bluuebunny/crossref_metadata_2025 huggingface dataset:
Phenotypic Analysis of Adhesion Molecules in First‐Trimester Decidual Tissue From Chorion Villus Samples
Authors: Haynes Mrk K. , Wapner Rnald L. , Jackson Lird G. , Smith J. Bruce
Published: September 2011

PROBLEM: First‐trimester decidua contain CD56bright /CD16neg lymphocytes that phenotypically resemble a subset of peripheral blood natural killer (NK) cells. Factors controlling their localization to decidua are unknown, but they may relate to trophoblast invasion, endometrial decidualization, and adhesion molecule expression.

METHOD OF STUDY: Ninety‐one chorion villous samples (CVS) were screened for the presence of decidua, and selected specimens were analyzed for the expression of adhesion molecule pairs using a panel of monoclonal antibodies.

RESULTS: Lymphoid cells in CVS‐derived decidua expressed CD56, PECAM, intracellular adhesion molecule‐1 (ICAM‐1), and the integrins LFA‐1, αEβ7, and α4β1, and co‐receptors for these molecules were expressed by decidual stromal cells, invasive trophoblasts, and venule endothelium. Some endothelium expressed a cuboidal phenotype.

CONCLUSIONS: The expression of complimentary pairs of adhesion molecules by maternal lymphoid cells and by either extravillous cytotrophoblast or decidual stromal cells supports the hypothesis that these cells interact within decidua. Also, both LFA‐1 and α4β1 may contribute to decidual localization of CD56bright NK cells.
Detection of Human Defensins in the Placenta
Authors: Svinarich David M. , Gomez Ricardo , Romero Roberto
Published: September 2011

PROBLEM: The placenta is a highly selective barrier against the hematogenous dissemination of infectious agents. Despite the presence of seemingly intact physical and immunologic barriers, infections nonetheless occur. These observations prompted the examination of placental tissue, amnion, and chorion for previously unrecognized protective mechanisms.

METHOD OF STUDY: Messenger RNA from term placenta, amnion, and chorion were reverse transcribed using a 3′ RACE adapter. 3′ rapid amplification of cDNA ends (RACE)‐polymerase chain reaction (PCR) was conducted on cDNA from these tissues to detect the presence of human defensins. Southern analysis and partial sequence analysis were subsequently performed to confirm identity.

RESULTS: PCR amplification of placental, amnion, and chorion cDNA yielded a 468‐bp product and a weakly detectable band of 300 bp. Southern analysis demonstrated two corresponding hybridizing bands in the placenta, amnion, and chorion but not from a negative cDNA control. Partial sequence analysis of the 468‐bp product from placenta confirmed the presence of either defensin 1 or 3 in human placenta.

CONCLUSIONS: The human placenta, amnion, and chorion express defensins at the level of transcription. These findings suggest that a novel and previously unrecognized mechanism of protecting the fetus against infection may be present within these tissues.
Gonadotropins Do Not Induce Antiphospholipid Antibodies
Authors: Franklin R. D. , Bronson R. A. , Kutteh W. H.
Published: September 2011

PROBLEM: To determine whether the increased incidence of antiphospholipid antibodies (APAs) in women undergoing assisted reproduction might be secondary to superovulation with gonadotropins, predisposing women to an abnormal immune response and thus inducing APAs.

METHOD OF STUDY: Women undergoing assisted reproduction with gonadotropins for the first time were selected and tested before the initiation of the stimulation cycle, during the cycle, and at the end of the cycle (group 1). Women who had undergone gonadotropin stimulation at least 60 days earlier (group 2) and normal, nonpregnant, fertile women (group 3) also were evaluated. Serum samples were assayed by the enzyme‐linked immunosorbent assay method.

RESULTS: Ten (20%) of 50 women in group 1 were positive for APAs. The 10 women who were positive for APAs remained positive throughout the treatment cycle. Positive antibodies were identified in 12 (24%) of 50 women in group 2, not significantly different from group 1 (P = 0.81). Antibodies were present in 2 of 50 normal fertile control subjects, significantly less frequently than in group 1 (P < 0.03) and in group 2 (P < 0.01).

CONCLUSIONS: These data suggest that gonadotropin administration and/or the ovarian response to stimulation does not predispose women to the induction of APAs. Moreover, the incidence of APAs in this population, which is higher than that found in normal fertile women, cannot be explained by cycle‐induced events.
Assessment of Progesterone‐Induced Acrosome Reaction by Biotinylated Monoclonal Antibody Probes
Authors: Lee Chi‐Yu Gregory , Khorasani Afsaneh Motamed , Dorjee Sonam
Published: September 2011

PROBLEM: To develop an immunohistochemical assay for determination of acrosome‐reacted human sperm and to study the effects of progesterone and cholesterol treatment on human sperm acrosome reaction.

METHOD OF STUDY: Three distinct anti‐sperm monoclonal antibodies were biotinylated and used as probes for assessment of acrosome reaction in a 30‐min immunohistochemical assay. Progesterone and/or cholesterol were added to sperm preparation to influence the acrosome reaction in different experimental conditions.

RESULTS: Percentages of acrosome‐intact sperm decreased significantly during the 18‐hr incubation. Acrosome reaction could be induced by progesterone as early as 2 hr after sperm incubation in human tubal fluid. The degree of progesterone‐induced acrosome reaction was time dependent and the optimal effect was reached by adding 10 μg/ml progesterone for 30 min incubation. Progesterone‐induced acrosome reaction was shown to be hormone‐concentration dependent with 50% stimulation at 1 μg/ml. Cholesterol (1 μg/ml) was found to inhibit progesterone‐induced acrosome reaction either by co‐incubation with human sperm during capacitation, or by simultaneous incubation with progesterone during acrosome reaction induction.

