bluuebunny/crossref_metadata_2025_split huggingface dataset:
Activity of the Rhodopseudomonas palustris p-Coumaroyl-Homoserine Lactone-Responsive Transcription Factor RpaR
Authors: Hirakawa Hidetada , Oda Yasuhiro , Phattarasukol Somsak , Armour Christopher D. , Castle John C. , Raymond Christopher K. , Lappala Colin R. , Schaefer Amy L. , Harwood Caroline S. , Greenberg E. Peter 
Published: March 2011

ABSTRACT

The
Rhodopseudomonas palustris
transcriptional regulator RpaR responds to the RpaI-synthesized quorum-sensing signal
p
-coumaroyl-homoserine lactone (
p
C-HSL). Other characterized RpaR homologs respond to fatty acyl-HSLs. We show here that RpaR functions as a transcriptional activator, which binds directly to the
rpaI
promoter. We developed an RNAseq method that does not require a ribosome depletion step to define a set of transcripts regulated by
p
C-HSL and RpaR. The transcripts include several noncoding RNAs. A footprint analysis showed that purified His-tagged RpaR (His
6
-RpaR) binds to an inverted repeat element centered 48.5 bp upstream of the
rpaI
transcript start site, which we mapped by S1 nuclease protection and primer extension analyses. Although
p
C-HSL-RpaR bound to
rpaI
promoter DNA, it did not bind to the promoter regions of a number of RpaR-regulated genes not in the
rpaI
operon. This indicates that RpaR control of these other genes is indirect. Because the RNAseq analysis allowed us to track transcript strand specificity, we discovered that there is
p
C-HSL-RpaR-activated antisense transcription of
rpaR
. These data raise the possibility that this antisense RNA or other RpaR-activated noncoding RNAs mediate the indirect activation of genes in the RpaR-controlled regulon.
DEAD-Box Proteins from Escherichia coli Exhibit Multiple ATP-Independent Activities
Authors: Zhao Xinliang , Jain Chaitanya 
Published: March 2011

ABSTRACT

DEAD-box proteins (DBPs) are a widespread class of ATP-dependent RNA helicases that play a key role in unwinding RNA duplexes. In recent years, certain DBPs have also been found to exhibit activities that do not require ATP. To gain a better understanding of prokaryotic RNA metabolism, we investigated whether
Escherichia coli
DBPs harbor any ATP-independent activities. We show that each of the four
E. coli
DBPs tested in this study can accelerate the association of cRNA molecules, can stimulate strand displacement, and can function as an RNA chaperone without utilizing ATP. To the best of our knowledge, these prokaryotic DBPs constitute the first examples of proteins that harbor each of these three activities. The identification of these auxiliary functions indicates that the
E. coli
DBPs are versatile factors that possess significant RNA remodeling activity in addition to their canonical RNA helicase activity and might therefore participate in a greater variety of cellular processes than has been previously appreciated.
Characterization of Mutants Deficient in the
l,d
-Carboxypeptidase (DacB) and WalRK (VicRK) Regulon, Involved in Peptidoglycan Maturation of Streptococcus pneumoniae Serotype 2 Strain D39
Authors: Barendt Skye M. , Sham Lok-To , Winkler Malcolm E. 
Published: March 2011

ABSTRACT

Peptidoglycan (PG) hydrolases play critical roles in the remodeling of bacterial cell walls during division. PG hydrolases have been studied extensively in several bacillus species, such as
Escherichia coli
and
Bacillus subtilis
, but remain relatively uncharacterized in ovococcus species, such as
Streptococcus pneumoniae
(pneumococcus). In this work, we identified genes that encode proteins with putative PG hydrolytic domains in the genome of
S. pneumoniae
strain D39. Knockout mutations in these genes were constructed, and the resulting mutants were characterized in comparison with the parent strain for growth, cell morphology, PG peptide incorporation, and in some cases, PG peptide composition. In addition, we characterized deletion mutations in nonessential genes of unknown function in the WalRK

Spn

two-component system regulon, which also contains the essential
pcsB
cell division gene. Several mutants did not show overt phenotypes, which is perhaps indicative of redundancy. In contrast, two new mutants showed distinct defects in PG biosynthesis. One mutation was in a gene designated
dacB
(
spd
_
0549
), which we showed encodes an
l,d
-carboxypeptidase involved in PG maturation. Notably,
dacB
mutants, similar to
dacA
(
d,d
-carboxypeptidase) mutants, exhibited defects in cell shape and septation, consistent with the idea that the availability of PG peptide precursors is important for proper PG biosynthesis. Epistasis analysis indicated that DacA functions before DacB in
d
-Ala removal, and immunofluorescence microscopy showed that DacA and DacB are located over the entire surface of pneumococcal cells. The other mutation was in WalRK

