bluuebunny/crossref_metadata_2025 huggingface dataset:
Magnetosome Expression of Functional Camelid Antibody Fragments (Nanobodies) in Magnetospirillum gryphiswaldense
Authors: Pollithy Anna , Romer Tina , Lang Claus , Müller Frank D. , Helma Jonas , Leonhardt Heinrich , Rothbauer Ulrich , Schüler Dirk
Published: July 2011

Numerous applications of conventional and biogenic magnetic nanoparticles (MNPs), such as in diagnostics, immunomagnetic separations, and magnetic cell labeling, require the immobilization of antibodies. This is usually accomplished by chemical conjugation, which, however, has several disadvantages, such as poor efficiency and the need for coupling chemistry. Here, we describe a novel strategy to display a functional camelid antibody fragment (nanobody) from an alpaca (
Lama pacos
) on the surface of bacterial biogenic magnetic nanoparticles (magnetosomes). Magnetosome-specific expression of a red fluorescent protein (RFP)-binding nanobody (RBP)
in vivo
was accomplished by genetic fusion of RBP to the magnetosome protein MamC in the magnetite-synthesizing bacterium
Magnetospirillum gryphiswaldense
. We demonstrate that isolated magnetosomes expressing MamC-RBP efficiently recognize and bind their antigen
in vitro
and can be used for immunoprecipitation of RFP-tagged proteins and their interaction partners from cell extracts. In addition, we show that coexpression of monomeric RFP (mRFP or its variant mCherry) and MamC-RBP results in intracellular recognition and magnetosome recruitment of RFP within living bacteria. The intracellular expression of a functional nanobody targeted to a specific bacterial compartment opens new possibilities for
in vivo
synthesis of MNP-immobilized nanobodies. Moreover, intracellular nanotraps can be generated to manipulate bacterial structures in live cells.
Horizontal Gene Transfer and Assortative Recombination within the Acinetobacter baumannii Clinical Population Provide Genetic Diversity at the Single
carO
Gene, Encoding a Major Outer Membrane Protein Channel
Authors: Mussi María Alejandra , Limansky Adriana S. , Relling Verónica , Ravasi Pablo , Arakaki Adrián , Actis Luis A. , Viale Alejandro M.
Published: July 2011

We described previously the presence in
Acinetobacter baumannii
of a novel outer membrane (OM) protein, CarO, which functions as an
l
-ornithine OM channel and whose loss was concomitant with increased carbapenem resistance among clonally related nosocomial isolates of this opportunistic pathogen. Here, we describe the existence of extensive genetic diversity at the
carO
gene within the
A. baumannii
clinical population. The systematic analysis of
carO
sequences from
A. baumannii
isolates obtained from public hospitals in Argentina revealed the existence of four highly polymorphic
carO
variants among them. Sequence polymorphism between the different
A. baumannii
CarO variants was concentrated in three well-defined protein regions that superimposed mostly to predicted surface-exposed loops. Polymorphism among
A. baumannii
CarO variants was manifested in differential electrophoretic mobilities, antigenic properties, abilities to form stable oligomeric structures, and
l
-ornithine influx abilities through the
A. baumannii
OM under
in vivo
conditions. Incongruence between the phylogenies of the clinical
A. baumannii
isolates analyzed and those of the
carO
variants they harbor suggests the existence of assortative (entire-gene)
carO
recombinational exchange within the
A. baumannii
population. Exchange of
carO
variants possessing differential characteristics mediated by horizontal gene transfer may constitute an
A. baumannii
population strategy to survive radically changing environmental conditions, such as the leap from inanimate sources to human hosts and vice versa, persistence in a compromised host, and/or survival in health care facilities.
Bacillus subtilis CodY Operators Contain Overlapping CodY Binding Sites
Authors: Wray Lewis V. , Fisher Susan H.
Published: July 2011

CodY is a global transcriptional regulator that is activated by branched-chain amino acids. A palindromic 15-bp sequence motif, AATTTTCNGAAAATT, is associated with CodY DNA binding. A gel mobility shift assay was used to examine the effect of pH on the binding of
Bacillus subtilis
CodY to the
hutPp
and
ureAp
3
promoters. CodY at pH 6.0 has higher affinity for DNA, more enhanced activation by isoleucine, and a lower propensity for nonspecific DNA binding than CodY at pH 8.0. DNase I footprinting was used to identify the CodY-protected regions in the
hutPp
and
ureAp
3
promoters. The CodY-protected sequences for both promoters were found to contain multiple copies of the 15-bp motif with 6-bp overlaps. Mutational analysis of the
hutPp
regulatory region revealed that two overlapping sequence motifs were required for CodY-mediated regulation. The presence of overlapping sequence motifs in the regulatory regions of many
B. subtilis
CodY-regulated genes suggests that CodY binds to native operators that contain overlapping binding sites.
Population-based cross-sectional study of barriers to utilisation of refraction services in South India: Rapid Assessment of Refractive Errors (RARE) Study
Authors: Marmamula Srinivas , Keeffe Jill E , Raman Usha , Rao Gullapalli N
Published: July 2011

Aim

To assess the barriers to the uptake of refraction services in the age group of 15–49 years in rural Andhra Pradesh, India.

Methods

A population-based cross-sectional study was conducted using cluster random sampling to enumerate 3300 individuals from 55 clusters. A validated questionnaire was used to elicit information on barriers to utilisation of services among individuals with uncorrected refractive error (presenting visual acuity <6/12 but improving to ≥6/12 on using a pinhole) and presbyopia (binocular near vision 35 years with binocular distance visual acuity of ≥6/12).