CONCLUSIONS: Assessment of human sperm acrosomal status by avidin‐biotin immunohistochemical assay can be a routine in clinical laboratories for male infertility services. Cholesterol can inhibit progesterone‐induced acrosome reaction, possibly by its modifications of sperm plasma membrane and/or interference of progesterone binding to its surface receptors.
Changes in Lymphoid Tissue After Treatment with a Gonadotropin Releasing Hormone Antagonist in the Neonatal Marmoset (Callithrix jacchus)
Authors: Mann David R. , Howie Sarah , Paulsen Douglas F. , Akinbami Mukaila A. , Lunn Stephen F. , Fraser Hamish M.
Published: September 2011

PROBLEM: The effect of neonatal treatment with a gonadotropin releasing hormone (GnRH) antagonist on the morphology and distribution of lymphocytes in lymphoid tissue of the infant marmoset was examined.

METHOD OF STUDY: From a screened panel of antihuman antibodies for specific immune cells, antibodies for the CD20 and CD3 antigens showed excellent reactivity with marmoset tissue. Five sets of marmoset twins were treated with either the GnRH antagonist or a vehicle from birth, and were euthanized at 7 to 9 (3 sets) or 16 to 20 weeks (2 sets) of age. The spleen, thymus, and inguinal lymph nodes from each animal were processed for immunocytochemistry, and the number of cells expressing the CD20 and CD3 antigens were quantified.

RESULTS: Control twins exhibited high plasma levels of testosterone, characteristic of the neonatal period, whereas testosterone concentrations were reduced (P = 0.001) to detection limits in the GnRH antagonist‐treated twins. Microscopic evaluation suggested that treatment reduced the volume and cellularity of the thymic cortex, resulting in a decrease in the cortical‐to‐medullary ratio. Treatment reduced (P = 0.046) the number of thymocytes expressing the B‐cell antigen (CD20) and marginally lowered (P = 0.067) the number expressing the T‐cell antigen (CD3) in the thymic medulla. In the spleens of treated animals, periarterial lymphatic sheaths were less prominent on microscopic examination, and there were marginally fewer (P = 0.064) CD3+ cells. Numbers of CD20+ lymphocytes in the peripheral white pulp of the spleen and in the germinal centers of the lymph nodes, or CD3+ cells in the paracortex and germinal centers of the lymph nodes, were not altered by treatment.

CONCLUSION: Neonatal treatment with a GnRH antagonist may alter maturational processes for B and T cells in the thymus and spleen of the marmoset and may deprive the immune system of its normal sensitivity to GnRH at a potentially critical time in development.
Placental Isoferritin Levels in Pregnant Patients with Systemic Lupus Erythematosus and/or Antiphospholipid Syndrome
Authors: Maymon R. , Bar J. , Sherman D. , Moroz C.
Published: September 2011

PROBLEM: Low serum placental isoferritin (PLF), an immunosuppressive cytokine‐like protein, was found in women with underlying placento‐vascular dysfunction, such as intrauterine growth retardation and preeclamptic toxemia. The possible contribution of this placental product in the assessment of pregnant patients with either systemic lupus erythematosus (SLE) and/or antiphospholipid syndrome (APS) was investigated.

METHOD OF STUDY: Seventy‐five healthy pregnant women used as controls and 25 preselected pregnant patients with either SLE and/or APS were enrolled in the study. Study patients were in remission during conception and all patients agreed to give 5 ml of venous blood at midgestation. The samples were frozen and analyzed retrospectively. After delivery, pregnancy outcomes were gathered from hospital records.

RESULTS: Seventeen (68%) women had uneventful pregnancies and deliveries (normal) whereas 8 (32%) showed pathologic obstetric outcomes. Mean midgestational serum PLF levels were similar in the control and normal outcome groups (87 U/ml), whereas significantly lower levels (37 U/ml) were measured in the pathologic outcome group. Using a cutoff level of 10 U/ml, 85% from the normal outcome group and 15% from the pathologic outcome group were above this threshold level, with 60% specificity and 100% sensitivity.

CONCLUSIONS: These preliminary data suggest that PLF values may reflect placento‐vascular functions. These may represent a predictive biomarker for developing obstetric complications in pregnant women with either SLE and/or APS.
Is the Expression of Classical HLA Class I Antigens on Trophoblast of Importance for Human Pregnancy?
Authors: CHRISTIANSEN OLE B. , MOHAPELOA HANNE P. , PEDERSEN BJØRN , ROSGAARD ANNI
Published: September 2011

PROBLEM: Human leukocyte antigen (HLA)‐C and possibly also HLA‐B seem to be expressed on the extravillous trophoblast. These antigens carry epitopes that function as ligands for natural killer (NK)‐cell‐inhibitory receptors. Antitrophoblast cytotoxicity mediated by decidual NK cells might be involved in miscarriage. We thus found it relevant to elucidate whether parental HLA‐C and ‐Bw polymorphism play a role in recurrent miscarriage (RM).