Spn

regulon gene
spd
_
0703
, which encodes a putative membrane protein that may function as a type of conserved streptococcal shape, elongation, division, and sporulation (SEDS) protein.
A Feasibility Study to Evaluate a Novel Drug Delivery Technique through Nasal/Sinus Mucosa Using a Biodegradable Polymer in a Guinea Pig Model
Authors: Jonnalagadda Sashikanth , Yu Vivian M. , Catalano Peter J. 
Published: March 2011

ObjectiveTargeted topical pharmaceuticals have fewer side effects than systemic therapy and present an interesting option to treat chronic sinus disease. A simple, dependable, resorbable drug delivery mechanism has been elusive. The goal of this study is to examine the feasibility of a novel bioresorbable synthetic polymer for drug delivery in nose and sinuses.Study DesignFeasibility study.SettingAnimal study.Subjects and MethodsPolyurethane sponges soaked in either triamcinolone or gentamicin were placed in the ethmoid cavities of 14 guinea pigs via an external approach; 2 additional animals served as controls. Serum levels of each drug were assayed at intervals up to 21 days. Histopathological examination of the relevant sinonasal anatomy of each animal was performed after 21 days.ResultsSerum levels of each drug were detectable between days 1 and 21. There were no significant differences in the histopathological examination of nasal mucosa in guinea pigs in which either drug was applied compared with control animals in which the bioabsorbable material was soaked in saline. The polyurethane sponge did not cause any foreign body reaction, granuloma, or polypoidal change to the sinus mucosa. Two animals developed a subclinical infection at the surgical site.ConclusionThe targeted use of topical pharmaceuticals via a synthetic bioresorbable nasal sponge dressing in this guinea pig model demonstrated minimal systemic absorption and minimal histopathological changes. This technology is currently under investigation in human clinical trials.
Balloon Dilation of the Cartilaginous Eustachian Tube
Authors: Poe Dennis S. , Silvola Juha , Pyykkö Ilmari 
Published: March 2011

Objectives(1) To translate techniques developed in a previous cadaver study of balloon dilation of the cartilaginous eustachian tube (ET) into clinical treatment for refractory dilatory dysfunction and (2) to study the safety/efficacy of the technique in a pilot clinical trial.Study DesignProspective with subjects as their own historical controls since June 2009.SettingRegional academic center.Subjects and MethodsEleven consecutive adult patients with longstanding otitis media with effusion (OME) who were unable to autoinsufflate their ET by Valsalva, swallow, or yawn and who had previous tympanostomies (average, 4.7). At the time of intervention, 5 of 11 had a tube; 2 of 11 had a tympanic membrane (TM) perforation. Four of 11 had intact TMs, 2 with OME and tympanogram type B and 2 with TM retraction and tympanogram types B and C. Balloon dilation of the cartilaginous ET was performed with sinus dilation instruments via transnasal endoscopic approach under general anesthesia in a day surgery setting. Inflation was to a maximum of 12 atm for 1 minute. Outcome measures: ability to Valsalva, rating of ET mucosal inflammation, tympanogram, and otomicroscopy findings.ResultsAll cases successfully dilated. Eleven of 11 could self‐insufflate by Valsalva (P <. 001); tympanograms were A (4/11), C (1/11), or open (6/11). All atelectases resolved. Procedures were well tolerated, without pain or complications related to dilation.ConclusionDilation of the cartilaginous ET appeared to be beneficial and without significant adverse effects in the treatment of ET dilatory dysfunction. Larger controlled trials with long‐term results are now justified and needed.
Intrathyroid Parathyroid Adenoma
Authors: Goodman Arnold , Politz Doug , Lopez Jose , Norman James 
Published: March 2011