Results

3095 (94%) were available for examination. Those with uncorrected refractive errors cited affordability as the main barrier to the uptake of eye-care services. Among people with uncorrected presbyopia, lack of ‘felt need’ was the leading barrier.

Conclusion

The barriers that were ‘relatively easy to change’ were reported by those with uncorrected refractive errors in contrast to ‘difficult to change’ barriers reported by those with uncorrected presbyopia. Together, the data on prevalence and an understanding of the barriers for the uptake of services are critical to the planning of refractive error services.
Rab38 targets to lamellar bodies and normalizes their sizes in lung alveolar type II epithelial cells
Authors: Zhang Linghui , Yu Kevin , Robert Kyle W. , DeBolt Kristine M. , Hong Nankang , Tao Jian-Qin , Fukuda Mitsunori , Fisher Aron B. , Huang Shaohui
Published: July 2011

Rab38 is a rat Hermansky-Pudlak syndrome gene that plays an important role in surfactant homeostasis in alveolar type II (ATII) pneumocytes. We examined Rab38 function in regulating lamellar body (LB) morphology in ATII cells. Quantitative electron microscopy revealed that LBs in ATII cells were ∼77% larger in Rab38-null fawn-hooded hypertension (FHH) than control Sprague-Dawley (SD) rats. Rab38 protein expression was restricted in lung epithelial cells but was not found in primary endothelial cells. In SD ATII cells, Rab38 protein level gradually declined during 5 days in culture. Importantly, endogenous Rab38 was present in LB fractions purified from SD rat lungs, and transiently expressed enhanced green fluorescent protein (EGFP)-tagged Rab38 labeled only the limiting membranes of a subpopulation (∼30%) of LBs in cultured ATII cells. This selective targeting was abolished by point mutations to EGFP-Rab38 and was not shared by Rab7 and Rab4b, which also function in the ATII cells. Using confocal microscopy, we established a method for quantitative evaluation of the enlarged LB phenotype temporally preserved in cultured FHH ATII cells. A direct causal relationship was established when the enlarged LB phenotype was reserved and then rescued by transiently reexpressed EGFP-Rab38 in cultured FHH ATII cells. This rescuing effect was associated with dynamic EGFP-Rab38 targeting to and on LB limiting membranes. We conclude that Rab38 plays an indispensible role in maintaining LB morphology and surfactant homeostasis in ATII pneumocytes.
Effect of Low-Fat Diets on Plasma Levels of NF-κB–Regulated Inflammatory Cytokines and Angiogenic Factors in Men with Prostate Cancer
Authors: Heymach John V. , Shackleford Terry J. , Tran Hai T. , Yoo Suk-Young , Do Kim-Anh , Wergin Melanie , Saintigny Pierre , Vollmer Robin T. , Polascik Thomas J. , Snyder Denise C. , Ruffin Mack T. , Yan Shaoyu , Dewhirst Mark , Kunnumakkara Ajaikumar B. , Aggarwal Bharat B. , Demark-Wahnefried Wendy
Published: July 2011

Diet, nutritional status, and certain dietary supplements are postulated to influence the development and progression of prostate cancer. Angiogenesis and inflammation are central to tumor growth and progression, but the effect of diet on these processes remains uncertain. We explored changes in 50 plasma cytokines and angiogenic factors (CAF) in 145 men with prostate cancer enrolled in a preoperative, randomized controlled phase II trial with four arms: control (usual diet), low-fat (LF) diet, flaxseed-supplemented (FS) diet, and FS+LS diet. The mean duration of dietary intervention was 30 to 31 days. Among the individual arms, the largest number of significant changes (baseline vs. preoperative follow-up) was observed in the LF arm, with 19 CAFs decreasing and one increasing (P < 0.05). Compared with the control arm, 6 CAFs—including proangiogenic factors (stromal-cell derived-1α) and myeloid factors (granulocyte-colony-stimulating factor, macrophage colony-stimulating factor)—all decreased in the LF arm compared with controls; three and four CAFs changed in the FS and FS+LF arms, respectively. Weight loss occurred in the LF arms and significantly correlated with VEGF decreases (P < 0.001). The CAFs that changed in the LF arm are all known to be regulated by NF-κB, and a pathway analysis identified NF-κB as the most likely regulatory network associated with these changes in the LF arm but not in the FS-containing arms. These results suggest that a LF diet without flaxseed may reduce levels of specific inflammatory CAFs and suggests that the NF-κB pathway may be a mediator of these changes. Cancer Prev Res; 4(10); 1590–8. ©2011 AACR.
Effects of Continuous-Flow Versus Pulsatile-Flow Left Ventricular Assist Devices on Myocardial Unloading and Remodeling
Authors: Kato Tomoko S. , Chokshi Aalap , Singh Parvati , Khawaja Tuba , Cheema Faisal , Akashi Hirokazu , Shahzad Khurram , Iwata Shinichi , Homma Shunichi , Takayama Hiroo , Naka Yoshifumi , Jorde Ulrich , Farr Maryjane , Mancini Donna M. , Schulze P. Christian
Published: July 2011

Background—

Continuous-flow left ventricular assist devices (LVAD) are increasingly used for patients with end-stage heart failure (HF). We analyzed the effects of ventricular decompression by continuous-flow versus pulsatile-flow LVADs on myocardial structure and function in this population.