METHOD OF STUDY: HLA‐C and ‐Bw investigations by DNA‐based techniques were undertaken in 35 couples with unexplained RM and in 30 couples with normal fecundity. The number of HLA‐C‐ and ‐Bw‐related supertypic specificities that can bind NK‐cell‐inhibitory receptors was evaluated in selected couples.

RESULTS: The proportions of couples with RM and control couples carrying four HLA‐C alleles with the same NK‐cell‐inhibitory supertypic specificities were equal. In 46% of studied couples with RM, all four HLA‐B alleles carried the HLA‐Bw6 supertypic specificity, which was significantly higher than the corresponding frequency (17%) in the control couples (P < 0.02).

CONCLUSIONS: The expression of polymorphic HLA‐C on trophoblasts does not seem to play a role in RM. Assuming that HLA‐B is expressed on trophoblasts, we may suggest that the revealed predominance of HLA‐Bw6 expression (which excludes the presence of HLA‐Bw4—protective antigens) may predispose a particular couple to the RM phenomenon.
Unique Biochemical Properties of Human Leukocyte Antigen‐E Allow for a Highly Specific Function in Immune Recognition
Authors: WEISS ELISABETH H. , CANNICH ASTRID , SPRINKS MATTHEW , FERNANDEZ NELSON , ULBRECHT MATTHIAS
Published: September 2011

PROBLEM: Does a correlation exist between the expression of human leukocyte antigen (HLA) class Ia and HLA‐E and what is its biological significance?

METHOD OF STUDY: HLA‐E transcripts were detected by reverse transcriptase‐polymerase chain reaction. Metabolically labeled HLA‐E heavy chains were immunoprecipited and analyzed by one‐dimensional isoelectric focusing. Mouse RMA‐S cells defective with regard to transporter associated with antigen processing (TAP) function were transfected with HLA‐E and human β2‐microglobulin to investigate TAP dependence of the cell‐surface expression of HLA‐E.

RESULTS: HLA‐E is transcribed regardless of the down‐regulation of polymorphic HLA class Ia expression. HLA‐E is transported to the cell surface in the absence of TAP‐con‐trolled peptide loading. In human cells, the amount of HLA‐E protein is very low regardless of the presence of correct peptide ligands.

CONCLUSIONS: HLA‐E regulates immune functions in cells that have down‐regulated the expression of polymorphic HLA‐class Ia molecules, either by preventing harmful natural killer cells from attacking targets that have physiologically decreased HLA‐class Ia expression or by activating effector cells against virus‐infected and tumor cells with impaired HLA‐class Ia expression.
Effect of Serum on Mouse Granulated Metrial Gland Cell Cytotoxicity
Authors: Stewart Dr. I.J. , Peel S.
Published: September 2011

PROBLEM: To examine factors affecting mouse granulated metrial gland cell cytotoxicity.

METHOD OF STUDY: Chromium‐release assays using mouse metrial gland cell suspensions targeted against Wehi 164 fibrosarcoma cells were used. Modulation of cellular cytotoxicity was investigated using an antibody. anti‐asialo‐GM1, to attempt depletion of effector cells and sera to determine if inhibitory factors are present in blood in vivo.

RESULTS: No reduction in cellular cytotoxicity was found following treatment of effector cells with asialo‐GM1 antibody, but there was a reduction following treatment with asialo‐GM1 antibody plus guinea pig serum and with guinea pig serum alone. Sera from pregnant, male, and SCID mice also reduced the level of cytotoxicity by metrial gland cell suspensions.

CONCLUSIONS: The reduction in cytotoxicity in the presence of serum indicates that there are factors in the blood which are inhibitory to granulated metrial gland cell cytotoxic activity in vivo. The resistance of mouse metrial gland cells to asialo‐GM1 antibody depletion is supportive of a natural cytotoxic (NC) lineage for this cell type.
Binding of Ovine Uterine Serpin to Lymphocytes
Authors: Liu Wen‐Jun , Peltier M.R. , Hansen P.J.
Published: September 2011

PROBLEM: The endometrium of the sheep produces a progesterone‐induced member of the serpin superfamily of serine proteinase inhibitors that can inhibit lymphocyte proliferation and reduce natural killer cell activity. Present results indicate that this molecule, called ovine uterine serpin (OvUS), can bind specifically to lymphocytes.

METHOD OF STUDY/RESULTS: Biotinylated OvUS bound to peripheral blood lymphocytes in a dose‐dependent and saturable manner. Binding was inhibited by OvUS, but not by several other proteins, including serpin‐enzyme complex (α1‐antitrypsin‐trypsin). Heparin blocked binding when added to the binding reaction or when used to pretreat lymphocytes. Both lymphocytes and Madin‐Darby bovine kidney (MDBK) cells also bound fluorescein isothiocyanate‐labeled OvUS.

