bluuebunny/crossref_metadata_2025 huggingface dataset:
Amino Acids 1055 to 1192 in the S2 Region of Severe Acute Respiratory Syndrome Coronavirus S Protein Induce Neutralizing Antibodies: Implications for the Development of Vaccines and Antiviral Agents
Authors: Keng Choong-Tat , Zhang Aihua , Shen Shuo , Lip Kuo-Ming , Fielding Burtram C. , Tan Timothy H. P. , Chou Chih-Fong , Loh Chay Boon , Wang Sifang , Fu Jianlin , Yang Xiaoming , Lim Seng Gee , Hong Wanjin , Tan Yee-Joo
Published: February 2005

The spike (S) protein of the severe acute respiratory syndrome coronavirus (SARS-CoV) interacts with cellular receptors to mediate membrane fusion, allowing viral entry into host cells; hence it is recognized as the primary target of neutralizing antibodies, and therefore knowledge of antigenic determinants that can elicit neutralizing antibodies could be beneficial for the development of a protective vaccine. Here, we expressed five different fragments of S, covering the entire ectodomain (amino acids 48 to 1192), as glutathione
S
-transferase fusion proteins in
Escherichia coli
and used the purified proteins to raise antibodies in rabbits. By Western blot analysis and immunoprecipitation experiments, we showed that all the antibodies are specific and highly sensitive to both the native and denatured forms of the full-length S protein expressed in virus-infected cells and transfected cells, respectively. Indirect immunofluorescence performed on fixed but unpermeabilized cells showed that these antibodies can recognize the mature form of S on the cell surface. All the antibodies were also able to detect the maturation of the 200-kDa form of S to the 210-kDa form by pulse-chase experiments. When the antibodies were tested for their ability to inhibit SARS-CoV propagation in Vero E6 culture, it was found that the anti-SΔ10 antibody, which was targeted to amino acid residues 1029 to 1192 of S, which include heptad repeat 2, has strong neutralizing activities, suggesting that this region of S carries neutralizing epitopes and is very important for virus entry into cells.
Protection of Rhesus Monkeys against Infection with Minimally Pathogenic Simian-Human Immunodeficiency Virus: Correlations with Neutralizing Antibodies and Cytotoxic T Cells
Authors: Quinnan Gerald V. , Yu Xiao-Fang , Lewis Mark G. , Zhang Peng Fei , Sutter Gerd , Silvera Peter , Dong Ming , Choudhary Anil , Sarkis Phuong T. N. , Bouma Peter , Zhang Zhiqiang , Montefiori David C. , VanCott Thomas C. , Broder Christopher C.
Published: February 2005

We studied the capacity of active immunization of rhesus monkeys with HIV-1 envelope protein (Env) to induce primary virus cross-reactive neutralizing antibodies to prevent infection following intravenous challenge with simian-human immunodeficiency virus (SHIV). Monkeys were immunized with the human immunodeficiency type 1 (HIV-1) strain R2 Env. Initially, the Env was expressed in vivo by an alphavirus replicon particle system, and then it was administered as soluble oligomeric gp140. Concurrently, groups of monkeys received expression vectors that encoded either simian immunodeficiency virus (SIV)
gag
/
pol
genes or no SIV genes in vivo to test the additional protective benefit of concurrent induction of virus-specific cell-mediated immune (CMI) responses. Groups of control monkeys received either the
gag
/
pol
regimen or sham immunizations. The antibodies induced by the Env immunization regimen neutralized diverse primary HIV-1 strains. Similarly, potent CMI responses were induced by the
gag
/
pol
regimen, as measured by gamma interferon enzyme-linked immunospot assays. Differences in the responses among groups of monkeys strongly suggested that there was interference between the Env and g
ag
/
pol
immunization regimens. Complete protection of some of the monkeys against infection after intravenous challenge with the partially pathogenic SHIV
DH12R (Clone 7)
was associated independently with both neutralizing antibody and CMI responses. Protection was associated with SHIV
DH12 (Clone 7)
serum neutralizing antibody titers of ≥1:80 or with cellular immune responses corresponding to >2,000 spot forming cells per 10
6
peripheral blood mononuclear cells. Immunization was also associated with a reduction in the magnitude and duration of virus load. Induction of cross-reactive, primary HIV-1-neutralizing antibodies is feasible and, when potent, may result in complete protection against infection with a heterologous challenge virus strain.
A Noninfectious Simian/Human Immunodeficiency Virus DNA Vaccine That Protects Macaques against AIDS
Authors: Singh Dinesh K. , Liu Zhenqian , Sheffer Darlene , Mackay Glenn A. , Smith Marilyn , Dhillon Sukhbir , Hegde Ramakrishna , Jia Fenglan , Adany Istvan , Narayan Opendra
Published: February 2005

