bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insulation of a synthetic hydrogen metabolism circuit in bacteria
Authors: Agapakis Christina M , Ducat Daniel C , Boyle Patrick M , Wintermute Edwin H , Way Jeffrey C , Silver Pamela A 
Published: February 2010

Abstract

Background
The engineering of metabolism holds tremendous promise for the production of desirable metabolites, particularly alternative fuels and other highly reduced molecules. Engineering approaches must redirect the transfer of chemical reducing equivalents, preventing these electrons from being lost to general cellular metabolism. This is especially the case for high energy electrons stored in iron-sulfur clusters within proteins, which are readily transferred when two such clusters are brought in close proximity. Iron sulfur proteins therefore require mechanisms to ensure interaction between proper partners, analogous to many signal transduction proteins. While there has been progress in the isolation of engineered metabolic pathways in recent years, the design of insulated electron metabolism circuits in vivo has not been pursued.

Results
Here we show that a synthetic hydrogen-producing electron transfer circuit in Escherichia coli can be insulated from existing cellular metabolism via multiple approaches, in many cases improving the function of the pathway. Our circuit is composed of heterologously expressed [Fe-Fe]-hydrogenase, ferredoxin, and pyruvate-ferredoxin oxidoreductase (PFOR), allowing the production of hydrogen gas to be coupled to the breakdown of glucose. We show that this synthetic pathway can be insulated through the deletion of competing reactions, rational engineering of protein interaction surfaces, direct protein fusion of interacting partners, and co-localization of pathway components on heterologous protein scaffolds.

Conclusions
Through the construction and characterization of a synthetic metabolic circuit in vivo, we demonstrate a novel system that allows for predictable engineering of an insulated electron transfer pathway. The development of this system demonstrates working principles for the optimization of engineered pathways for alternative energy production, as well as for understanding how electron transfer between proteins is controlled.
Ginger DNA transposons in eukaryotes and their evolutionary relationships with long terminal repeat retrotransposons
Authors: Bao Weidong , Kapitonov Vladimir V , Jurka Jerzy 
Published: February 2010

Abstract

Background
In eukaryotes, long terminal repeat (LTR) retrotransposons such as Copia, BEL and Gypsy integrate their DNA copies into the host genome using a particular type of DDE transposase called integrase (INT). The Gypsy INT-like transposase is also conserved in the Polinton/Maverick self-synthesizing DNA transposons and in the 'cut and paste' DNA transposons known as TDD-4 and TDD-5. Moreover, it is known that INT is similar to bacterial transposases that belong to the IS3, IS481, IS30 and IS630 families. It has been suggested that LTR retrotransposons evolved from a non-LTR retrotransposon fused with a DNA transposon in early eukaryotes. In this paper we analyze a diverse superfamily of eukaryotic cut and paste DNA transposons coding for INT-like transposase and discuss their evolutionary relationship to LTR retrotransposons.

Results
A new diverse eukaryotic superfamily of DNA transposons, named Ginger (for 'Gypsy INteGrasE Related') DNA transposons is defined and analyzed. Analogously to the IS3 and IS481 bacterial transposons, the Ginger termini resemble those of the Gypsy LTR retrotransposons. Currently, Ginger transposons can be divided into two distinct groups named Ginger1 and Ginger2/Tdd. Elements from tshe Ginger1 group are characterized by approximately 40 to 270 base pair (bp) terminal inverted repeats (TIRs), and are flanked by CCGG-specific or CCGT-specific target site duplication (ssTSsD) sequences. The Ginger1-encoded transposases contain an approximate 400 amino acid N-terminal portion sharing high amino acid identity to the entire Gypsy-encoded integrases, including the YPYY motif, zinc finger, DDE domain, and, importantly, the GPY/F motif, a hallmark of Gypsy and endogenous retrovirus (ERV) integrases. Ginger1 transposases also contain additional C-terminal domains: ovarian tumor (OTU)-like protease domain or Ulp1 protease domain. In vertebrate genomes, at least two host genes, which were previously thought to be derived from the Gypsy integrases, apparently have evolved from the Ginger1 transposase genes. We also introduce a second Ginger group, designated Ginger2/Tdd, which includes the previously reported DNA transposon TDD-4.