ObjectiveIt has been taught that a missing parathyroid adenoma can be within the thyroid. Therefore, thyroid lobectomy is appropriate when an adenoma cannot be found. Unfortunately, this technique is often futile. The purpose of this study is to examine the frequency of unsuccessful thyroid lobectomy in parathyroid surgery and to look at the true incidence and location of intrathyroid parathyroid adenomas (iT‐PAs).Study DesignA retrospective chart review of 11,163 patients undergoing parathyroid surgery identifying the location of more than 40,000 parathyroid glands.SettingA tertiary care center specializing in parathyroid surgery.Subjects and MethodsA total of 1163 reoperations for persistent primary hyperparathyroidism (PHPT) were examined for the incidence and outcomes of thyroid lobectomy performed to find iT‐PA. A second study examined 10,000 patients undergoing first‐time parathyroidectomy to classify the location and incidence of iT‐PA.ResultsThyroid lobectomy had been previously unsuccessfully performed in 77% cases of PHPT undergoing reoperation. Two or fewer glands were found in 82% prior to lobectomy. The adenoma was subsequently found on the lobectomy side in 64% and on the opposite side in 36%. True iT‐PA occurred in only 0.7% of 10,000 primary cases. Another 1.2% were closely adherent to or partially within the thyroid substance. The most common location was the lower lateral quadrant of the thyroid.ConclusionThe incidence of true iT‐PA is less than 1%, occurring in predictable locations. Thyroid lobectomy for a missing parathyroid adenoma is typically unsuccessful and should only rarely, if ever, be performed.
Matrix metalloproteinase 12 overexpression in myeloid lineage cells plays a key role in modulating myelopoiesis, immune suppression, and lung tumorigenesis
Authors: Qu Peng , Yan Cong , Du Hong 
Published: March 2011

AbstractMatrix metalloproteinase 12 (MMP12) is a macrophage-secreting proteinase. To fully understand the function of MMP12 in myeloid lineage cells, a myeloid-specific c-fms-rtTA/(TetO)7-CMV-MMP12 bitransgenic mouse model was created. In this bitransgenic system, induction of MMP12 abnormally elevated frequencies and numbers of common myeloid progenitor (CMP) and granulocyte/macrophage progenitor (GMP) populations, and decreased the frequency and number of the megakaryocyte/erythrocyte progenitor (MEP) population in the bone marrow (BM). The CD11b+/Gr-1+ immature cell population was systemically increased in multiple organs. Both in vitro and in vivo studies showed an immunosuppressive function on T-cell proliferation and function by CD11b+/Gr-1+ immature cells from MMP12-overexpressing bitransgenic mice. MMP12 directly stimulated lineage-negative (Lin−) progenitor cells to differentiate into CD11b+/Gr-1+ immature cells that showed immunosuppression on T-cell proliferation and function in vitro. Regulatory T cells (Tregs) were increased. In the lung, the concentration of IL-6 was increased, which aberrantly activated oncogenic Stat3 and increased expression of Stat3 downstream genes in epithelial tumor progenitor cells. Spontaneous emphysema and lung adenocarcinoma were sequentially developed after MMP12 overexpression. BM chimeras confirmed that the MMP12-induced myeloid cell autonomous defect led to abnormal myelopoiesis, immune suppression, and lung adenocarcinoma.
Priming of the vascular endothelial growth factor signaling pathway by thrombospondin-1, CD36, and spleen tyrosine kinase
Authors: Kazerounian Shideh , Duquette Mark , Reyes Millys A. , Lawler James T. , Song Keli , Perruzzi Carole , Primo Luca , Khosravi-Far Roya , Bussolino Federico , Rabinovitz Isaac , Lawler Jack 
Published: March 2011

Abstract
CD36 plays a critical role in the inhibition of angiogenesis through binding to the type 1 repeats of thrombospondin-1 (TSP-1) and activating Fyn tyrosine kinase and MAPK pathways. Here, we reveal a novel association of CD36 with VEGFR-2 and spleen tyrosine kinase (Syk). We also address the correlation between the expression of CD36 and Syk by demonstrating that overexpression of CD36 in HUVECs up-regulates endogenous Syk expression. We also define a new role for TSP-1 and CD36 in the activation of the VEGFR-2 signaling pathway that requires Syk. Our findings also identify a role for Syk as a stimulator of VEGF-A–induced angiogenesis by increasing phosphorylation of Y1175 in VEGFR-2, which is a major tyrosine for promoting VEGF-A–induced endothelial cell migration. Together, these studies introduce a new signaling pathway for TSP-1, CD36, and Syk, and address the role of these proteins in regulating the angiogenic switch.
A transient definitive erythroid lineage with unique regulation of the β-globin locus in the mammalian embryo
Authors: McGrath Kathleen E. , Frame Jenna M. , Fromm George J. , Koniski Anne D. , Kingsley Paul D. , Little Jane , Bulger Michael , Palis James 
Published: March 2011

