bluuebunny/crossref_metadata_2025 huggingface dataset:
Hydrogen plasma treatment for improved conductivity in amorphous aluminum doped zinc tin oxide thin films
Authors: Morales-Masis M. , Ding L. , Dauzou F. , Jeangros Q. , Hessler-Wyser A. , Nicolay S. , Ballif C.
Published: September 2014

Improving the conductivity of earth-abundant transparent conductive oxides (TCOs) remains an important challenge that will facilitate the replacement of indium-based TCOs. Here, we show that a hydrogen (H2)-plasma post-deposition treatment improves the conductivity of amorphous aluminum-doped zinc tin oxide while retaining its low optical absorption. We found that the H2-plasma treatment performed at a substrate temperature of 50 °C reduces the resistivity of the films by 57% and increases the absorptance by only 2%. Additionally, the low substrate temperature delays the known formation of tin particles with the plasma and it allows the application of the process to temperature-sensitive substrates.
Effects of q-profile structure on turbulence spreading: A fluctuation intensity transport analysis
Authors: Yi S. , Kwon J. M. , Diamond P. H. , Hahm T. S.
Published: September 2014

This paper studies effects of q-profile structure on turbulence spreading. It reports results of numerical experiments using global gyrokinetic simulations. We examine propagation of turbulence, triggered by an identical linear instability in a source region, into an adjacent, linearly stable region with variable q-profile. The numerical experiments are designed so as to separate the physics of turbulence spreading from that of linear stability. The strength of turbulence spreading is measured by the penetration depth of turbulence. Dynamics of spreading are elucidated by fluctuation intensity balance analysis, using a model intensity evolution equation which retains nonlinear diffusion and damping, and linear growth. It is found that turbulence spreading is strongly affected by magnetic shear s, but is hardly altered by the safety factor q itself. There is an optimal range of modest magnetic shear which maximizes turbulence spreading. For high to modest shear values, the spreading is enhanced by the increase of the mode correlation length with decreasing magnetic shear. However, the efficiency of spreading drops for sufficiently low magnetic shear even though the mode correlation length is comparable to that for the case of optimal magnetic shear. The reduction of spreading is attributed to the increase in time required for the requisite nonlinear mode-mode interactions. The effect of increased interaction time dominates that of increased mode correlation length. Our findings of the reduction of spreading and the increase in interaction time at weak magnetic shear are consistent with the well-known benefit of weak or reversed magnetic shear for core confinement enhancement. Weak shear is shown to promote locality, as well as stability.
Effects of confinements on morphology of InxGa1−xAs thin film grown on sub-micron patterned GaAs substrate: Elastoplastic phase field model
Authors: Arjmand M. , Deng J. , Swaminathan N. , Morgan D. , Szlufarska I.
Published: September 2014

An elastoplastic phase field model is developed to investigate the role of lateral confinement on morphology of thin films grown heteroepitaxially on patterned substrates. Parameters of the model are chosen to represent InxGa1−xAs thin films growing on GaAs patterned with SiO2. We determined the effect of misfit strain on morphology of thin films grown in 0.5 μm patterns with non-uniform deposition flux. Growth of islands inside patterns can be controlled by non-uniformity of deposition flux, misfit strain between film and the substrate, and also strain energy relaxation due to plastic deformation. Our results show that the evolution of island morphology depends non-monotonically on indium content and associated misfit strain due to coupling between the plastic relaxation and the confinements effects. Low indium concentration (0%–40%) causes formation of instabilities with relatively long wavelengths across the width of the pattern. Low surface diffusion (due to low indium concentration) and fewer islands across the pattern (due to small misfit strain) lead to formation and growth of islands near the walls driven by overflow flux. Further increase in indium concentration (40%–75%) increases the lattice mismatch and surface diffusivity of the film, and also activates plastic deformation mechanism, which leads to coalescence of islands usually away from the edges. By further increasing the indium concentration (up to 100%), plastic deformation relaxes most of the strain energy density of the film, which prevents formation of instabilities in the film. Hence, in this case, islands are only formed near the walls.
Dipole moment-tuned packing of TiO2 nanocrystals into monolayer films by electrophoretic deposition
Authors: Gonzalo-Juan I. , Krejci A. J. , Rodriguez M. A. , Zhou Y. , Fichthorn K. A. , Dickerson J. H.
Published: September 2014