Conclusions
The Ginger superfamily represents eukaryotic DNA transposons closely related to LTR retrotransposons. Ginger elements provide new insights into the evolution of transposable elements and certain transposable element (TE)-derived genes.
Risk of breast cancer among daughters of mothers with diabetes: a population-based cohort study
Authors: Stephansson Olof , Granath Fredrik , Ekbom Anders , Michels Karin B 
Published: February 2010

Abstract
Introduction
Diabetes during pregnancy is related to enhanced fetal growth, which has been associated with increased breast cancer risk. Whether daughters of mothers with a diagnosis of diabetes have an increased risk of breast cancer is not known.

Methods
We performed a retrospective cohort study of daughters of mothers with diabetes by linkage of the Swedish Multigeneration, Cause-of-Death and Patient Register between 1952 and 2005. Breast cancer cases were ascertained by linkage with the Swedish Cancer Register between 1958 and 2005. Standardized incidence ratios (SIRs) of breast cancer were calculated assuming a Poisson distribution for the observed cases.

Results
We identified 291,360 daughters of mothers with a diagnosis of diabetes before or after birth between 1952 and 2005. Among the daughters, 7,956 cases of breast cancer were diagnosed between 1964 and 2005. The total time of follow-up was 12,173,821 person years. The expected number of breast cancer cases was 9,204, resulting in an SIR of 0.86 (95% CI, 0.85 to 0.88). The decrease in risk associated with maternal diabetes was stronger for premenopausal (< 55 years of age) than postmenopausal (≥ 55 years of age) breast cancer (SIR 0.83 and 0.91, respectively). Among daughters of mothers with diabetes, a history of breast cancer in the mother increased the risk of breast cancer in the daughter (SIR 1.43, 1.32 to 1.54).

Conclusions
Daughters of mothers with a lifetime history of diabetes were at a decreased risk of breast cancer. The strongest negative association was found among premenopausal breast cancer.
ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing
Authors: Li Guoliang , Fullwood Melissa J , Xu Han , Mulawadi Fabianus Hendriyan , Velkov Stoyan , Vega Vinsensius , Ariyaratne Pramila Nuwantha , Mohamed Yusoff Bin , Ooi Hong-Sain , Tennakoon Chandana , Wei Chia-Lin , Ruan Yijun , Sung Wing-Kin 
Published: February 2010

AbstractChromatin interaction analysis with paired-end tag sequencing (ChIA-PET) is a new technology to study genome-wide long-range chromatin interactions bound by protein factors. Here we present ChIA-PET Tool, a software package for automatic processing of ChIA-PET sequence data, including linker filtering, mapping tags to reference genomes, identifying protein binding sites and chromatin interactions, and displaying the results on a graphical genome browser. ChIA-PET Tool is fast, accurate, comprehensive, user-friendly, and open source (available at http://chiapet.gis.a-star.edu.sg).
An alternatively spliced CXCL16 isoform expressed by dendritic cells is a secreted chemoattractant for CXCR6+ cells
Authors: van der Voort Robbert , Verweij Viviènne , de Witte Theo M , Lasonder Edwin , Adema Gosse J , Dolstra Harry 
Published: February 2010

Abstract
A secreted isoform of the chemokine CXCL16 contributes to the interaction between dendritic cells and CXCR6+ lymphocytes.
DC are professional APCs that initiate and regulate adaptive immune responses by interacting with naïve and memory T cells. Chemokines released by DC play an essential role in T cell recruitment and in the maintenance of antigen-specific T cell-DC conjugates. Here, we characterized the expression of the T cell-attracting chemokine CXCL16 by murine DC. We demonstrate that through alternative RNA splicing, DC not only express the previously characterized transmembrane CXCL16 isoform, which can be cleaved from the cell surface, but also a novel isoform lacking the transmembrane and cytoplasmic domains. Transfection of HEK293 cells shows that this novel isoform, termed CXCL16v, is not expressed on the cell membrane but is secreted as a protein of ∼10 kDa. Quantitative PCR demonstrates that CXCL16v is broadly expressed in lymphoid and nonlymphoid tissues resembling the tissue distribution of DC. Indeed, CXCL16v mRNA is expressed significantly by spleen DC and BM-DC. Moreover, we show that mature DC have increased CXCL16v mRNA levels and express transmembrane and soluble CXCL16 proteins. Finally, we show that CXCL16v specifically attracts cells expressing the chemokine receptor CXCR6. Our data demonstrate that mature DC express secreted, transmembrane, and cleaved CXCL16 isoforms to recruit and communicate efficiently with CXCR6+ lymphoid cells.
TAF1 Differentially Enhances Androgen Receptor Transcriptional Activity via Its N-Terminal Kinase and Ubiquitin-Activating and -Conjugating Domains
Authors: Tavassoli Peyman , Wafa Latif A. , Cheng Helen , Zoubeidi Amina , Fazli Ladan , Gleave Martin , Snoek Robert , Rennie Paul S. 
Published: February 2010