Methods and Results—

Sixty-one patients who underwent LVAD implantation as bridge-to-transplant were analyzed (pulsatile-flow LVAD: group P, n=31; continuous-flow LVAD: group C, n=30). Serial echocardiograms, serum levels of brain natriuretic peptide (BNP), and extracellular matrix biomarkers (ECM) were compared between the groups. Myocardial BNP and ECM gene expression were evaluated in a subset of 18 patients. Postoperative LV ejection fraction was greater (33.2±12.6% versus 17.6±8.8%,
P
<0.0001) and the mitral E/E′ was lower (9.9±2.6 versus 13.2±3.8,
P
=0.0002) in group P versus group C. Postoperative serum levels of BNP, metalloproteinases (MMP)-9, and tissue inhibitor of MMP (TIMP)-4 were significantly lower in group P compared with group C (BNP: 552.6±340.6 versus 965.4±805.7 pg/mL,
P
<0.01; MMP9: 309.0±220.2 versus 475.2±336.9 ng/dL,
P
<0.05; TIMP4: 1490.9±622.4 versus 2014.3±452.4 ng/dL,
P
<0.001). Myocardial gene expression of ECM markers and BNP decreased in both groups; however, expression of TIMP-4 decreased only in group P (
P
=0.024).

Conclusions—

Mechanical unloading of the failing myocardium using pulsatile devices is more effective as indicated by echocardiographic parameters of systolic and diastolic LV function as well as dynamics of BNP and ECM markers. Therefore, specific effects of pulsatile mechanical unloading on the failing myocardium may have important implications for device selection especially for the purpose of bridge-to-recovery in patients with advanced HF.
Mouse FLRT2 Interacts with the Extracellular and Intracellular Regions of FGFR2
Authors: Wei K. , Xu Y. , Tse H. , Manolson M.F. , Gong S.-G.
Published: July 2011

Fibroblast Growth Factor (FGF) signaling is known to be critical in mediating key developmental events during craniofacial development. Recent evidence suggests that members of the Fibronectin (F) Leucine (L) Rich (R) Transmembrane (T), FLRT, family modulate FGF signaling. FLRT2 has a highly specific pattern of expression during craniofacial development, in close relationship with FGFR2. We therefore characterized FLRT2/FGFR2 interactions in the context of craniofacial development and showed, by co-immunoprecipitation and GST pulldown assays with embryonic craniofacial tissue lysates, that FLRT2 interacted with FGFR2. Yeast two-hybrid assays further showed that the intracellular regions of both proteins interacted in addition to the interactions in the extracellular portions. The extracellular Leucine Rich Repeats domain of FLRT2 contributed to the interactions with the extracellular regions of FGFR2. Interactions in the intracellular regions of the 2 proteins were mediated by the C-tail domain in FLRT2. Furthermore, cells stably transfected with FLRT2 shRNAs or FLRT2 cDNA exhibited a concomitant decrease and increase, respectively, in FGFR2 protein, mRNA, and ERK phosphorylation levels, suggesting a positive feedback regulatory loop of FLRT2 on FGF signaling in craniofacial tissues. We propose that FLRT2-FGFR2 interactions represent a potential mechanism for regulation of FGF signaling by FLRT2 during craniofacial development.
Calibrating information users’ views on relevance: A social representations approach
Authors: Ju Boryung , Gluck Myke
Published: July 2011

The purpose of this study is to investigate how information users view the concept of relevance and make their judgement(s) on relevant information through the framework of social representations theory. More specifically, this study attempts to address the questions of what users view as the constituent concepts of relevance, what are core and peripheral concepts of relevance, and how these concepts are structured by applying a structural analysis approach of social representations theory. We employ a free word association method for data collection. Two hundred and forty four information users of public and academic libraries responded to questionnaires on their relevance judgement criteria. Collected data were content analysed and assessed using weighted frequency, similarity measure, and core/periphery measurements to identify key elements of relevance and to differentiate core and periphery elements of relevance. Results show that four out of 26 emerged elements (concepts) are core and 22 are periphery elements of the concept of relevance. The findings of this study provide a quantitative measure of weighing various elements of relevance and the internal structure of the concept of relevance from users’ perspectives providing enhancements for search algorithms with quantitative metadata support.
History and Simulation/Gaming: Living With Two Solitudes
Authors: Corbeil Pierre
Published: July 2011

The History and Simulation/Gaming special issue should be understood as being bi-directional. The historical theme refers to the use of games and simulations, to the study of history, and to the place of history—or perhaps, simply the dimension of time and change—in the use and design of games. Historians in universities, designers and players of the well-known historical games, and the gamers who read and contribute to this journal seem to belong to distinct classes. This special issue, a modest undertaking in length and scope, is an attempt to bridge the chasm between the two classes. A sense of history can be a source of strength, intellectual or otherwise. The articles in this special issue are an opportunity for historians, gamers, and historical gamers to briefly connect.
Macrophage Colony Stimulating Factor-Induced Macrophage Differentiation Influences Myotube Elongation
Authors: Keeling Sara , Deashinta Nadia , Howard Katherine M. , Vigil Sara , Moonie Sheniz , Schneider Barbara St. Pierre
Published: July 2011

Background:

Unaccustomed exercise, high-intensity dynamic sports activities, or the resumption of normal weight-bearing after a period of disuse can induce skeletal muscle injury, which activates an inflammatory response followed by muscle regeneration. Specific subsets of macrophages are involved in muscle regeneration. But the exact role of macrophage differentiation during muscle regeneration remains to be elucidated.

Objective:

The objective of the study was to examine the effect of macrophage colony stimulating factor (M-CSF)-differentiated, lipopolysaccharides (LPS)-stimulated-macrophage-conditioned medium on muscle-cell proliferation, fusion, and elongation, which are key events during muscle regeneration and myogenesis.