CONCLUSIONS: Results suggest that OvUS can interact with lymphocytes and other cells through binding to a cell surface molecule. Such binding may indicate that inhibition of lymphocyte activation by OvUS involves 1) binding of OvUS to a cell surface receptor or 2) competitive inhibition of binding between OvUS and a co‐activation molecule required for lymphocyte activation.
A NARRATIVE OF POWER: TOWER COLLIERY AS AN EXAMPLE OF WORKER CONTROL THROUGH COOPERATIVE WORK ORGANIZATION
Authors: Smith Russell , Arthur Len , Cato Molly Scott , Keenoy Tom
Published: September 2011

This essay addresses the nature and limits of democracy in a work organization through charting the history and progress of the Tower coal mine in South Wales as a worker‐owned producer cooperative and as a productive mine. Methodologically, the research relies on site observations, individual and group interviews at all “levels” of the organization, published documents, the cooperative archives, and the extensive and intensive local newspaper reportage. During its 13 years as a workers' cooperative, Tower expanded production in an increasingly competitive market, increased employment, opened up new markets, made a significant social contribution to the local economy, and overcame production difficulties, which would likely have shut down a privately owned enterprise. Significantly, all these were achieved through a management process based on direct democracy. Despite government strictures governing the mine industry, management control was exercised through a network of mutually interconnecting democratic processes and procedures. These included annual shareholders meetings, monthly board meetings, weekly production meetings, and daily shift production meetings led by elected “shift captains.” These were complemented by a continual process of largely informal consultation. Such processes generated criticism and disagreement as much as consensus and even overt conflict on occasions. The essay details the establishment and development of Tower Cooperative, identifying and discussing crucial questions, including: What happened to the nature of management authority? What happened to the nature of the employment relationship? What was the complex role of the union in the cooperative? The essay also evaluates the tensions over Tower's 13‐year history as a cooperative.
DOMESTIC WORKERS AND COOPERATIVES: BEYONDCARE GOES BEYOND CAPITALISM, A CASE STUDY IN BROOKLYN, NEW YORK
Authors: Estey Ken
Published: September 2011

Worker‐owned and worker‐managed cooperatives have a long history in the U.S. They pose an alternative to workplaces structured within capitalism that are hierarchical and do not feature collective decision‐making. The short history of the cooperative movement in this article sets the context for a study of workers in Brooklyn, who are also immigrants, in the field of child care. These workers face additional hurdles to full empowerment at work as they lack comprehensive labor law protection and must contend with the under‐enforcement of existing laws in the U.S. Home‐based child care is inherently isolated and does not foster opportunities for workers to organize in traditional ways. These conditions create a compelling rationale for workers to resist their exploitation through self‐organization and the creation of worker cooperatives. This article will describe how the BeyondCare child care cooperative in Sunset Park, Brooklyn offers its worker owners control over their labor and unfettered access to their earnings. BeyondCare is a useful case study because it is a worker cooperative made up of immigrant women who have learned from other immigrant worker owners how to create meaningful living‐wage labor. The worker owners offer a timely example about the power of immigrant women to reach into a privatized place in the U.S. economy—home‐based labor—and to recreate that work into something that works for them.
NAPL Source Zone Depletion Model and Its Application to Railroad‐Tank‐Car Spills
Authors: Marruffo Amanda , Yoon Hongkyu , Schaeffer David J. , Barkan Christopher P. L. , Saat Mohd Rapik , Werth Charles J.
Published: September 2011

We developed a new semi‐analytical source zone depletion model (SZDM) for multicomponent light nonaqueous phase liquids (LNAPLs) and incorporated this into an existing screening model for estimating cleanup times for chemical spills from railroad tank cars that previously considered only single‐component LNAPLs. Results from the SZDM compare favorably to those from a three‐dimensional numerical model, and from another semi‐analytical model that does not consider source zone depletion. The model was used to evaluate groundwater contamination and cleanup times for four complex mixtures of concern in the railroad industry. Among the petroleum hydrocarbon mixtures considered, the cleanup time of diesel fuel was much longer than E95, gasoline, and crude oil. This is mainly due to the high fraction of low solubility components in diesel fuel. The results demonstrate that the updated screening model with the newly developed SZDM is computationally efficient, and provides valuable comparisons of cleanup times that can be used in assessing the health and financial risk associated with chemical mixture spills from railroad‐tank‐car accidents.
Field Test of the Superconducting Gravimeter as a Hydrologic Sensor
Authors: Wilson Clark R. , Scanlon Bridget , Sharp John , Longuevergne Laurent , Wu Hongqiu
Published: September 2011

We report on a field test of a transportable version of a superconducting gravimeter (SG) intended for groundwater storage monitoring. The test was conducted over a 6‐month period at a site adjacent to a well in the recharge zone of the karstic Edwards Aquifer, a major groundwater resource in central Texas. The purpose of the study was to assess requirements for unattended operation of the SG in a field setting and to obtain a gravimetric estimate of aquifer specific yield. The experiment confirmed successful operation of the SG, but water level changes were small (<0.3 m) leading to uncertainty in the estimate of specific yield. Barometric pressure changes were the dominant cause of both water level variations and non‐tidal gravity changes. The specific yield estimate (0.26) is larger than most published values and dependent mainly on low frequency variations in residual gravity and water level time series.
Probiotics in the management of gastrointestinal disease: Analysis of the attitudes and prescribing practices of gastroenterologists and surgeons
Authors: CORDINA Claire , SHAIKH Irshad , SHRESTHA Sussie , CAMILLERI‐BRENNAN John
Published: September 2011

OBJECTIVE:  Probiotics are increasingly advocated in the management of various gastrointestinal disorders. The aim of this study was to investigate the current attitudes and prescribing practices of surgeons and gastroenterologists for probiotics in the treatment of gastrointestinal disorders.

METHODS:  A questionnaire was designed to look at the frequency of probiotic prescribing, types of probiotics used, indications for and duration of treatment and clinicians' experiences with probiotic use. A total of 220 questionnaires were mailed to consultant gastroenterologists and surgeons practicing in the UK.