AbstractA transient erythromyeloid wave of definitive hematopoietic progenitors (erythroid/myeloid progenitors [EMPs]) emerges in the yolk sac beginning at embryonic day 8.25 (E8.25) and colonizes the liver by E10.5, before adult-repopulating hematopoietic stem cells. At E11.5, we observe all maturational stages of erythroid precursors in the liver and the first definitive erythrocytes in the circulation. These early fetal liver erythroblasts express predominantly adult β-globins and the definitive erythroid-specific transcriptional modifiers c-myb, Sox6, and Bcl11A. Surprisingly, they also express low levels of “embryonic” βH1-, but not εy-, globin transcripts. Consistent with these results, RNA polymerase and highly modified histones are found associated with βH1- and adult globin, but not εy-globin, genes. E11.5 definitive proerythroblasts from mice transgenic for the human β-globin locus, like human fetal erythroblasts, express predominately human γ-, low β-, and no ε-globin transcripts. Significantly, E9.5 yolk sac–derived EMPs cultured in vitro have similar murine and human transgenic globin expression patterns. Later liver proerythroblasts express low levels of γ-globin, while adult marrow proerythroblasts express only β-globin transcripts. We conclude that yolk sac–derived EMPs, the first of 2 origins of definitive erythropoiesis, express a unique pattern of globin genes as they generate the first definitive erythrocytes in the liver of the mammalian embryo.
Carney Complex: case report and review
Authors: Borkar Shirish S , Kamath Sevagur G , Kashyap Nitin , Sagar Sunil CV , Rao Lakshmi , Warrier Raj , Chauhan Aman 
Published: March 2011

Abstract
Carney complex is a very rare multiple neoplasia syndrome with cardiac, cutaneous, and neural tumours with a variety of pigmented lesion of skin. We are reporting a rare case of carney complex in which left atrial myxoma with superficial angiomyxoma, giant cell tumour of bone and lentigines showed a unique association. This patient underwent successful surgical excision of left atrial myxoma under cardiopulmonary bypass.
RNAi-mediated knockdown of cyclooxygenase2 inhibits the growth, invasion and migration of SaOS2 human osteosarcoma cells: a case control study
Authors: Zhao Qinghua , Wang Chuan , Zhu Jiaxue , Wang Lei , Dong Shuanghai , Zhang Guoqiao , Tian Jiwei 
Published: March 2011

Abstract

Background
Cyclooxygenase2 (COX-2), one isoform of cyclooxygenase proinflammatory enzymes, is responsible for tumor development, invasion and metastasis. Due to its role and frequent overexpression in a variety of human malignancies, including osteosarcoma, COX-2 has received considerable attention. However, the function of COX-2 in the pathogenesis of cancer is not well understood. We examined the role of COX-2 in osteosarcoma.

Methods
We employed lentivirus mediated-RNA interference technology to knockdown endogenous gene COX-2 expression in human osteosarcoma cells (SaOS2) and analyzed the phenotypical changes. The effect of COX-2 treatment on the proliferation, cell cycle, invasion and migration of the SaOS2 cells were assessed using the MTT, flow cytometry, invasion and migration assays, respectively. COX-2, vascular endothelial growth factor (VEGF), epidermal growth factor (EGF), basic fibroblast growth factor (bFGF) mRNA and protein expression were detected by RT-PCR and western blotting.

Results
Our results indicate that a decrease of COX-2 expression in human osteosarcoma cells significantly inhibited the growth, decreased the invasion and migration ability of SaOS2 cells. In addition, it also reduced VEGF, EGF and bFGF mRNA and protein expression.