Simian/human immunodeficiency virus SHIV
KU2
replicates with extremely high titers in macaques. In order to determine whether the DNA of the viral genome could be used as a vaccine if the DNA were rendered noninfectious, we deleted the reverse transcriptase gene from SHIV
KU2
and inserted this DNA (Δ
rt
SHIV
KU2
) into a plasmid that was then used to test gene expression and immunogenicity. Transfection of Jurkat and human embryonic kidney epithelial (HEK 293) cells with the DNA resulted in production of all of the major viral proteins and their precursors and transient export of a large quantity of the Gag p27 into the supernatant fluid. As expected, no infectious virus was produced in these cultures. Four macaques were injected intradermally with 2 mg of the DNA at 0, 8, and 18 weeks. The animals developed neutralizing antibodies and low enzyme-linked immunospot assay (E-SPOT) titers against SHIV
KU2
. These four animals and two unvaccinated control animals were then challenged with heterologous SHIV89.6P administered into their rectums. The two control animals developed viral RNA titers exceeding 10
6
copies/ml of plasma, and these titers were accompanied by the loss of CD4
+
T cells by 2 weeks after challenge. The two control animals died at weeks 8 and 16, respectively. All four of the immunized animals became infected with the challenge virus but developed lower titers of viral RNA in plasma than the control animals, and the titers decreased over time in three of the four macaques. The fourth animal remained viremic and died at week 47. Whereas the control animals failed to develop E-SPOT responses, all four of the immunized animals developed anamnestic E-SPOT responses after challenge. The animal that died developed the highest E-SPOT response and was the only one that produced neutralizing antibodies against the challenge virus. These results established that noninfectious DNA of pathogenic SHIV could be used as a vaccine to prevent AIDS, even though the immunological assays used did not predict the manner in which the challenge virus would replicate in the vaccinated animals.
Glycoprotein M Is an Essential Lytic Replication Protein of the Murine Gammaherpesvirus 68
Authors: May Janet S. , Colaco Susanna , Stevenson Philip G.
Published: February 2005

All herpesviruses encode a homolog of glycoprotein M (gM), which appears to function in virion morphogenesis. Despite its conservation, gM is inessential for the lytic replication of alphaherpesviruses. In order to address the importance of gM in gammaherpesviruses, we disrupted it in the murine gammaherpesvirus 68 (MHV-68). The mutant virus completely failed to propagate in normally permissive fibroblasts. The defective genome was rescued by either homologous recombination to restore the wild-type gM in situ or the insertion of an ectopic, intergenic expression cassette encoding gM into the viral genome. Thus, gM was essential for the lytic replication of MHV-68.
Complex Formation among Murine Cytomegalovirus US22 Proteins Encoded by Genes M139, M140, and M141
Authors: Karabekian Zaruhi , Hanson Laura K. , Slater Jacquelyn S. , Krishna Neel K. , Bolin Lisa L. , Kerry Julie A. , Campbell Ann E.
Published: February 2005

The murine cytomegalovirus (MCMV) proteins encoded by US22 genes M139, M140, and M141 function, at least in part, to regulate replication of this virus in macrophages. Mutant MCMV having one or more of these genes deleted replicates poorly in macrophages in culture and in the macrophage-dense environment of the spleen. In this report, we demonstrate the existence of stable complexes formed by the products of all three of these US22 genes, as well as a complex composed of the products of M140 and M141. These complexes form in the absence of other viral proteins; however, the pM140/pM141 complex serves as a requisite binding partner for the M139 gene products. Products from all three genes colocalize to a perinuclear region of the cell juxtaposed to or within the
cis
-Golgi region but excluded from the
trans
-Golgi region. Interestingly, expression of pM141 redirects pM140 from its predominantly nuclear residence to the perinuclear, cytoplasmic locale where these US22 proteins apparently exist in complex. Thus, complexing of these nonessential, early MCMV proteins likely confers a function(s) independent of each individual protein and important for optimal replication of MCMV in its natural host.
Large-Scale Molecular Characterization of Adeno-Associated Virus Vector Integration in Mouse Liver
Authors: Nakai Hiroyuki , Wu Xiaolin , Fuess Sally , Storm Theresa A. , Munroe David , Montini Eugenio , Burgess Shawn M. , Grompe Markus , Kay Mark A.
Published: February 2005

Recombinant adeno-associated virus (rAAV) vector holds promise for gene therapy. Despite a low frequency of chromosomal integration of vector genomes, recent studies have raised concerns about the risk of rAAV integration because integration occurs preferentially in genes and accompanies chromosomal deletions, which may lead to loss-of-function insertional mutagenesis. Here, by analyzing 347 rAAV integrations in mice, we elucidate novel features of rAAV integration: the presence of hot spots for integration and a strong preference for integrating near gene regulatory sequences. The most prominent hot spot was a harmless chromosomal niche in the rRNA gene repeats, whereas nearly half of the integrations landed near transcription start sites or CpG islands, suggesting the possibility of activating flanking cellular disease genes by vector integration, similar to retroviral gain-of-function insertional mutagenesis. Possible cancer-related genes were hit by rAAV integration at a frequency of 3.5%. In addition, the information about chromosomal changes at 218 integration sites and 602 breakpoints of vector genomes have provided a clue to how vector terminal repeats and host chromosomal DNA are joined in the integration process. Thus, the present study provides new insights into the risk of rAAV-mediated insertional mutagenesis and the mechanisms of rAAV integration.
BAYESIAN NETWORK LEARNING WITH FEATURE ABSTRACTION FOR GENE-DRUG DEPENDENCY ANALYSIS
Authors: CHANG JEONG-HO , HWANG KYU-BAEK , JUNE OH S. , ZHANG BYOUNG-TAK
Published: February 2005