Method:

Murine C2C12 myoblasts were cultured in conditioned medium obtained from PU5-1R macrophages that were (a) undifferentiated, unstimulated; (b) M-CSF-differentiated, unstimulated; (c) undifferentiated, LPS-stimulated; or (d) M-CSF-differentiated, LPS-stimulated. Myoblast proliferation ratio, nuclei number, and length were measured.

Results:

C2C12 cells cultured in conditioned medium from M-CSF-differentiated, LPS-stimulated macrophages had significantly more nuclei and greater length than cells cultured in conditioned medium from undifferentiated, LPS-stimulated macrophages. Dilution and denaturization of the M-CSF-differentiated, LPS-stimulated-macrophage medium prevented a marked increase in C2C12 nuclei number and length. However, the C2C12 myoblast proliferation ratio was significantly greater in conditioned medium from undifferentiated, LPS-stimulated macrophages than in conditioned medium from M-CSF-differentiated, LPS-stimulated macrophages.

Conclusions:

M-CSF-differentiated, LPS-stimulated macrophages may influence myogenesis and the early and terminal stages of muscle regeneration. This knowledge may aid in developing therapies that will directly expedite muscle repair and lead to faster rehabilitation and reduced rehabilitation costs.
Psychosocial and Biological Indicators of Depression in the Caregiving Population
Authors: Clark Michele C. , Nicholas Jennifer M. , Wassira Lucas N. , Gutierrez Antonio P.
Published: July 2011

Estimates suggest that 25–50% of family caregivers experience depression. Recent research has linked psychological stress and depression symptoms to increased cytokine activity. This study was designed to investigate the predictors of high cytokine levels and their influence with personality factors on depression in a caregiving population. The authors examined the relationship between caregiving burden and depression through the influence of sociotropy, autonomy, and cytokine levels in a sample of 106 caregivers who were actively caring for an elderly dependent in the community. Though the authors did not establish a mediation model, they found that the personality sub-factors of sociotropy, predicted tumor necrosis factor receptor (TNFR1) levels, while burden significantly predicted interleukin-6 and C-reactive protein (CRP) levels. Additionally, burden and TNFR1 levels predicted depression, with greater burden and TNFR1 levels predicting increased depression severity. Study findings point to a need for early interventions for caregivers to prevent increases in stress and cytokine levels and the development of depression.
Differential niche and Wnt requirements during acute myeloid leukemia progression
Authors: Lane Steven W. , Wang Yingzi J. , Lo Celso Cristina , Ragu Christine , Bullinger Lars , Sykes Stephen M. , Ferraro Francesca , Shterental Sebastian , Lin Charles P. , Gilliland D. Gary , Scadden David T. , Armstrong Scott A. , Williams David A.
Published: July 2011

Hematopoietic stem cells (HSCs) engage in complex bidirectional signals with the hematopoietic microenvironment (HM), and there is emerging evidence that leukemia stem cells (LSCs) may use similar interactions. Using a syngeneic retroviral model of MLL-AF9 induced acute myeloid leukemia (AML), we have identified 2 different stages of leukemia progression, propagated by “pre-LSCs” and established leukemia (LSCs) and compared the homing properties of these distinctive entities to that of normal HSCs. The homing and microlocalization of pre-LSCs was most similar to long-term HSCs and was dependent on cell-intrinsic Wnt signaling. In contrast, the homing of established LSCs was most similar to that of committed myeloid progenitors and distinct from HSCs. Although osteoblast-derived Dickkopf-1, a potent Wnt inhibitor known to impair HSC function, dramatically impaired normal HSC localization within the bone marrow, it did not affect pre-LSCs, LSC homing, or AML development. Mechanistically, cell-intrinsic Wnt activation was observed in human and murine AML samples, explaining the independence of MLL-AF9 LSCs from niche-derived Wnt signals. These data identify differential engagement of HM associated with leukemic progression and identify an LSC niche that is physically distinct and independent of the constraints of Wnt signaling that apply to normal HSCs.
CD38 and chronic lymphocytic leukemia: a decade later
Authors: Malavasi Fabio , Deaglio Silvia , Damle Rajendra , Cutrona Giovanna , Ferrarini Manlio , Chiorazzi Nicholas
Published: July 2011

This review highlights a decade of investigations into the role of CD38 in CLL. CD38 is accepted as a dependable marker of unfavorable prognosis and as an indicator of activation and proliferation of cells when tested. Leukemic clones with higher numbers of CD38+ cells are more responsive to BCR signaling and are characterized by enhanced migration. In vitro activation through CD38 drives CLL proliferation and chemotaxis via a signaling pathway that includes ZAP-70 and ERK1/2. Finally, CD38 is under a polymorphic transcriptional control after external signals. Consequently, CD38 appears to be a global molecular bridge to the environment, promoting survival/proliferation over apoptosis. Together, this evidence contributes to the current view of CLL as a chronic disease in which the host's microenvironment promotes leukemic cell growth and also controls the sequential acquisition and accumulation of genetic alterations. This view relies on the existence of a set of surface molecules, including CD38, which support proliferation and survival of B cells on their way to and after neoplastic transformation. The second decade of studies on CD38 in CLL will tell if the molecule is an effective target for antibody-mediated therapy in this currently incurable leukemia.
The Impact of Tariff Structure on Customer Retention, Usage, and Profitability of Access Services
Authors: Iyengar Raghuram , Jedidi Kamel , Essegaier Skander , Danaher Peter J.
Published: July 2011

Past research in marketing and psychology suggests that pricing structure may influence consumers' perception of value. In the context of two commonly used pricing schemes, pay-per-use and two-part tariff, we evaluate the impact of pricing structure on consumer preferences for access services. To this end, we develop a utility-based model of consumer retention and usage of a new service. A notable feature of the model is its ability to capture the pricing structure effect and measure its impact on consumer retention, usage, and pricing policy.