Conclusions
The COX-2 signaling pathway may provide a novel therapeutic target for the treatment of human osteosarcoma.
Comarketing Alliances: Should You Contract on Actions or Outcomes?
Authors: Chennamaneni Pavan Rao , Desiraju Ramarao 
Published: March 2011

Comarketing alliances often involve multiple partners, and a given partner's marketing efforts on behalf of the alliance can indirectly affect the demand of the other partners. Individual partners, however, can ignore the effects of such an externality and invest suboptimally to the detriment of the alliance. This paper examines the relative effectiveness of outcome- and action-based contracts in providing the alliance partners with the incentives to invest appropriately. We develop a mathematical model in which a focal firm (e.g., Sony) contracts with two partners (e.g., McDonald's and Old Navy) when each of these partners is privately informed about the impact of the alliance on its demand. Our analysis evaluates the strengths and weaknesses of outcome- (or output-) and action-based (or input-based) contracts in settings with varying levels of the demand externality. We find that when there is either no externality or a relatively weak positive externality, there is a strict preference for output-based contracts; that preference, however, is reversed with a sufficiently strong positive externality. This paper explains the underlying rationale for these findings. This paper was accepted by Preyas Desai, marketing.
The Threat from Within: Account Managers' Concern About Opportunism by Their Own Team Members
Authors: Murtha Brian R. , Challagalla Goutam , Kohli Ajay K. 
Published: March 2011

It is well known that transaction-specific investments (TSIs) made in customers by account managers makes them vulnerable to opportunism by customers (i.e., the targets of the investments). The present research shows that TSIs made in customers by account managers can also lead them to be concerned about internal opportunism by nontargets of the investments (e.g., information technology or finance specialists in their own teams). Furthermore, it shows that concern about internal opportunism leads account managers to engage in internal blocking of their own team members (i.e., restricting their access to customers and to customer information), which results in lower performance with customers. This phenomenon is a conundrum in that account managers interested in stronger performance with customers appear to block the very functional specialists who can help them attain better performance. This research also identifies two types of continuities (account manager–customer continuity and specialist–customer continuity) that moderate the relationship between TSIs and concern about internal opportunism. Building on the literature in economics and organization theory, our research suggests that cross-functional teams that are designed to bring different functional areas together are more complex to manage than previously believed. This paper was accepted by Pradeep Chintagunta and Preyas Desai, special issue editors. This paper was accepted by Pradeep Chintagunta and Preyas Desai, special issue editors.
An Experimental Study of Information Revelation Policies in Sequential Auctions
Authors: Cason Timothy N. , Kannan Karthik N. , Siebert Ralph 
Published: March 2011

Theoretical models of information asymmetry have identified a trade-off between the desire to learn and the desire to prevent an opponent from learning private information. This paper reports a laboratory experiment that investigates if actual bidders account for this trade-off, using a sequential procurement auction with private cost information and varying information revelation policies. Specifically, the Complete Information Revelation Policy, where all submitted bids are revealed between auctions, is compared to the Incomplete Information Revelation Policy, where only the winning bid is revealed. The experimental results are largely consistent with the theoretical predictions. For example, bidders pool with other types to prevent an opponent from learning significantly more often under a Complete Information Revelation Policy. Also as predicted, the procurer pays less when employing an Incomplete Information Revelation Policy only when the market is highly competitive. Bids are usually more aggressive than the risk-neutral quantitative prediction, which is broadly consistent with risk aversion. This paper was accepted by Teck Ho, decision analysis.
The Value of Fast Fashion: Quick Response, Enhanced Design, and Strategic Consumer Behavior
Authors: Cachon Gérard P. , Swinney Robert 
Published: March 2011

A fast fashion system combines quick response production capabilities with enhanced product design capabilities to both design “hot” products that capture the latest consumer trends and exploit minimal production lead times to match supply with uncertain demand. We develop a model of such a system and compare its performance to three alternative systems: quick-response-only systems, enhanced-design-only systems, and traditional systems (which lack both enhanced design and quick response capabilities). In particular, we focus on the impact of each of the four systems on “strategic” or forward-looking consumer purchasing behavior, i.e., the intentional delay in purchasing an item at the full price to obtain it during an end-of-season clearance. We find that enhanced design helps to mitigate strategic behavior by offering consumers a product they value more, making them less willing to risk waiting for a clearance sale and possibly experiencing a stockout. Quick response mitigates strategic behavior through a different mechanism: by better matching supply to demand, it reduces the chance of a clearance sale. Most importantly, we find that although it is possible for quick response and enhanced design to be either complements or substitutes, the complementarity effect tends to dominate. Hence, when both quick response and enhanced design are combined in a fast fashion system, the firm typically enjoys a greater incremental increase in profit than the sum of the increases resulting from employing either system in isolation. Furthermore, complementarity is strongest when customers are very strategic. We conclude that fast fashion systems can be of significant value, particularly when consumers exhibit strategic behavior. This paper was accepted by Yossi Aviv, operations management.