Combined analysis of the microarray and drug-activity datasets has the potential of revealing valuable knowledge about various relations among gene expressions and drug activities in the malignant cell. In this paper, we apply Bayesian networks, a tool for compact representation of the joint probability distribution, to such analysis. For the alleviation of data dimensionality problem, the huge datasets were condensed using a feature abstraction technique. The proposed analysis method was applied to the NCI60 dataset () consisting of gene expression profiles and drug activity patterns on human cancer cell lines. The Bayesian networks, learned from the condensed dataset, identified most of the salient pairwise correlations and some known relationships among several features in the original dataset, confirming the effectiveness of the proposed feature abstraction method. Also, a survey of the recent literature confirms the several relationships appearing in the learned Bayesian network to be biologically meaningful.
PROTEIN SIDE-CHAIN PACKING PROBLEM: A MAXIMUM EDGE-WEIGHT CLIQUE ALGORITHMIC APPROACH
Authors: DUKKA BAHADUR K. C. , TOMITA ETSUJI , SUZUKI JUN'ICHI , AKUTSU TATSUYA
Published: February 2005

"Protein Side-chain Packing" has an ever-increasing application in the field of bio-informatics, dating from the early methods of homology modeling to protein design and to the protein docking. However, this problem is computationally known to be NP-hard.

In this regard, we have developed a novel approach to solve this problem using the notion of a maximum edge-weight clique. Our approach is based on efficient reduction of protein side-chain packing problem to a graph and then solving the reduced graph to find the maximum clique by applying an efficient clique finding algorithm developed by our co-authors. Since our approach is based on deterministic algorithms in contrast to the various existing algorithms based on heuristic approaches, our algorithm guarantees of finding an optimal solution.

We have tested this approach to predict the side-chain conformations of a set of proteins and have compared the results with other existing methods. We have found that our results are favorably comparable or better than the results produced by the existing methods. As our test set contains a protein of 494 residues, we have obtained considerable improvement in terms of size of the proteins and in terms of the efficiency and the accuracy of prediction.
ACTIVE SITE PREDICTION FOR COMPARATIVE MODEL STRUCTURES WITH THEMATICS
Authors: SHEHADI IHSAN A. , ABYZOV ALEXEJ , UZUN ALPER , WEI YING , MURGA LEONEL F. , ILYIN VALENTIN , ONDRECHEN MARY JO
Published: February 2005

THEMATICS (Theoretical Microscopic Titration Curves) is a simple, reliable computational predictor of the active sites of enzymes from structure. Our method, based on well-established Finite Difference Poisson–Boltzmann techniques, identifies the ionisable residues with anomalous predicted titration behavior. A cluster of two or more such perturbed residues is a very reliable predictor of the active site. The protein does not have to bear any resemblance in sequence or structure to any previously characterized protein, but the method does require the three-dimensional structure. We now present evidence that THEMATICS can also locate the active site in structures built by comparative modeling from similar structures. Results are given for a total of 21 sets of proteins, including 21 templates and 83 comparative model structures. Detailed results are presented for three sets of orthologous proteins (Triosephosphate isomerase, 6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase, and Aspartate aminotransferase) and for one set of human homologues of Aldose reductase with different functions. THEMATICS correctly locates the active site in the model structures. This suggests that the method can be applicable to a much larger set of proteins for which an experimentally determined structure is unavailable. With a few exceptions, the predicted active sites in the comparative model structures are similar to that of the corresponding template structure.
A TABU SEARCH ALGORITHM FOR POST-PROCESSING MULTIPLE SEQUENCE ALIGNMENT
Authors: RIAZ TARIQ , YI WANG , LI KUO-BIN
Published: February 2005

Tabu search is a meta-heuristic approach that is proven to be useful in solving combinatorial optimization problems. We implement the adaptive memory features of tabu search to refine a multiple sequence alignment. Adaptive memory helps the search process to avoid local optima and explores the solution space economically and effectively without getting trapped into cycles. The algorithm is further enhanced by introducing extended tabu search features such as intensification and diversification. The neighborhoods of a solution are generated stochastically and a consistency-based objective function is employed to measure its quality. The algorithm is tested with the datasets from BAliBASE benchmarking database. We have observed through experiments that tabu search is able to improve the quality of multiple alignments generated by other software such as ClustalW and T-Coffee. The source code of our algorithm is available at .
INTEGRATION OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY TO UNDERSTAND PROTEIN-DNA RECOGNITION MECHANISM
Authors: SARAI AKINORI , SIEBERS JORG , SELVARAJ SAMUEL , GROMIHA M. MICHAEL , KONO HIDETOSHI
Published: February 2005

Transcription factors play essential role in the gene regulation in higher organisms, binding to multiple target sequences and regulating multiple genes in a complex manner. In order to decipher the mechanism of gene regulation, it is important to understand the molecular mechanism of protein-DNA recognition. Here we describe a strategy to approach this problem, using various methods in bioinformatics and computational biology. We have used a knowledge-based approach, utilizing rapidly increasing structural data of protein-DNA complexes, to derive empirical potential functions for the specific interactions between bases and amino acids as well as for DNA conformation, from the statistical analyses on the structural data. Then these statistical potentials are used to quantify the specificity of protein-DNA recognition. The quantification of specificity has enabled us to establish the structure-function analysis of transcription factors, such as the effects of binding cooperativity on target recognition. The method is also applied to real genome sequences, predicting potential target sites. We are also using computer simulations of protein-DNA interactions and DNA conformation in order to complement the empirical method. The integration of these approaches together will provide deeper insight into the mechanism of protein-DNA recognition and improve the target prediction of transcription factors.
EFFICIENT CONSTRAINED MULTIPLE SEQUENCE ALIGNMENT WITH PERFORMANCE GUARANTEE
Authors: CHIN FRANCIS Y. L. , HO N. L. , LAM T. W. , WONG PRUDENCE W. H.
Published: February 2005