Using data from a pricing field experiment for a new telecommunication service, we find that consumers derive lower utility from consumption under a two-part tariff than pay-per-use pricing, resulting in lower retention of customers and lower usage of the service. Specifically, our demand analysis shows that a two-part tariff structure leads to an average decline of 10.5% in the annual retention rate and an average decrease of 38.7% in yearly usage relative to pay-per-use pricing after controlling for income effects. Despite the higher customer churn and lower usage, we find that the two-part tariff is still the profit-maximizing pricing structure. However, our results show that if firms ignore the pricing structure (or access fee) effect, then they would overcharge customers for the access fee and undercharge them for the per-minute price. Translated in terms of profitability, the failure to account for the access fee effect leads to a reduction of 11% in firm profit.
New Product Diffusion Decisions Under Supply Constraints
Authors: Shen Wenjing , Duenyas Izak , Kapuscinski Roman
Published: July 2011

Two recent papers on managing new product diffusion decisions under production constraints reach somewhat contradictory conclusions. Ho et al. (Ho, T.-H., S. Savin, C. Terwiesch. 2002. Managing demand and sales dynamics in new product diffusion under supply constraint. Management Sci. 48(2) 187–206) show that it is never optimal to refuse to satisfy any customers when the firm has inventory of the product. On the other hand, in a very similar model, Kumar and Swaminathan (Kumar, S., J. M. Swaminathan. 2003. Diffusion of innovations under supply constraints. Oper. Res. 51(6) 866–879) show that production constraints may in fact lead a firm to reject customers' orders even when the firm has the inventory to satisfy them (to slow down new product diffusion). We provide a counterexample to the results of Ho et al. (2002) and show that in their and Kumar and Swaminathan's (2003) models, it may be optimal to deny customers a product in inventory. We provide a generalization of both models that includes the ability to dynamically price the product (and also allows capacity and production costs to vary over time). We show that the unintuitive but optimal behavior of denying customers products that are in inventory disappears when the firm can dynamically set prices.

This paper was accepted by Candace A. Yano, operations and supply chain management.
Microarray Analysis of the Infrapatellar Fat Pad in Knee Osteoarthritis: Relationship with Joint Inflammation
Authors: GANDHI RAJIV , TAKAHASHI MARK , VIRTANEN CARL , SYED KHALID , DAVEY J. RODERICK , MAHOMED NIZAR N.
Published: July 2011

Objective.

To examine differences in genes involved in fat metabolism, energy homeostasis, adipogenesis, and inflammation between endstage and early-stage knee osteoarthritis (OA) infrapatellar fat pads (IFP).

Methods.

Twenty-nine endstage and 5 early-stage primary OA IFP were harvested at knee surgery. Total RNA was extracted, labeled, and hybridized to whole-genome expression arrays. Unsupervised analysis of all samples using principal components analysis or 2-way hierarchical clustering showed groupings based on tissue source and disease. Statistical testing identified sets of genes that displayed differences between the 2 fat types. Western blot analysis was performed for protein expression of an identified gene of interest.

Results.

The 29 IFP demonstrated an elevation in the expression of adipokines such as adiponectin and leptin. A statistically significant increased expression was seen for genes of adipogenesis, such as peroxisome proliferator-activated receptor-γ (PPAR-γ), diacylglycerol acyltransferase 2 (DGAT2), cluster of differentiation (CD36), and thyroid hormone responsive spot (THRSP) in the severe OA fat pads as compared to the controls. A subset of 5 patients in the endstage OA group were consistently similar in gene expression to early OA tissue. Protein expression of PPAR-γ2 was 5.4-fold and PPAR-γ1 was 1.4-fold greater in endstage versus early OA tissue.

Conclusion.

Endstage OA fat pads demonstrated a significant upregulation of genes for fat metabolism and energy homeostasis and a mixed result for inflammatory cytokines.
The Longitudinal Outcome of Fibromyalgia: A Study of 1555 Patients
Authors: WALITT BRIAN , FITZCHARLES MARY-ANN , HASSETT AFTON L. , KATZ ROBERT S. , HÄUSER WINFRIED , WOLFE FREDERICK
Published: July 2011

Objective.

To describe the diagnosis status and outcome of patients diagnosed with fibromyalgia (FM) by US rheumatologists.

Methods.

We assessed 1555 patients with FM with detailed outcome questionnaires during 11,006 semiannual observations for up to 11 years. At entry, all patients satisfied American College of Rheumatology preliminary 2010 FM criteria modified for survey research. We determined diagnosis status, rates of improvement, responder subgroups, and standardized mean differences (effect sizes) between start and study completion scores of global well-being, pain, sleep problems, and health related quality of life. (QOL)

Results.

The 5-year improvement rates were pain 0.4 (95% CI 0.2, 0.5), fatigue 0.4 (95% CI 0.2, 0.05), and global 0.0 (95% CI −0.1, 0.1). The standardized mean differences were patient global 0.03 (95% CI −0.02, 0.08), pain 0.22 (95% CI 0.16, 0.28), sleep problems 0.20 (95% CI 0.14, 0.25), physical component summary of the Short-form 36 (SF-36) 0.11 (95% CI −0.14, −0.07), and SF-36 mental component summary 0.03 (95% CI −0.07, 0.02). Patients switched between criteria-positive and criteria-negative states, with 716 patients (44.0%) failing to meet criteria at least once during 4228.5 patient-years (7448 observations). About 10% of patients had substantial improvement and about 15% had moderate improvement of pain. Overall, FM severity worsened in 35.9% and pain in 38.6%.