RESULTS:  The overall response rate was 80.5%, of which 69.5% of respondents said they recommended or prescribed probiotic food supplements to their patients, including 53.4% of surgeons and 80.8% of gastroenterologists (P = 0.00013). The most popular probiotic supplements among surgeons were probiotic‐containing yoghurt and drinks (79.5% and 71.8%, respectively), whereas VSL#3 was more popular with gastroenterologists (83.3%). The most popular indications were irritable bowel syndrome (70.7% of prescribers) and pouchitis (67.5% of prescribers). Many respondents prescribed long‐term probiotics. Most consultants had been prescribing probiotics for a period of 1 to 5 years.

CONCLUSION:  Probiotics are popular among gastroenterologists and surgeons in the UK for the treatment of gastrointestinal disorders. Further evidence to support their routine use, by way of large, well‐designed randomized controlled trials, is necessary.
Hydrogen production by recombinant Escherichia coli strains
Authors: Maeda Toshinari , Sanchez‐Torres Viviana , Wood Thomas K.
Published: September 2011

The production of hydrogen via microbial biotechnology is an active field of research. Given its ease of manipulation, the best‐studied bacterium Escherichia coli has become a workhorse for enhanced hydrogen production through metabolic engineering, heterologous gene expression, adaptive evolution, and protein engineering. Herein, the utility of E. coli strains to produce hydrogen, via native hydrogenases or heterologous ones, is reviewed. In addition, potential strategies for increasing hydrogen production are outlined and whole‐cell systems and cell‐free systems are compared.
Community‐based interference against integration of Pseudomonas aeruginosa into human salivary microbial biofilm
Authors: He X. , Hu W. , He J. , Guo L. , Lux R. , Shi W.
Published: September 2011

As part of the human gastrointestinal tract, the oral cavity represents a complex biological system and harbors diverse bacterial species. Unlike the gut microbiota, which is often considered a health asset, studies of the oral commensal microbiota have been largely limited to their implication in oral conditions such as dental caries and periodontal disease. Less emphasis has been given to their potential beneficial roles, especially the protective effects against oral colonization by foreign or pathogenic bacteria. In this study, we used salivary microbiota derived from healthy human subjects to investigate protective effects against colonization and integration of Pseudomonas aeruginosa, an opportunistic bacterial pathogen, into developing or pre‐formed salivary biofilms. When co‐cultivated in saliva medium, P. aeruginosa persisted in the planktonic phase, but failed to integrate into the salivary microbial community during biofilm formation. Furthermore, in saliva medium supplemented with sucrose, the oral microbiota inhibited the growth of P. aeruginosa by producing lactic acid. More interestingly, while pre‐formed salivary biofilms were able to prevent P. aeruginosa colonization, the same biofilms recovered from mild chlorhexidine gluconate treatment displayed a shift in microbial composition and showed a drastic reduction in protection. Our study indicates that normal oral communities with balanced microbial compositions could be important in effectively preventing the integration of foreign or pathogenic bacterial species, such as P. aeruginosa.
An Argument for the Use of Multiple Segment Stents in Curved Arteries
Authors: Kasiri Saeid , Kelly Daniel J.
Published: September 2011

Stenting of curved arteries is generally perceived to be more challenging than straight vessels. Conceptually implanting multiple shorter stents rather than a single longer stent into such a curved artery represents a promising concept, but little is known about the impact of such an approach. The objective of this study is to evaluate the effectiveness of using a multiple segment stent rather than a single long stent to dilate a curved artery using the finite element method. A double segment stent (DSS) and a single segment stent (SSS) were modeled. The stents were compared when expanded into a model of a curved artery. The model predicts that the DSS provides higher flexibility, more conformity, and lower recoil in comparison to the SSS. The volume of arterial tissue experiencing high levels of stress due to stent implantation is also reduced for the DSS. It is suggested that a multiple segment stenting system is a potential solution to the problem of higher rates of in-stent restenosis in curved arteries and mechanically challenging environments.
Complete Sequence of pJIE143, a
pir
-Type Plasmid Carrying IS
Ecp1-bla
CTX-M-15
from an Escherichia coli ST131 Isolate
Authors: Partridge Sally R. , Ellem Justin A. , Tetu Sasha G. , Zong Zhiyong , Paulsen Ian T. , Iredell Jonathan R.
Published: September 2011

pJIE143 (34 kb), from an
Escherichia coli
ST131 isolate, carries
bla
CTX-M-15
but could not be typed using the standard PCR-based replicon-typing primer set. Complete sequencing revealed a backbone with similarity to IncX plasmids, including a
pir
-like gene encoding a π-like replication protein and iterons related to those of other IncX plasmids. The 2.971-kb IS
Ecp1-bla
CTX-M-15
-orf477Δ transposition unit often found within Tn
2
is inserted just beyond the end of
pir
, flanked by 5-bp direct repeats.
Protecting the content integrity of digital imagery with fidelity preservation
Authors: Lin Pei-Yu , Lee Jung-San , Chang Chin-Chen
Published: September 2011

Fragile watermarking is applied to protect the content integrity of digital images. The main concerns related to watermarking include retaining the quality of the watermarked image and retaining the ability to detect whether any manipulation has occurred. Because recent watermarking techniques seriously distort the quality of the protected image after embedding the authentication code into the image content, attention has been drawn to how to satisfy both the need for image fidelity and detection ability. To account for the influence from both essentials, a novel algorithm is proposed in this article. The new scheme utilizes a weighted-sum function to embed (
n
+ 1) authentication bits into a block with 2

n

pixels by modifying only one original pixel with (±1). With fewer authentication codes, the new process can protect the content of the image. The experimental results demonstrate that the approach can guarantee the fidelity of the watermarked image while retaining tamper-proof functionality.
Incorporating household structure into a discrete-event simulation model of tuberculosis and HIV
Authors: Mellor Georgina R. , Currie Christine S. M. , Corbett Elizabeth L.
Published: September 2011