The constrained multiple sequence alignment problem is to align a set of sequences of maximum length n subject to a given constrained sequence, which arises from some knowledge of the structure of the sequences. This paper presents new algorithms for this problem, which are more efficient in terms of time and space (memory) than the previous algorithms,15 and with a worst-case guarantee on the quality of the alignment. Saving the space requirement by a quadratic factor is particularly significant as the previous O(n4)-space algorithm has limited application due to its huge memory requirement. Experiments on real data sets confirm that our new algorithms show improvements in both alignment quality and resource requirements.
LPA2 receptor mediates mitogenic signals in human colon cancer cells
Authors: Yun C. Chris , Sun Hong , Wang Dongsheng , Rusovici Raluca , Castleberry Amanda , Hall Randy A. , Shim Hyunsuk
Published: February 2005

Lysophosphatidic acid (LPA) is a mediator of multiple cellular responses. LPA mediates its effects predominantly through the G protein-coupled receptors LPA1, LPA2, and LPA3. In the present work, we studied LPA2-mediated signaling using human colon cancer cell lines, which predominantly express LPA2. LPA2 activated Akt and Erk1/2 in response to LPA. LPA mediated Akt activation was inhibited by pertussis toxin (PTX), whereas Erk1/2 activation was completely inhibited by a blocker of phospholipase Cβ, U-73122. LPA also induced interleukin-8 (IL-8) synthesis in the colon cancer cells by primarily activating LPA2 receptor. We also found that LPA2 interacts with Na+/H+ exchanger regulatory factor 2 (NHERF2). Activation of Akt and Erk1/2 was significantly attenuated by silencing of NHERF2 expression by RNA interference, suggesting a pivotal role of NHERF2 in LPA2-mediated signaling. We found that expression of LPA2 was elevated, whereas expression of LPA1 downregulated in several types of cancers, including ovarian and colon cancer. We conclude that LPA2 is the major LPA receptor in colon cancer cells and cellular signals by LPA2 are largely mediated through its ability to interact with NHERF2.
Contrast and Temporal Frequency-Related Adaptation in the Pretectal Nucleus of the Optic Tract
Authors: Ibbotson M. R.
Published: February 2005

In mammals, many cells in the retino-geniculate-cortical pathway adapt during stimulation with high contrast gratings. In the visual cortex, adaptation to high contrast images reduces sensitivity at low contrasts while only moderately affecting sensitivity at high contrasts, thus generating rightward shifts in the contrast response functions (contrast gain control). Similarly, motion adaptation at particular temporal frequencies (TFs) alters the temporal tuning properties of cortical cells. For the first time in any species, this paper investigates the influence of motion adaptation on both the contrast and TF responses of neurons in the retino-pretectal pathway by recording from direction-selective neurons in the nucleus of the optic tract (NOT) of the marsupial wallaby, Macropus eugenii. This species is of interest because its NOT receives almost all input directly from the retina, with virtually none from the visual cortex (unlike cats and primates). All NOT cells show changes in their contrast response functions after adaptation, many revealing contrast gain control. Contrast adaptation is direction-dependent, preferred directions producing the largest changes. The lack of cortical input suggests that contrast adaptation is generated independently from the cortex in the NOT or retina. Motion adaptation also produces direction-selective effects on the TF tuning of NOT neurons by shifting the location of the optimum TF. Cells that show strong adaptation to contrast also tend to show large changes in TF tuning, suggesting similar intracellular mechanisms. The data are discussed in terms of the generality of contrast adaptation across mammalian species and across unconnected brain regions within the same species.
Countermanding Eye-Head Gaze Shifts in Humans: Marching Orders Are Delivered to the Head First
Authors: Corneil Brian D. , Elsley James K.
Published: February 2005

The countermanding task requires subjects to cancel a planned movement on appearance of a stop signal, providing insights into response generation and suppression. Here, we studied human eye-head gaze shifts in a countermanding task with targets located beyond the horizontal oculomotor range. Consistent with head-restrained saccadic countermanding studies, the proportion of gaze shifts on stop trials increased the longer the stop signal was delayed after target presentation, and gaze shift stop-signal reaction times (SSRTs: a derived statistic measuring how long it takes to cancel a movement) averaged ∼120 ms across seven subjects. We also observed a marked proportion of trials (13% of all stop trials) during which gaze remained stable but the head moved toward the target. Such head movements were more common at intermediate stop signal delays. We never observed the converse sequence wherein gaze moved while the head remained stable. SSRTs for head movements averaged ∼190 ms or ∼70–75 ms longer than gaze SSRTs. Although our findings are inconsistent with a single race to threshold as proposed for controlling saccadic eye movements, movement parameters on stop trials attested to interactions consistent with a race model architecture. To explain our data, we tested two extensions to the saccadic race model. The first assumed that gaze shifts and head movements are controlled by parallel but independent races. The second model assumed that gaze shifts and head movements are controlled by a single race, preceded by terminal ballistic intervals not under inhibitory control, and that the head-movement branch is activated at a lower threshold. Although simulations of both models produced acceptable fits to the empirical data, we favor the second alternative as it is more parsimonious with recent findings in the oculomotor system. Using the second model, estimates for gaze and head ballistic intervals were ∼25 and 90 ms, respectively, consistent with the known physiology of the final motor paths. Further, the threshold of the head movement branch was estimated to be 85% of that required to activate gaze shifts. From these results, we conclude that a commitment to a head movement is made in advance of gaze shifts and that the comparative SSRT differences result primarily from biomechanical differences inherent to eye and head motion.
Recommendations for Blood Pressure Measurement in Humans and Experimental Animals
Authors: Kurtz Theodore W. , Griffin Karen A. , Bidani Anil K. , Davisson Robin L. , Hall John E.
Published: February 2005

