune murine models suggest that environmental and/or infectious agents can exacerbate autoimmune reactions, and a model of PBC has been described in which polyinosinic-polycytidylic acid (poly I:C), a viral RNA mimetic and Toll-like receptor 3 (TLR-3) agonist induces low-titre AMAs and in mild portal infiltrates. We took advantage of our established model to determine whether immunization with 2OA-BSA coupled with poly I:C alters the disease process. Indeed, the addition of poly I:C produces a profound exacerbation of autoimmune cholangitis, including a significant increase in CD8+ infiltrating T cells, as well as a marked increase of proinflammatory cytokines. In addition, mice have evidence of fibrosis. These findings lend support to the concept that besides breakdown of self-tolerance, there is a requirement of a second ‘hit’ during the breakdown process that leads to disease which more faithfully mimics human PBC.