AbstractAberrant expression of androgen receptor (AR) coregulators has been linked to progression of prostate cancers to castration resistance. Using the repressed transactivator yeast two-hybrid system, we found that TATA binding protein-associated factor 1 (TAF1) interacted with the AR. In tissue microarrays, TAF1 was shown to steadily increase with duration of neoadjuvant androgen withdrawal and with progression to castration resistance. Glutathione S-transferase pulldown assays established that TAF1 bound through its acetylation and ubiquitin-activating/conjugating domains (E1/E2) directly to the AR N terminus. Coimmunoprecipitation and ChIP assays revealed colocalization of TAF1 and AR on the prostate-specific antigen promoter/enhancer in prostate cancer cells. With respect to modulation of AR activity, overexpression of TAF1 enhanced AR activity severalfold, whereas small interfering RNA knockdown of TAF1 significantly decreased AR transactivation. Although full-length TAF1 showed enhancement of both AR and some generic gene transcriptional activity, selective AR coactivator activity by TAF1 was demonstrated in transactivation experiments using cloned N-terminal kinase and E1/E2 functional domains. In keeping with AR coactivation by the ubiquitin-activating and -conjugating domain, TAF1 was found to greatly increase the cellular amount of polyubiquitinated AR. In conclusion, our results indicate that increased TAF1 expression is associated with progression of human prostate cancers to the lethal castration-resistant state. Because TAF1 is a coactivator of AR that binds and enhances AR transcriptional activity, its overexpression could be part of a compensatory mechanism adapted by cancer cells to overcome reduced levels of circulating androgens.
Topical Lidocaine Gel and Mammography Methotrexate Overdose Safety Caps that do not Protect Children
Authors: Cohen Michael R. 
Published: February 2010

These medication errors have occurred in health care facilities at least once. They will happen again—perhaps where you work. Through education and alertness of personnel and procedural safeguards, they can be avoided. You should consider publishing accounts of errors in your newsletters and/or presenting them at your inservice training programs. Your assistance is required to continue this feature. The reports described here were received through the Institute for Safe Medication Practices (ISMP) Medication Errors Reporting Program. Any reports published by ISMP will be anonymous. Comments are also invited; the writers' names will be published if desired. ISMP may be contacted at the address shown below. Errors, close calls, or hazardous conditions may be reported directly to ISMP through the ISMP Web site ( www.ismp.org ), by calling 800-FAIL-SAFE, or via e-mail at ismpinfo@ismp.org . ISMP guarantees the confidentiality and security of the information received and respects reporters' wishes as to the level of detail included in publications.
Relation of Natriuretic Peptides and Midregional Proadrenomedullin to Cardiac Chamber Volumes by Computed Tomography in Patients without Heart Failure: From the ROMICAT Trial
Authors: Truong Quynh A , Siegel Emily , Karakas Mahir , Januzzi James L , Bamberg Fabian , Mahabadi Amir A , Dasdemir Selcuk , Brady Thomas J , Bergmann Andreas , Kunde Jan , Nagurney John T , Hoffmann Udo , Koenig Wolfgang 
Published: February 2010

Abstract
Background: Stress myocyte biomarkers are used prognostically in patients with cardiovascular disease. We examined associations between amino-terminal pro–B-type natriuretic peptide (NT-proBNP), midregional pro–A-type natriuretic peptide (MR-proANP), and midregional proadrenomedullin (MR-proADM) concentrations and cardiac chamber volumes in chest pain patients without heart failure by use of computed tomography (CT).
Methods: At the time of 64-slice CT scan, we acquired plasma and serum samples for these biomarkers from 346 patients [mean (SD) age 53 (12) years, 65% men]. Left atrial volume (LAV) and left ventricular volumes at end-diastole (LVEDV) and end-systole (LVESV) were measured and indexed to body surface area (LAVI, LVEDI, LVESI).
Results: Concentrations of both natriuretic peptides were correlated with LAV and LAVI (r = 0.19–0.32, all P ≤ 0.0005) and MR-proADM with LV volumes and indices (r = −0.14 to −0.21, all P ≤ 0.01). NT-proBNP and MR-proANP concentrations were higher in the top quartiles of patients than the lowest quartiles using LAV and LAVI, whereas MR-proADM concentrations were lower in the top quartiles of LV measures. In adjusted analyses, patients had 2- to 4-fold increased risk of LA enlargement for every incremental increase in log10NT-proBNP [LAV odds ratio (OR) 2.4, P = 0.03; LAVI OR 4.0, P = 0.003] and 10- to 13-fold increased risk of LA enlargement for every incremental increase in log10MR-proANP (LAV OR 10.7, P = 0.009; LAVI OR 13.1, P = 0.004).
Conclusions: In patients without heart failure, both NT-proBNP and MR-proANP concentrations are independently associated with LA enlargement, whereas MR-proADM concentrations are correlated with LV volumes. This may partially explain the well-recognized value of natriuretic peptides for use in risk stratification.
Evaluation and Repair of Thin Brick Veneer Facades
Authors: Leafblad Janelle L. , Searls Carolyn L. 
Published: February 2010