In experimental animals, as in humans, techniques for measuring blood pressure (BP) have improved considerably over the past decade. In this document, we present recommendations for measuring BP in experimental animals with the goal of helping investigators select optimal methods for BP monitoring in the research laboratory. The advantages and disadvantages of various BP measurement methods are discussed and specific recommendations are provided for selecting the optimal technique depending on the study objective. Although indirect techniques that permit only sporadic measurements of BP may be suitable for some purposes, methods for directly measuring BP are generally preferred because of their ability to monitor the highly dynamic nature of BP in a comprehensive fashion. Selection of the methods to be used should ultimately be guided by the study objectives to insure that the techniques chosen are appropriate for the experimental questions being explored.
Can Zipf's law be adapted to normalize microarrays?
Authors: Lu Tim , Costello Christine M , Croucher Peter JP , Häsler Robert , Deuschl Günther , Schreiber Stefan
Published: February 2005

Background

Normalization is the process of removing non-biological sources of variation between array experiments. Recent investigations of data in gene expression databases for varying organisms and tissues have shown that the majority of expressed genes exhibit a power-law distribution with an exponent close to -1 (i.e. obey Zipf's law). Based on the observation that our single channel and two channel microarray data sets also followed a power-law distribution, we were motivated to develop a normalization method based on this law, and examine how it compares with existing published techniques. A computationally simple and intuitively appealing technique based on this observation is presented.

Results

Using pairwise comparisons using MA plots (log ratio vs. log intensity), we compared this novel method to previously published normalization techniques, namely global normalization to the mean, the quantile method, and a variation on the loess normalization method designed specifically for boutique microarrays. Results indicated that, for single channel microarrays, the quantile method was superior with regard to eliminating intensity-dependent effects (banana curves), but Zipf's law normalization does minimize this effect by rotating the data distribution such that the maximal number of data points lie on the zero of the log ratio axis. For two channel boutique microarrays, the Zipf's law normalizations performed as well as, or better than existing techniques.

Conclusion

Zipf's law normalization is a useful tool where the Quantile method cannot be applied, as is the case with microarrays containing functionally specific gene sets (boutique arrays).
Individual patient data meta-analysis : Cervical stitch (cerclage) for preventing pregnancy loss in women
Authors: Tudur-Smith Catrin , Jorgensen Andrea L , Alfirevic Zarko , Williamson Paula R
Published: February 2005

Background

Cervical cerclage is a surgical procedure involving suturing the cervix with a purse type stitch to keep it closed during pregnancy. This procedure has been used widely in the management of pregnancies considered at high risk of preterm delivery. Several observational studies into the efficacy of cervical cerclage have claimed high rates of successful pregnancy outcome in women with a poor obstetric history attributed to cervical incompetence. However, a recent aggregate data Cochrane review found no such conclusive evidence from seven included randomised studies. Current data suggests that cervical cerclage is likely to benefit women considered to be 'at very high risk' of a second trimester miscarriage due to a cervical factor, however identifying such women remains elusive and many women may be treated unnecessarily. Undertaking an individual patient data (IPD) meta-analysis of the studies will allow us to investigate whether treatment is more effective in particular subgroups. Such an analysis will also provide a more powerful analysis of the predictors of preterm delivery and pregnancy loss, including ultrasound measurement of cervical length, and will allow a more complete analysis of 'time to event' outcomes.

Methods/Design

The analysis will include data from randomised trials comparing the intervention of elective cerclage versus no cerclage or bedrest to prevent miscarriage or pre-term labour. A specific list of data will be requested for each trial, including demographic and obstetric history data. The primary outcomes of interest will be neonatal mortality/morbidity. Attention will also be given to secondary outcomes such as time from randomisation to delivery, preterm delivery before 32 weeks and maternal morbidity. An intention to treat analysis will be performed, with attention paid to assessing clinical and statistical heterogeneity. Multilevel models with patients and trials as the two levels will be explored to investigate treatment effect on various outcomes. Patient-level covariates will be incorporated into the models in an attempt to account for statistical heterogeneity as well as to investigate interactions with treatment effect.