Human immunodeficiency virus (HIV) increases the risks of developing tuberculosis (TB) disease following infection, and speeds up disease progression. This has had a devastating effect on TB epidemics in sub-Saharan Africa, where incidence rates have more than trebled in the past twenty years. Current control methods for TB disease have failed to keep pace with this growth, and there is an urgent need to find TB control strategies that are effective in high-HIV prevalent settings. This article describes a discrete-event simulation model of endemic TB that includes the effects of HIV and of household structure on the transmission dynamics of TB. Incorporating a social structure allows us to compare the effectiveness of contact-tracing interventions with case-finding targeted at high risk groups. We describe the modeling of the household structure in some detail, as this has applications to the modeling of other infectious diseases.
Increasing the effectiveness of directory caches by deactivating coherence for private memory blocks
Authors: Cuesta Blas A. , Ros Alberto , Gómez María E. , Robles Antonio , Duato José F.
Published: September 2011

To meet the demand for more powerful high-performance shared-memory servers, multiprocessor systems must incorporate efficient and scalable cache coherence protocols, such as those based on directory caches. However, the limited directory cache size of the increasingly larger systems may cause frequent evictions of directory entries and, consequently, invalidations of cached blocks, which severely degrades system performance.

A significant percentage of the referred memory blocks are only accessed by one processor (even in parallel applications) and, therefore, do not require coherence maintenance. Taking advantage of techniques that dynamically identify those private blocks, we propose to deactivate the coherence protocol for them and to treat them as uniprocessor systems do. The protocol deactivation allows directory caches to omit the tracking of an appreciable quantity of blocks, which reduces their load and increases their effective size. Since the operating system collaborates on the detection of private blocks, our proposal only requires minor modifications.

Simulation results show that, thanks to our proposal, directory caches can avoid the tracking of about 57% of the accessed blocks and their capacity can be better exploited. This contributes either to shorten the runtime of parallel applications by 15% while keeping directory cache size or to maintain system performance while using directory caches 8 times smaller.
Demand-driven software race detection using hardware performance counters
Authors: Greathouse Joseph L. , Ma Zhiqiang , Frank Matthew I. , Peri Ramesh , Austin Todd
Published: September 2011

Dynamic data race detectors are an important mechanism for creating robust parallel programs. Software race detectors instrument the program under test, observe each memory access, and watch for inter-thread data sharing that could lead to concurrency errors. While this method of bug hunting can find races that are normally difficult to observe, it also suffers from high runtime overheads. It is not uncommon for commercial race detectors to experience 300x slowdowns, limiting their usage.

This paper presents a hardware-assisted demand-driven race detector. We are able to observe cache events that are indicative of data sharing between threads by taking advantage of hardware available on modern commercial microprocessors. We use these to build a race detector that is only enabled when it is likely that inter-thread data sharing is occurring. When little sharing takes place, this demand-driven analysis is much faster than contemporary continuous-analysis tools without a large loss of detection accuracy. We modified the race detector in Intel(R) Inspector XE to utilize our hardware-based sharing indicator and were able to achieve performance increases of 3x and 10x in two parallel benchmark suites and 51x for one particular program.
Moguls
Authors: Sun Guangyu , Hughes Christopher J. , Kim Changkyu , Zhao Jishen , Xu Cong , Xie Yuan , Chen Yen-Kuang
Published: September 2011

In recent years, the increasing number of processor cores and limited increases in main memory bandwidth have led to the problem of the
bandwidth wall
, where memory bandwidth is becoming a performance bottleneck. This is especially true for emerging latency-insensitive, bandwidth-sensitive applications. Designing the memory hierarchy for a platform with an emphasis on maximizing bandwidth within a fixed power budget becomes one of the key challenges. To facilitate architects to quickly explore the design space of memory hierarchies, we propose an analytical performance model called Moguls. The Moguls model estimates the performance of an application on a system, using the bandwidth demand of the application for a range of cache capacities and the bandwidth provided by the system with those capacities. We show how to extend this model with appropriate approximations to optimize a cache hierarchy under a power constraint. The results show how many levels of cache should be designed, and what the capacity, bandwidth, and technology of each level should be. In addition, we study memory hierarchy design with hybrid memory technologies, which shows the benefits of using multiple technologies for future computing systems.
The role of optics in future high radix switch design
Authors: Binkert Nathan , Davis Al , Jouppi Norman P. , McLaren Moray , Muralimanohar Naveen , Schreiber Robert , Ahn Jung Ho
Published: September 2011

For large-scale networks, high-radix switches reduce hop and switch count, which decreases latency and power. The ITRS projections for signal-pin count and per-pin bandwidth are nearly flat over the next decade, so increased radix in electronic switches will come at the cost of less per-port bandwidth. Silicon nanophotonic technology provides a long-term solution to this problem. We first compare the use of photonic I/O against an all-electrical, Cray YARC inspired baseline. We compare the power and performance of switches of radix 64, 100, and 144 in the 45, 32, and 22 nm technology steps. In addition with the greater off-chip bandwidth enabled by photonics, the high power of electrical components inside the switch becomes a problem beyond radix 64.