Abstract
Thin brick veneer is an exterior cladding system of brick from 3/8 to 3/4 in. thick attached to a substrate, used to imitate standard size brick veneer walls. There are three basic types of adhered installations with many variations within each type: brick precast into panels, panelized wall systems, and site-adhered thin brick. The most widely used system is thin brick site-adhered to exterior cement plaster or concrete walls with a bonding mortar, often with open joints. Building codes provide little guidance for adhered veneer. We have observed debonding of individual brick units, debonding of brick panels, cracking and spalling of brick due to corrosion of underlying elements, and water leakage. Repairs to thin brick veneer systems often consist of testing for loose brick units, removing and re-adhering brick units, and pointing the joints between brick units. The objectives of this paper are to review available construction systems using adhered thin brick veneer, codes and standards, discuss our experience in investigating failures of these systems, and present our recommendations for repairs and for new construction.
Three-Dimensional Assessment of the Eruption Path of the Canine in Individuals with Bone-Grafted Alveolar Clefts Using Cone Beam Computed Tomography
Authors: Oberoi Snehlata , Gill Pawandeep , Chigurupati Radhika , Hoffman William Y. , Hatcher David C. , Vargervik Karin 
Published: February 2010

Objective To evaluate the eruption path of the permanent maxillary canine during a 1-year period after secondary alveolar bone grafting and to (1) compare the canine eruption path on the cleft and noncleft side, (2) examine the number of congenially missing lateral incisors and the rate of canine impaction, and (3) examine the relationship between the eruption status of the canine and timing of alveolar bone grafting relative to age and canine root development using cone beam computed tomography (CBCT). Methods Cone beam computed tomography scans for 17 nonsyndromic unilateral cleft lip and palate (UCLP), and four bilateral cleft lip and palate (BCLP) consecutive cases of alveolar bone grafting surgery were obtained after orthodontic expansion and before alveolar bone grafting and at least 1 year postsurgery on the Hitachi MercuRay CBCT machine. The DICOM files were imported into Dolphin 3D Imaging 10.5 and reoriented for consistency. The X, Y, and Z coordinates were determined for the canine cusp tip and root tip on both the cleft and noncleft sides. The direction of movement of the canine in 1 year was determined. Results Most canines on both the cleft and noncleft sides moved incisally, facially, and mesially. Twelve percent of the canines on the cleft side appeared to require surgical exposure. Eighty percent of the canines had less than half root development at the time of bone grafting. The amount of root development did not affect the outcome in terms of eruption amount or direction. Conclusions Most canines on both the cleft and noncleft side moved incisally, facially, and mesially.
Validation of the NVSCA Registry for Common Oral Clefts: Study Design and First Results
Authors: Rozendaal Anna M. , Luijsterburg Antonius J.M. , Mohangoo Ashna D. , Ongkosuwito Edwin M. , Anthony Sabine , Vermeij-Keers Christi 
Published: February 2010