Discussion

Predictive models generated from our analysis should lead to more effective counselling of women at risk and a more cost effective use of cerclage.
Role of Infection in In Vitro Fertilization Treatment
Authors: COCCIA M E , CAMMILLI F , GINOCCHIONI L , RIZZELLO F
Published: February 2005

Abstract: With the increasing demand for assisted reproductive techniques (ARTs), it is important to consider how to manage infection. Three main positive factors that contribute to successful in vitro fertilization (IVF) cycles are maternal age, the ovarian hyperstimulation protocol used, and the number and quality of transferred embryos. Negative factors include contamination and infection. This paper describes the issues relating to infection during IVF and proposes guidelines to control infection and to increase laboratory safety.
Effects of Vaginal Progesterone on Pain and Uterine Contractility in Patients with Threatened Abortion before Twelve Weeks of Pregnancy
Authors: PALAGIANO A , BULLETTI C , PACE M C , DE ZIEGLER D , CICINELLI E , IZZO A
Published: February 2005

Abstract: Fifty women with previous diagnosis of inadequate luteal phase and threatened abortion underwent a prospective, randomized, double‐blind study in one medical center carried out with a parallel trial. The primary objective was to establish the effects of vaginal progesterone (Crinone 8%) in reducing both pain and uterine contractions (UCs). The gel with or without (placebo) vaginal progesterone was administered once a day since the diagnosis of threatened abortion and for 5 days. The efficacy on pain symptom amelioration was evaluated by a 5‐score intensity gradation, while the UCs were evaluated by ultrasound. The secondary objective of the study was to evaluate the outcome of the pregnancies. The use of progesterone was effective both on pain relief and on the frequency of the UCs that decreased after 5 days of vaginal progesterone administration (P < 0.005). The evaluation of the ongoing pregnancy and spontaneous abortion in both study groups after 60 days showed that 4 patients of group A and 8 patients of group B miscarried (P < 0.05). In conclusion, patients with threatened abortion benefit from vaginal progesterone by a reduction of UCs and pain. The use of vaginal progesterone improved the outcome of pregnancies complicated by threatened abortion and previous diagnosis of inadequate luteal phase.
Differential Effects of Lipopolysaccharide and Thrombin on Interleukin‐8 Expression in Syncytiotrophoblasts and Endothelial Cells: Implications for Fetal Survival
Authors: MA YUEHONG , KADNER SUSAN S. , GULLER SETH
Published: February 2005

Abstract: Syncytiotrophoblasts (SCTs) are directly bathed by maternal blood and, as such, are in direct contact with proinflammatory stimuli present in the maternal circulation. The extent and nature of cytokine responses induced in SCTs play a central role in the maintenance of pregnancy. Thrombin is a critical mediator of tissue factor‐initiated blood coagulation. Thrombin has been more recently demonstrated to induce cytokine expression and inflammation in several cell types. To dissect the patterns of regulation of cytokine production in the placental villus, we compared the effects of thrombin and lipopolysaccharide (LPS) treatments on cytokine expression in SCTs and endothelial cells. For studies, primary cultures of cytotrophoblasts from human term placentas were differentiated to SCTs. We observed that the presence of thrombin only modestly enhanced interleukin‐8 (IL‐8) levels in SCTs in a manner that was not dose‐dependent. Conversely, SCTs were exquisitely sensitive to LPS, the presence of which induced approximately a 10‐fold increase in IL‐8 levels with an EC50∼ 1 ng/mL. Northern blotting and real‐time PCR results indicated that LPS (but not thrombin) treatment induced a >4‐fold increase in levels of IL‐8 mRNA. The addition of the anti‐inflammatory steroid, dexamethasone, significantly reduced the LPS‐mediated increase in levels of IL‐8 in SCTs. Conversely, in human umbilical vein endothelial cells, thrombin and LPS treatments induced 10‐ and 20‐fold increases in IL‐8 expression, respectively. These results indicate that LPS, but not thrombin, promotes proinflammatory processes in SCTs, with cell‐type specificity. The inability of thrombin in the intervillous space to evoke inflammatory responses in SCTs may constitute an important aspect of fetal survival. Conversely, our results suggest that SCTs do play a key role in infection‐associated changes in placental cytokine expression.
Roles of cell-adhesion molecules nectin 1 and nectin 3 in ciliary body development
Authors: Inagaki Maiko , Irie Kenji , Ishizaki Hiroyoshi , Tanaka-Okamoto Miki , Morimoto Koji , Inoue Eiji , Ohtsuka Toshihisa , Miyoshi Jun , Takai Yoshimi
Published: February 2005

Nectins are Ca2+-independent immunoglobulin-like cell-cell-adhesion molecules consisting of four members. Nectins homophilically and heterophilically trans-interact to form a variety of cell-cell junctions, including cadherin-based adherens junctions in epithelial cells and fibroblasts in culture, synaptic junctions in neurons, and Sertoli cell-spermatid junctions in the testis, in cooperation with, or independently of, cadherins. To further explore the function of nectins, we generated nectin 1–/– and nectin 3–/– mice. Both nectin 1–/– and nectin 3–/– mice showed a virtually identical ocular phenotype, microphthalmia, accompanied by a separation of the apex-apex contact between the pigment and non-pigment cell layers of the ciliary epithelia. Immunofluorescence and immunoelectron microscopy revealed that nectin 1 and nectin 3, but not nectin 2, localized at the apex-apex junctions between the pigment and non-pigment cell layers of the ciliary epithelia. However, nectin 1–/– and nectin 3–/– mice showed no impairment of the apicolateral junctions between the pigment epithelia where nectin 1, nectin 2 and nectin 3 localized, or of the apicolateral junctions between the non-pigment epithelia where nectin 2 and nectin 3, but not nectin 1, localized. These results indicate that the heterophilic trans-interaction between nectin 1 and nectin 3 plays a sentinel role in establishing the apex-apex adhesion between the pigment and non-pigment cell layers of the ciliary epithelia that is essential for the morphogenesis of the ciliary body.
Genetics of shoulder girdle formation: roles of Tbx15 and aristaless-like genes
Authors: Kuijper Sanne , Beverdam Annemiek , Kroon Carla , Brouwer Antje , Candille Sophie , Barsh Gregory , Meijlink Frits
Published: February 2005