Conclusion.

Although we found no average clinically meaningful improvement in symptom severity overall, 25% had at least moderate improvement of pain over time. The result that emerged from this longitudinal study was one of generally continuing high levels of self-reported symptoms and distress for most patients, but a slight trend toward improvement.
Uveitis-Associated Epitopes of Retinal Antigens Are Pathogenic in the Humanized Mouse Model of Uveitis and Identify Autoaggressive T Cells
Authors: Mattapallil Mary J. , Silver Phyllis B. , Mattapallil Joseph J. , Horai Reiko , Karabekian Zaruhi , McDowell J. Hugh , Chan Chi-Chao , James Eddie A. , Kwok William W. , Sen H. Nida , Nussenblatt Robert B. , David Chella S. , Caspi Rachel R.
Published: July 2011

Noninfectious uveitis is a leading cause of blindness and thought to involve autoimmune T cell responses to retinal proteins (e.g., retinal arrestin [soluble-Ag (S-Ag)]). There are no known biomarkers for the disease. Susceptibility is associated with HLA, but little is known about susceptible class II alleles or the potentially pathogenic epitopes that they present. Using a humanized HLA-transgenic mouse model of S-Ag–induced autoimmune uveitis, we identified several susceptible and resistant alleles of HLA-DR and -DQ genes and defined pathogenic epitopes of S-Ag presented by the susceptible alleles. The sequences of these epitopes overlap with some previously identified peptides of S-Ag (“M” and “N”), known to elicit memory responses in lymphocytes of uveitis patients. HLA-DR–restricted, S-Ag–specific CD4+ T cells could be detected in blood and draining lymph nodes of uveitic mice with HLA class II tetramers and transferred the disease to healthy mice. Importantly, tetramer-positive cells were detected in peripheral blood of a uveitis patient. To our knowledge, these findings provide the first tangible evidence that an autoimmune response to retina is causally involved in pathogenesis of human uveitis, demonstrating the feasibility of identifying and isolating retinal Ag-specific T cells from uveitis patients and may facilitate their development as biomarkers for the disease.
Deinococcus daejeonensis sp. nov., isolated from sludge in a sewage disposal plant
Authors: Srinivasan Sathiyaraj , Kim Myung Kyum , Lim Sangyong , Joe Minho , Lee Myungjin
Published: July 2011

A Gram-stain-positive, strictly aerobic, spherical, non-motile red-pigmented bacterial strain, designated MJ27T, was isolated from a sludge sample of the Daejeon sewage disposal plant in South Korea. A polyphasic approach was used to study the taxonomic position of strain MJ27T. Strain MJ27T shared highest 16S rRNA gene sequence similarity with

Deinococcus grandis

DSM 3963T (98.8 %),

Deinococcus caeni

Ho-08T (97.5 %) and

Deinococcus aquaticus

PB314T (96.6 %.); levels of sequence similarity with the type strains of other

Deinococcus

species were less than 96.0 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MJ27T belonged to the clade formed by members of the genus

Deinococcus

in the family

Deinococcaceae

. The G+C content of the genomic DNA of strain MJ27T was 67.6 mol%. The chemotaxonomic characteristics of strain MJ27T were typical of members of the genus

Deinococcus

, with MK-8 as the predominant respiratory quinone, C16 : 1ω7c, C15 : 1ω6c, C16 : 0 and C15 : 0 as major fatty acids (>12 %), ornithine as the diamino acid in the cell-wall peptidoglycan and resistance to gamma radiation [D10 (dose required to reduce the bacterial population by tenfold) >9 kGy]. The low levels of DNA–DNA relatedness reported here (5.3±1.5–29.2±2.3 %) indicate that strain MJ27T represents a species that is separate from its closest relatives in the genus

Deinococcus

. On the basis of phylogenetic inference, fatty acid profile and other phenotypic properties, strain MJ27T is considered to represent a novel species of the genus

Deinococcus

, for which the name Deinococcus daejeonensis sp. nov. is proposed. The type strain is MJ27T ( = KCTC 13751T = JCM 16918T).
The Candida albicans GAP Gene Family Encodes Permeases Involved in General and Specific Amino Acid Uptake and Sensing
Authors: Kraidlova Lucie , Van Zeebroeck Griet , Van Dijck Patrick , Sychrová Hana
Published: July 2011

The
Saccharomyces cerevisiae
general amino acid permease Gap1 (
Sc
Gap1) not only mediates the uptake of most amino acids but also functions as a receptor for the activation of protein kinase A (PKA). Fungal pathogens can colonize different niches in the host, each containing various levels of different amino acids and sugars. The
Candida albicans
genome contains six genes homologous to the
S. cerevisiae GAP1
. The expression of these six genes in
S. cerevisiae
showed that the products of all six
C. albicans
genes differ in their transport capacities.
C. albicans
Gap2 (
Ca
Gap2) is the true orthologue of
Sc
Gap1 as it transports all tested amino acids. The other
Ca
Gap proteins have narrower substrate specificities though
Ca
Gap1 and
Ca
Gap6 transport several structurally unrelated amino acids.
Ca
Gap1,
Ca
Gap2, and
Ca
Gap6 also function as sensors. Upon detecting some amino acids, e.g., methionine, they are involved in a rapid activation of trehalase, a downstream target of PKA. Our data show that
CaGAP
genes can be functionally expressed in
S. cerevisiae
and that
Ca
Gap permeases communicate to the intracellular signal transduction pathway similarly to
Sc
Gap1.
Identification of the Lipopolysaccharide Core of Yersinia pestis and Yersinia pseudotuberculosis as the Receptor for Bacteriophage φA1122
Authors: Kiljunen Saija , Datta Neeta , Dentovskaya Svetlana V. , Anisimov Andrey P. , Knirel Yuriy A. , Bengoechea José A. , Holst Otto , Skurnik Mikael
Published: July 2011