Objective Since 1997 the Dutch Association for Cleft Palate and Craniofacial Anomalies (NVSCA) has maintained a national registry of congenital craniofacial anomalies. This study validates data on three common oral cleft categories (cleft lip/alveolus = CL/A; cleft lip/alveolus and palate = CL/AP; and cleft palate = CP) and general items. Design Retrospective observational study. Setting All 15 Dutch cleft palate teams registered presurgery patients with common oral clefts (n = 2553) from 1997 to 2003. Patients A random sample of 250 cases was used; 13 cases were excluded. Main Outcome Measures The corresponding medical data were reviewed; these medical data served to validate the NVSCA registry data. Prevalence comparisons, 2 × 2 tables and validity measures were performed. Results The cleft categories most accurately recorded were CL/A and CP. Both categories had an observed agreement of 98%, kappa of 0.94, and a sensitivity and specificity of 97%. Cleft lip/alveolus and palate had an observed agreement of 95%, kappa of 0.89, a sensitivity of 90%, and a specificity of 99%. Regarding the general items, observed agreement and kappa were highest for adoption/foster child (99%; 0.76) and lowest for remarks about pregnancy (63%; 0.20). Sensitivity ranged from 25% (consanguinity) to 97% (white mother) and specificity was high for all items (93%) except for white father and mother (approximately 35%). Conclusions The NVSCA registry is a valuable tool for quality improvement and research because validity on all three common oral cleft categories is very good. Validity on the general items is reasonable to satisfying and appears to be related to the type of information.
Three-Dimensional Morphologic Nasal Surface Characteristics that Predict the Extremes of Esthetics in Patients with Repaired Cleft Lip and Palate
Authors: Russell Kathy A. , Milne Andrew D. , Varma Devesh , Josephson Keith , Lee J. Michael 
Published: February 2010

Objective The purposes of this study were (1) to develop imaging methods and objective numeric parameters to describe nose morphology, and (2) to correlate those parameters with nasal esthetics for patients with clefts. Methods A total of 28 patients with repaired complete unilateral cleft lip and palate (CUCLP) and 20 age- and gender-matched individuals without clefts were identified. A panel of orthodontists rated and ranked nasal esthetics from nose casts for the cleft group. Best and worst esthetic cleft groups were established from the cast assessments. Three-dimensional surface coordinates of the casts were digitally mapped with an electromagnetic tracking device. Digitized nasal images were oriented, voxelated, sliced, and mathematically curve-fitted. Maximum difference, percent area difference, and maximum and minimum derivative differences between cleft and noncleft and between right and left nose sides were calculated. Differences in parameters between groups were assessed with the use of analysis of variance (ANOVA) and t tests, and correlations with esthetics were assessed with the Spearman rank correlation test. Results Differences were seen between cleft and noncleft and best and worst esthetic groups for all four parameters ( p < .05). The best esthetic cleft group had (1) lower percent area difference ( p < .0001), (2) lower maximum difference ( p < .001), and (3) smaller differences in slope of the nose in the coronal plane ( p < .0001) than the worst esthetic cleft group. Conclusions Maximum difference and maximum derivative difference and, to a lesser degree, percent area difference can be used to identify differences between cleft and noncleft nasal morphology and to assess levels of nasal esthetics for patients with CUCLP.
Motor and Sensory Nerve Conduction Are Affected Differently by Ice Pack, Ice Massage, and Cold Water Immersion
Authors: Herrera Esperanza , Sandoval Maria C. , Camargo Diana M. , Salvini Tania F. 
Published: February 2010

BackgroundIt is well known that reducing tissue temperature changes sensory and motor nerve conduction. However, few studies have compared the effect of different cold modalities on nerve conduction parameters.ObjectiveThe purpose of this study was to compare the effects of ice pack, ice massage, and cold water immersion on the conduction parameters of the sural (sensorial) and tibial motor nerves.DesignAn experimental study was conducted in which the participants were randomly assigned to 1 of 3 intervention groups (n=12 per group). Independent variables were cold modality and pre- and post-cooling measurement time. Dependent variables were skin temperature and nerve conduction parameters.MethodsThirty-six people who were healthy, with a mean (SD) age of 20.5 (1.9) years, participated in the study. Each group received 1 of the 3 cold modalities, applied to the right calf region for 15 minutes. Skin temperature and nerve conduction parameters were measured before and immediately after cooling.ResultsAll 3 modalities reduced skin temperature (mean=18.2°C). There also was a reduction in amplitude and an increase in latency and duration of the compound action potential. Ice massage, ice pack, and cold water immersion reduced sensory nerve conduction velocity (NCV) by 20.4, 16.7, and 22.6 m/s and motor NCV by 2.5, 2.1, and 8.3 m/s, respectively. Cold water immersion was the most effective modality in changing nerve conduction parameters.LimitationsThe cooling area of the ice massage and ice pack was smaller than that of the cold water immersion. The examiner was not blinded to the treatment group. The population included only participants who were healthy and young.ConclusionsAll 3 modalities were effective in reducing skin temperature and changing sensory conduction at a physiological level that is sufficient to induce a hypoalgesic effect. The results suggest that cold water immersion, as applied in this study, is the most indicated modality for inducing therapeutic effects associated with the reduction of motor nerve conduction.