We propose an optical switch architecture that exploits highspeed optical interconnects to build a flat crossbar with multiplewriter, single-reader links. Unlike YARC, which uses small buffers at various stages, the proposed design buffers only at input and output ports. This simplifies the design and enables large buffers, capable of handling ethernet-size packets. To mitigate head-of-line blocking and maximize switch throughput, we use an arbitration scheme that allows each port to make eight requests and use two grants. The bandwidth of the optical crossbar is also doubled to to provide a 2x internal speedup. Since optical interconnects have high static power, we show that it is critical to balance the use of optical and electrical components to get the best energy efficiency. Overall, the adoption of photonic I/O allows 100,000 port networks to be constructed with less than one third the power of equivalent all-electronic networks. A further 50% reduction in power can be achieved by using photonics within the switch components. Our best optical design performs similarly to YARC for small packets while consuming less than half the power, and handles 80% more load for large message traffic.
Enhancement of Oral Bioavailability of Puerarin by Polybutylcyanoacrylate Nanoparticles
Authors: Zhao Lixia , Liu Anchang , Sun Min , Gu Jinsong , Wang Haigang , Wang Shuang , Zhang Jing , Guo Chenyu , Duan Rui , Zhai Guangxi
Published: September 2011

The interest using novel drug delivery systems to improve oral bioavailability of drug with poor solubility is increasing. In this study, a new oral delivery system, polybutylcyanoacrylate nanoparticles (PBCNs), was introduced to improve the oral bioavailability of puerarin (PUE). PUE-loaded PBCN was successfully prepared by anionic polymerization method. Characterization of PUE-loaded PBCN was evaluated with morphology, size, zeta potential, and in vitro release study. The PBCN loading PUE exhibited a spherical shape under transmission electron microscopy with an average size of 159.4 nm, and the zeta potential was −15.0 mV. The in vitro release of PUE-loaded PBCN showed an initial burst release followed by a sustained release. Physicochemical state of PUE in PBCN was investigated by differential scanning colorimetry, X-ray diffraction, and Fourier transform infrared spectroscopy. The results indicated that PUE in PBCN was in a noncrystalline state. The oral pharmacokinetic study in rats showed that the relative bioavailability of PUE-encapsulated PBCN to the crude PUE was more than 550%. It can be concluded that PBCN as an oral drug carrier can significantly improve the oral bioavailability of PUE.
Intraosseous Cavernous Hemangioma of Inferior Turbinate: A Rare Case Report
Authors: Akiner M. N. , Akturk M. T. , Demirtas M. , Atmis E. O.
Published: September 2011

Objectives. To investigate hemangiomas in the differential diagnosis of the nasal cavity neoplasms, even though it is an extremely rare mesenchymal tumor of the nasal cavity, and the world literature was reviewed.Case Report. A 57-year-old woman applied to our department with a 5-year history of left-sided nasal obstruction without history of epistaxis, nasal packaging, or facial trauma. Anterior rhinoscopic examination revealed a mass originating from inferior turbinate that completely obstructs the left nasal cavity. Paranasal computed tomography (CT) showed that the bony mass originated from the anterior part of the left inferior turbinate. Surrounding tissues were normal, and there was not any erosion or destruction. Mass was excised by the endoscopic approach. Histological diagnosis was reported as osseous cavernous hemangioma.Conclusion. Hemangiomas are a rare cause of intranasal masses. Its unusual site and masked presentation makes the differential diagnosis difficult. When a bony hard, well-shaped mass was seen in the nasal cavity, the possibility of intraosseous hemangioma must be remembered.
Worries and Concerns among Inflammatory Bowel Disease Patients Followed Prospectively over One Year
Authors: Jelsness-Jørgensen Lars-Petter , Moum Bjørn , Bernklev Tomm
Published: September 2011

Disease-related worries are frequently reported in inflammatory bowel disease (IBD), but longitudinal assessments of these worries are scarce. In the present study, patients completed the rating form of IBD patient concerns (RFIPC) at three occasions during one year. One-way analysis of variance (ANO VA),t-tests, bivariate correlation, and linear regression analyses were used to analyse data. The validity and reliability of the Norwegian RFIPC was tested. A total of 140 patients were included (V1), ulcerative colitis (UC)n= 92, Crohn's disease (CD)n= 48, mean age 46.9 and 40.0-year old, respectively. The highest rated worries included having an ostomy bag, loss of bowel control, and reduced energy levels. Symptoms were positively associated with more worries. A pattern of IBD-related worries was consistent over a period of one year. Worries about undergoing surgery or having an ostomy bag seemed to persist even when symptoms improved. The Norwegian RFIPC is valid and reliable.
Existence of Positive Periodic Solutions for a Class of n‐Species Competition Systems with Impulses
Authors: Guo Peilian , Liu Yansheng
Published: September 2011

By using the fixed point theorem on cone, some sufficient conditions are obtained on the existence of positive periodic solutions for a class of n‐species competition systems with impulses. Meanwhile, we point out that the conclusion of (Yan, 2009) is incorrect.
Use of Near-Infrared Spectroscopic Analysis of Second Trimester Amniotic Fluid to Assess Preterm Births
Authors: Power Kristin M. , Sanchez-Galan Javier E. , Luskey Gary W. , Koski Kristine G. , Burns David H.
Published: September 2011