φA1122 is a T7-related bacteriophage infecting most isolates of
Yersinia pestis
, the etiologic agent of plague, and used by the CDC in the identification of
Y. pestis
. φA1122 infects
Y. pestis
grown both at 20°C and at 37°C. Wild-type
Yersinia pseudotuberculosis
strains are also infected but only when grown at 37°C. Since
Y. pestis
expresses rough lipopolysaccharide (LPS) missing the O-polysaccharide (O-PS) and expression of
Y. pseudotuberculosis
O-PS is largely suppressed at temperatures above 30°C, it has been assumed that the phage receptor is rough LPS. We present here several lines of evidence to support this. First, a rough derivative of
Y. pseudotuberculosis
was also φA1122 sensitive when grown at 22°C. Second, periodate treatment of bacteria, but not proteinase K treatment, inhibited the phage binding. Third, spontaneous φA1122 receptor mutants of
Y. pestis
and rough
Y. pseudotuberculosis
could not be isolated, indicating that the receptor was essential for bacterial growth under the applied experimental conditions. Fourth, heterologous expression of the
Yersinia enterocolitica
O:3 LPS outer core hexasaccharide in both
Y. pestis
and rough
Y. pseudotuberculosis
effectively blocked the phage adsorption. Fifth, a gradual truncation of the core oligosaccharide into the Hep/Glc (
l
-
glycero
-
d
-
manno-
heptose/
d
-glucopyranose)-Kdo/Ko (3-deoxy-
d
-
manno
-oct-2-ulopyranosonic acid/
d
-
glycero
-
d
-
talo-
oct-2-ulopyranosonic acid) region in a series of LPS mutants was accompanied by a decrease in phage adsorption, and finally, a
waaA
mutant expressing only lipid A, i.e., also missing the Kdo/Ko region, was fully φA1122 resistant. Our data thus conclusively demonstrated that the φA1122 receptor is the Hep/Glc-Kdo/Ko region of the LPS core, a common structure in
Y. pestis
and
Y. pseudotuberculosis
.
Identification of the P3 Promoter and Distinct Roles of the Two Promoters of the SaeRS Two-Component System in Staphylococcus aureus
Authors: Jeong Do-Won , Cho Hoonsik , Lee Hyunwoo , Li Chunling , Garza Joshua , Fried Melinda , Bae Taeok
Published: July 2011

In
Staphylococcus aureus
, the SaeRS two-component system (TCS) encoded by the
saePQRS
operon controls expression of major virulence factors, such as coagulase and alpha-hemolysin. The
saePQRS
operon has two promoters: P1 and P3. The P1 promoter, a strong promoter, is autoinduced and can transcribe all four genes. Compared with P1, P3 shows fairly low but constitutive promoter activity, and it transcribes only
saeR
and
saeS
, the two genes encoding response regulator SaeR and sensor kinase SaeS. However, the role of each promoter in
sae
signaling has not been rigorously defined. In this study, we found that the genuine transcription start site (TSS) of P3 is located 78 nucleotides downstream of the previously reported TSS. Subsequently, the P3 promoter sequence was identified and validated by mutagenesis analyses. Deletion of the
saePQ
region including the P1 promoter did not significantly alter the expression patterns of coagulase and alpha-hemolysin, two well-known
sae
target genes. Due to its L18P substitution in a transmembrane domain, SaeS in strain Newman has a constitutive kinase activity. Interestingly, the mutation also rendered the protein unstable, but the protein stability was restored by SaeQ, suggesting a possible SaeQ-SaeS interaction. Ironically, the same mutation seems to increase mRNA stability. SaeR appears to be stabilized by SaeS, possibly by a protein-protein interaction. Chromosomal mutation of P1 did not affect the expression pattern of coagulase and alpha-hemolysin. Based on these results, we conclude that transcription of
saeRS
from P3 is sufficient for target gene activation and that P1 is not involved in the activation.
PGI synthase overexpression protects against bleomycin-induced mortality and is associated with increased Nqo 1 expression
Authors: Zhou Weisong , Dowell Dustin R. , Geraci Mark W. , Blackwell Timothy S. , Collins Robert D. , Polosukhin Vasiliy V. , Lawson William E. , Wu Pingsheng , Sussan Thomas , Biswal Shyam , Goleniewska Kasia , O'Neal Jamye , Newcomb Dawn C. , Toki Shinji , Morrow Jason D. , Peebles R. Stokes
Published: July 2011

The mortality rate for acute lung injury (ALI) is reported to be between 35–40%, and there are very few treatment strategies that improve the death rate from this condition. Previous studies have suggested that signaling through the prostaglandin (PG) I2 receptor may protect against bleomycin-induced ALI in mice. We found that mice that overexpress PGI synthase (PGIS) in the airway epithelium were significantly protected against bleomycin-induced mortality and had reduced parenchymal consolidation, apoptosis of lung tissue, and generation of F2-isoprostanes compared with littermate wild-type controls. In addition, we show for the first time in both in vivo and in vitro experiments that PGI2 induced the expression of NADP (H): quinoneoxidoreductase 1 (Nqo 1), an enzyme that prevents the generation of reactive oxygen species. PGI2 induction of Nqo 1 provides a possible novel mechanism by which this prostanoid protects against bleomycin-induced mortality and identifies a potential therapeutic target for human ALI.
Evaluating Criteria for English Learner Reclassification: A Causal-Effects Approach Using a Binding-Score Regression Discontinuity Design with Instrumental Variables
Authors: Robinson Joseph P.
Published: July 2011