The diverse cellular contributions to the skeletal elements of the vertebrate shoulder and pelvic girdles during embryonic development complicate the study of their patterning. Research in avian embryos has recently clarified part of the embryological basis of shoulder formation. Although dermomyotomal cells provide the progenitors of the scapular blade, local signals appear to have an essential guiding role in this process. These signals differ from those that are known to pattern the more distal appendicular skeleton. We have studied the impact of Tbx15, Gli3, Alx4 and related genes on formation of the skeletal elements of the mouse shoulder and pelvic girdles. We observed severe reduction of the scapula in double and triple mutants of these genes. Analyses of a range of complex genotypes revealed aspects of their genetic relationship, as well as functions that had been previously masked due to functional redundancy. Tbx15 and Gli3 appear to have synergistic functions in formation of the scapular blade. Scapular truncation in triple mutants of Tbx15, Alx4 and Cart1indicates essential functions for Alx4 and Cart1 in the anterior part of the scapula, as opposed to Gli3 function being linked to the posterior part. Especially in Alx4/Cart1 mutants, the expression of markers such as Pax1, Pax3 and Scleraxis is altered prior to stages when anatomical aberrations are visible in the shoulder region. This suggests a disorganization of the proximal limb bud and adjacent flank mesoderm, and is likely to reflect the disruption of a mechanism providing positional cues to guide progenitor cells to their destination in the pectoral girdle.
Band 3 modifications inPlasmodium falciparum-infected AA and CC erythrocytes assayed by autocorrelation analysis using quantum dots
Authors: Tokumasu Fuyuki , Fairhurst Rick M. , Ostera Graciela R. , Brittain Nathaniel J. , Hwang Jeeseong , Wellems Thomas E. , Dvorak James A.
Published: February 2005

The molecular stability of hemoglobin is critical for normal erythrocyte functions, including oxygen transport. Hemoglobin C (HbC) is a mutant hemoglobin that has increased oxidative susceptibility due to an amino acid substitution (β6: Glu to Lys). The growth of Plasmodium falciparum is abnormal in homozygous CC erythrocytes in vitro, and CC individuals show innate protection against severe P. falciparum malaria. We investigated one possible mechanism of innate protection using a quantum dot technique to compare the distribution of host membrane band 3 molecules in genotypically normal (AA) to CC erythrocytes. The high photostability of quantum dots facilitated the construction of 3D cell images and the quantification of fluorescent signal intensity. Power spectra and 1D autocorrelation analyses showed band 3 clusters on the surface of infected AA and CC erythrocytes. These clusters became larger as the parasites matured and were more abundant in CC erythrocytes. Further, average cluster size (500 nm) in uninfected (native) CC erythrocytes was comparable with that of parasitized AA erythrocytes but was significantly larger (1 μm) in parasitized CC erythrocytes. Increased band 3 clustering may enhance recognition sites for autoantibodies, which could contribute to the protective effect of hemoglobin C against malaria.
PML bodies: a meeting place for genomic loci?
Authors: Ching Reagan W. , Dellaire Graham , Eskiw Christopher H. , Bazett-Jones David P.
Published: February 2005

Promyelocytic leukemia (PML) bodies have been implicated in a variety of cellular processes, such as cell-cycle regulation, apoptosis, proteolysis, tumor suppression, DNA repair and transcription. Despite this, the function of PML bodies is still unknown. Direct and indirect evidence supports the hypothesis that PML bodies interact with specific genes or genomic loci. This includes the finding that the stability of PML bodies is affected by cell stress and changes in chromatin structure. PML bodies also facilitate the transcription and replication of double-stranded DNA viral genomes. Moreover, PML bodies associate with specific regions of high transcriptional activity in the cellular genome. We propose that PML bodies functionally interact with chromatin and are important for the regulation of gene expression.
A comparative study on the degradation of cotton linters induced by carbonate and hydroxyl radicals generated from peroxynitrite
Authors: Carlsson Magnus , Stenman David , Merényi Gábor , Reitberger Torbjörn
Published: February 2005

Carbonate (CO3
•−) and hydroxyl (HO•) radicals were chemically produced in cotton linter suspensions using peroxynitrite as a radical precursor. Both radicals could degrade cotton linters, as shown by viscosity and GPC-SEC measurements. As evidenced by the viscosity measurements, the presence of oxygen during the cotton linter treatments slightly increased cellulose degradation by both radicals. For the carbonate radical, more than 90% of the viscosity losses could be recovered by reductive NaBH4 treatment before measuring the viscosity, whereas only approximately 40% of the viscosity was recovered after hydroxyl radical degradation and subsequent NaBH4 treatment. This indicates that carbonate radicals mainly abstract H-atoms adjacent to hydroxyl groups, i.e., at C2, C3 and C6. This intramolecular selectivity may reflect a polar effect, whereby hydrogen atom abstractions from these positions are favoured. In addition, abstraction at C6 would be sterically and statistically favoured.
Biomechanical pulping of spruce wood chips with Streptomyces cyaneus CECT 3335 and handsheet characterization
Authors: Hernández Manuel , Hernández-Coronado M. Jesus , Pérez M. Isabel , Revilla Esteban , Villar Juan C. , Ball Andrew S. , Viikari Liisa , Arias M. Enriqueta
Published: February 2005