This pilot study investigated the possibility that metabolomic differences exist in second trimester of women delivering at term (≥37 weeks,n=216) and preterm (≤35 weeks,n=11). For this retrospective study, biobanked AF samples underwent near-infrared (NIR) spectral analysis using wavelengths from 700 to 1050 nm. Spectral data was compressed then optimized by multilinear regression to create a calibration model. The resultant model was able to classify term and preterm births based on differing AF metabolomic profiles with a sensitivity and specificity of 100%. When groups were classified using a prematurity index (PI), there was a statistical difference (P<0.001) between the predicted preterm group (PI0.77±0.08) and the term group (PI1.00±0.02). In conclusion,the 2ndtrimester AF samples showed distinct differences in metabolomic profiles between patients delivering preterm as compared to those at term in functional groups related to proteins, carbohydrates, fats, polyols, and water.
Changes in Serum S100A12 and sRAGE Associated with Improvement of the PaO2/FiO2 Ratio following PMX-DHP Therapy for Postoperative Septic Shock
Authors: Takahashi G. , Hoshikawa K. , Matsumoto N. , Shozushima T. , Onodera C. , Kan S. , Akitomi S. , Kikkawa T. , Tomisawa Y. , Kojika M. , Sato N. , Inoue Y. , Suzuki K. , Wakabayashi G. , Endo S.
Published: September 2011

Background: Endotoxin (Et) adsorption therapy with a column of polymyxin B-immobilized fibers (PMX) is effective in improving the partial pressure of arterial oxygen/fraction of inspired oxygen ratio (PaO2/FiO2 ratio) and increasing mean arterial blood pressure (MAP) in sepsis. S100A12 and soluble receptor for advanced glycation end product (sRAGE) are useful as early markers of acute lung injury. Purpose: To investigate the effect of improving the PaO2/FiO2 ratio by PMX-direct hemoperfusion (PMX-DHP) on production of S100A12 and sRAGE. Subjects and Methods: Sepsis patients after surgery for perforation of the lower gastrointestinal tract were adopted as the subjects. We retrospectively reviewed the cases of 20 patients on mechanical ventilation and continuous administration of norepinephrine. We recorded PaO2/FiO2 ratio, MAP, and norepinephrine doses. S100A12, sRAGE, and Et levels were measured before and after PMX-DHP. Results: The PaO2/FiO2 ratio and MAP improved significantly after PMX-DHP (p < 0.05). S100A12 and Et decreased significantly after PMX-DHP (p < 0.05). No differences were observed in sRAGE. Conclusion: S100A12 is useful as a marker that reflected improvement in the PaO2/FiO2 ratio after PMX-DHP. We consider PMX-DHP to be useful as adjunctive therapy for sepsis that reduces the Et and corrects the pathology in the early stage.
Lateral self-association of VWF involves the Cys2431-Cys2453 disulfide/dithiol in the C2 domain
Authors: Ganderton Tim , Wong Jason W. H. , Schroeder Christina , Hogg Philip J.
Published: September 2011

VWF is a plasma protein that binds platelets to an injured vascular wall during thrombosis. When exposed to the shear forces found in flowing blood, VWF molecules undergo lateral self-association that results in a meshwork of VWF fibers. Fiber formation has been shown to involve thiol/disulfide exchange between VWF molecules. A C-terminal fragment of VWF was expressed in mammalian cells and examined for unpaired cysteine thiols using tandem mass spectrometry (MS). The VWF C2 domain Cys2431-Cys2453 disulfide bond was shown to be reduced in approximately 75% of the molecules. Fragments containing all 3 C domains or just the C2 domain formed monomers, dimers, and higher-order oligomers when expressed in mammalian cells. Mutagenesis studies showed that both the Cys2431-Cys2453 and nearby Cys2451-Cys2468 disulfide bonds were involved in oligomer formation. Our present findings imply that lateral VWF dimers form when a Cys2431 thiolate anion attacks the Cys2431 sulfur atom of the Cys2431-Cys2453 disulfide bond of another VWF molecule, whereas the Cys2451-Cys2468 disulfide/dithiol mediates formation of trimers and higher-order oligomers. These observations provide the basis for exploring defects in lateral VWF association in patients with unexplained hemorrhage or thrombosis.
Selection of organisms for the co-evolution-based study of protein interactions
Authors: Herman Dorota , Ochoa David , Juan David , Lopez Daniel , Valencia Alfonso , Pazos Florencio
Published: September 2011

Background

The prediction and study of protein interactions and functional relationships based on similarity of phylogenetic trees, exemplified by the mirrortree and related methodologies, is being widely used. Although dependence between the performance of these methods and the set of organisms used to build the trees was suspected, so far nobody assessed it in an exhaustive way, and, in general, previous works used as many organisms as possible. In this work we asses the effect of using different sets of organism (chosen according with various phylogenetic criteria) on the performance of this methodology in detecting protein interactions of different nature.

Results

We show that the performance of three mirrortree-related methodologies depends on the set of organisms used for building the trees, and it is not always directly related to the number of organisms in a simple way. Certain subsets of organisms seem to be more suitable for the predictions of certain types of interactions. This relationship between type of interaction and optimal set of organism for detecting them makes sense in the light of the phylogenetic distribution of the organisms and the nature of the interactions.

Conclusions

In order to obtain an optimal performance when predicting protein interactions, it is recommended to use different sets of organisms depending on the available computational resources and data, as well as the type of interactions of interest.