When English learners are “reclassified” as fluent English proficient, often their instructional setting changes, including a significant reduction in or elimination of English language development services. Depending on a child's language skills, this instructional change could hinder future development or provide needed opportunities for learning advanced material. By establishing assessment-based guidelines for reclassification, policy makers have tremendous influence on when these settings change. The author highlights this policy lever for guiding reclassification decisions and identifies a method for rigorously evaluating whether the threshold for transitioning between settings is appropriate. This method—binding-score regression discontinuity with an instrumental variable—was then implemented to obtain unbiased effects of reclassification on academic outcomes for students on the cusp of meeting reclassification criteria to provide credible policy recommendations for maintaining or shifting assessment-based reclassification thresholds. The method detailed here can be used by policy makers to evaluate their own assessment-based guidelines.
A Didactic Presentation of Snijders’s lz* Index of Person Fit With Emphasis on Response Model Selection and Ability Estimation
Authors: Magis David , Raîche Gilles , Béland Sébastien
Published: July 2011

This paper focuses on two likelihood-based indices of person fit, the index lz and the Snijders’s modified index lz*. The first one is commonly used in practical assessment of person fit, although its asymptotic standard normal distribution is not valid when true abilities are replaced by sample ability estimates. The lz* index is a generalization of lz, which corrects for this sampling variability. Surprisingly, it is not yet popular in the psychometric and educational assessment community. Moreover, there is some ambiguity about which type of item response model and ability estimation method can be used to compute the lz* index. The purpose of this article is to present the index lz* in a simple and didactic approach. Starting from the relationship between lz and lz*, we develop the framework according to the type of logistic item response theory (IRT) model and the likelihood-based estimators of ability. The practical calculation of lz* is illustrated by analyzing a real data set about language skill assessment.
The costs and benefits of working with one's spouse: A two‐sample examination of spousal support, work–family conflict, and emotional exhaustion in work‐linked relationships
Authors: Halbesleben Jonathon R. B. , Wheeler Anthony R. , Rossi Ana Maria
Published: July 2011

Although the prevalence of employees working within the same workplace or occupation with their spouse has increased, relatively little research has examined their experiences. On the basis of the boundary and conservation of resources (COR) theories, we argue that higher levels of work–family role integration among work‐linked couples will lead to higher levels of spousal support resources and lower levels of work–family conflict. This will, in turn, lead to lower emotional exhaustion among employees in a work‐linked relationship. Among two samples of employees in a variety of occupations, we found that being in a work‐linked relationship was associated with both higher spousal instrumental support as well as different forms of work–family conflict. The interaction between spousal support and work–family conflict was associated with emotional exhaustion. We discuss the implications of these findings for boundary and COR theories in terms of movement of resources across work–family boundaries and resource relevance in the strain process. Copyright © 2011 John Wiley & Sons, Ltd.
Successful management of osteoradionecrotic precoccygeal defect with the free latissimus dorsi muscle flap: Case report and literature review
Authors: Lin Chin‐Ta , Chen Shyi‐Gen , Chen Tim‐Mo , Dai Niann‐Tzyy , FU Ju‐Peng , Chang Shun‐Chen
Published: July 2011

Perineal wound complications following abdominoperineal resection (APR) are still frequent and most troublesome complications. We report the case of a 79‐year‐old male found to have the huge precoccygeal defect with infection after APR for rectal carcinoma. Before surgery, the patient received a complete course of chemoradiation therapy to treat for downgrade staging of the rectal malignancy. Extensive debridement of the perianal wound was performed for three times, followed by perianal reconstruction and packing and augmentation of the precoccygeal dead space with free latissimus dorsi (LD) muscle flap. Although persisted wound infection was still observed after reconstruction, the patient still led a good result after one time of further debridement and split‐thickness skin graft. We selected free LD muscle flap to fill and seal off the large pelvic dead space without the needs to change the jackknife position of the patient after debridement. To the best of our knowledge, this is the first case reported in the literature with the radiation‐associated perianal wound infection after APR reconstructed successfully by free LD muscle flap. © 2011 Wiley‐Liss, Inc. Microsurgery, 2011.
Isolation of Pure Phospholipid Fraction from Egg Yolk
Authors: Gładkowski Witold , Chojnacka Anna , Kiełbowicz Grzegorz , Trziszka Tadeusz , Wawrzeńczyk Czesław
Published: July 2011

The phospholipid (PL) fraction from egg yolk was isolated and purified. In the procedure applied (method 2) the egg yolk was extracted with ethanol, precipitated using acetone chilled to −20 °C and washed using acetone. The purity of the samples was checked by HPLC analysis using a Charged Aerosol Detector (CAD). The results were compared with those obtained for the phospholipid fraction isolated and purified by deoiling yolk before extraction and the precipitation of PL with acetone chilled to 4 °C (method 1). The use of acetone chilled to −20 °C to precipitate and wash the phospholipids yielded the phospholipid fraction with 100% purity (78.7 ± 0.2 of phosphatidylcholine and 21.3 ± 0.2 of phosphatidylethanolamine). When deoiling and the 4 °C purification process was used (method 1) 0.4 ± 0.1% cholesterol and some traces of triacylglycerols remained in the PL fraction.