The actinobacteriumStreptomyces cyaneusCECT 3335 was evaluated for its ability to delignify spruce wood chips (Picea abies) after 2 weeks of incubation prior to refiner mechanical pulping. Weight loss of the chips during the treatment ranged from 2% to 3%. Chemicalanalysis of the treated wood showed an increase in acid-soluble lignin content concomitant with a notable increase in the acid/aldehyde+ketone [AC/(AL+KE)] ratio of the lignin compared with the control. Structural alterations in wood cell walls were observed by optical and scanning microscopy using astra blue-safranin staining and cryosections stained with gold/palladium, respectively. A gradual loss of lignin from the lumen towards the middle lamella and incipient defiberization could be observed. The estimation of specific energy for the defibration and refining stages of treated pulp showed a 24% reduction in the energy required, largely due to a 30% saving in the defibration of chips. The analysis of handsheets obtained from treated pulp showed a notable improvement in some strength properties, such as breaking length, tear index and stretch. In addition, the high Gurley air resistance value indicates more packing of the voids of the fiber network. These results demonstrate for the first time the suitability ofStreptomyces cyaneusfor biomechanical pulping purposes.
Mass loss and moisture dynamics of Scots pine (Pinus sylvestris L.) exposed outdoors above ground in Sweden
Authors: Rydell Åsa , Bergström Mikael , Elowson Torbjörn
Published: February 2005

The durability of 566 Scots pine (Pinus sylvestris) samples was tested during a period of 9 years of exposure to weather in Sweden. The parameters investigated were heartwood/sapwood, origin, surface treatment, end-seal, storage and drying method, annual ring width and density. The weight was measured on 67 occasions during 9 years in order to assess the moisture content of the samples. The mass loss was determined for each sample at the end of the trial. Sapwood had a higher moisture uptake and a higher mass loss compared with heartwood. Even if sapwood was painted with an impermeable paint and then end-sealed, it still had higher average moisture content than heartwood. The results also demonstrated that sapwood was more sensitive to different handling conditions than heartwood. Sapwood was sensitive to air-drying and water storage, which was evident in the higher moisture uptake. In terms of mass loss, some differences were evident but they were not statistically significant due to the large standard deviation of the sapwood samples from water-stored logs. The only positive influence of water storage was on samples end-dipped in oil. One explanation could be that water storage led to increased permeability due to bacterial attack, which in turn enhanced the penetration of the oil. Heartwood had low and stable moisture dynamics during the test period, almost independent of treatment or handling conditions. No correlation with moisture uptake or mass loss was evident among annual ring width, origin or density.
The influence of cation and anion structure of new quaternary ammonium salts on adsorption and leaching
Authors: Zabielska-Matejuk Jadwiga
Published: February 2005

This study examined the effect of cation and anion chemical structure of new quaternary ammonium and imidazolium compounds (QAC, bis-QAC, IC, bis-IC) on the adsorption onto Scots pine wood (Pinus sylvestris L.) and resistance to water leaching. The group of copper (II) modified QACs, containing copper-chloro-acetate complexes in the anion structure, was also examined. The length of alkyl hydrophobic substituents in the cation structure significantly influences adsorption. The adsorption characteristics were statistically related to the alkyl chain length of new quaternary ammonium salts (quantitative correlations between CMC and adsorption values). Bis-ICs adsorb onto Scots pine wood with the greatest difficulty and the slowest and are also leached to the greatest degree. A varied adsorption of chloride ion cations and a several times higher leaching of chlorides than cations of the examined salts from the saturated wood were observed. The anion modification of bis-QAC and bis-IC of copper-chloro-acetate complexes causes decreased adsorption and resistance to the leaching of these salts. As a result of the performed regression analysis of Langmuir and Freundlich adsorption isotherms, it was found that the adsorption of the examined compounds onto wood was governed by both chemical and physical processes. New quaternary ammonium and imidazolium compounds represent potential wood preservatives.
Comparison of Pinus taeda L. wood property calibrations based on NIR spectra from the radial-longitudinal and radial-transverse faces of wooden strips
Authors: Schimleck Laurence R. , Stürzenbecher Reinhard , Mora Christian , David Jones P. , Daniels Richard F.
Published: February 2005

When a radial strip is cut from an increment core it can potentially be cut with two orientations: parallel to longitudinal tracheids, i.e., a radial-longitudinal (RL) strip (the orientation of SilviScan samples), or at an orientation of 90° to the tracheids, i.e., a radial-transverse (RT) strip. Both strips could be used for near-infrared (NIR) analysis, but it is unknown how calibrations based on RT-face NIR spectra compare with those based on RL-face NIR spectra. A total of 20 Pinus taeda L. (loblolly pine) RL strips were characterized in terms of air-dry density, microfibril angle (MFA), stiffness and several tracheid morphological characteristics. NIR spectra were collected in 10-mm increments from the RL and RT faces of matching strips and used to develop calibrations for each property. In general, RL-face NIR spectra gave calibrations that provided stronger relationships. Differences between the two sets of calibrations were small, indicating that either face could be used for NIR analysis.