The magnitude of the electric dipole moment of TiO2 nanocrystals was tuned as a function of the shape of the nanocrystal to facilitate the formation of tightly-packed monolayers, fabricated by electrophoretic deposition. The dipole moment aided the formation of monolayers with quasi-hexagonal ordering. Voronoi tessellation analysis confirmed that nanorods facilitated higher degrees of order than nanospheres. Thermal and dilatometric analyses demonstrate that the nanocrystals' sintering temperature was reduced below 1250 °C—a useful development for device applications.
Enhancement of energy storage in epitaxial PbZrO3 antiferroelectric films using strain engineering
Authors: Ge Jun , Remiens Denis , Dong Xianlin , Chen Ying , Costecalde Jean , Gao Feng , Cao Fei , Wang Genshui
Published: September 2014

We demonstrate an approach to enhance the energy storage density W of antiferroelectric film through simple altering a crystallographic orientation of the substrate. We reveal that the antiferroelectric phase stability of PbZrO3 can be enhanced for the (110) or (111) SrTiO3 substrate orientation, thus suppresses the antiferroelectric-ferroelectric phase transition to higher electric field with ∼120 kV/cm increment. In addition, the polarization values of these films are also favorably increased hence increases W by 5.3 J/cm3 at 700 kV/cm. The observed enhancement is found to originate from a high sensitivity of phase transition to mechanical confinements due to the volume expansion at the transition.
Effect of thermal annealing and oxygen partial pressure on the swelling of HfO2/SiO2/Si metal-oxide-semiconductor structure grown by rf sputtering: A synchrotron x-ray reflectivity study
Authors: Biswas Debaleen , Md Faruque Sk Abdul Kader , Sinha Anil Kumar , Upadhyay Anuj , Chakraborty Supratic
Published: September 2014

As-grown and rapid thermal annealed thin HfO2 films, deposited on Si(100) substrate by reactive rf sputtering at various partial pressures of O2 and Ar, are studied by synchrotron x-ray reflectivity. The growth of interfacial layer (IL) of SiO2 is more or less linear with the decrease in oxygen partial pressure (pO2) in the O2/Ar mixture. The thickest oxide is found to be grown at the minimum oxygen partial pressure (pO2). It is observed that the IL swells upon annealing at higher temperature, and swelling is maximum for the sample grown in minimum pO2. The surface roughness and thickness of the HfO2 films decrease upon annealing indicating a denser film. The HfO2/Si interface roughness is also decreased upon annealing. Therefore, lower annealing temperature and higher pO2 is to be set to reduce the IL thickness and for higher dielectric constant and larger oxide capacitance. High frequency capacitance-voltage (C–V) measurement on the devices, annealed at higher temperature, further shows the necessity for optimization of pO2 during the deposition of HfO2 film to minimize the fixed oxide charge density of metal-oxide-semiconductor devices.
Absolute supercurrent switch in ferromagnetic/superconducting/ferromagnetic trilayers operating at T > 4.2 K
Authors: Stamopoulos D. , Aristomenopoulou E. , Manios E.
Published: September 2014

Artificial (CoO-)Co/Nb/Co trilayers (TLs) are studied by means of magnetization, transport, and magnetic force microscopy measurements. By using these TLs as a model system, we provide definite means to distinguish the exchange-fields and stray-fields based magnetoresistance effects observed in relevant Ferromagnetic/Superconducting/Ferromagnetic (FM/SC/FM) structures. Accordingly, we isolate and exclusively focus on the stray-fields version, to report a complete supercurrent switch, ΔR/Rnor ≈ 100%, achieved at operating temperature T > 4.2 K. Detailed series of Co(60 nm)/Nb(dNb)/Co(60 nm) TLs are studied, in which all crucial parameters that relate to the outer Co layers and to the Nb interlayer were systematically varied to unveil the factors that motivate and/or promote the observed effect. We propose a compact model that fairly captures the underlying physics of the Co(60 nm)/Nb(dNb)/Co(60 nm) TLs studied here and can be generalized to assist understanding of the relevant processes in every kind of FM/SC/FM TLs. The presented results and accompanying model are both provocative for basic research and attractive for the design of cryogenic devices.
Controllable spin-charge transport in strained graphene nanoribbon devices
Authors: Diniz Ginetom S. , Guassi Marcos R. , Qu Fanyao
Published: September 2014

We theoretically investigate the spin-charge transport in two-terminal device of graphene nanoribbons in the presence of a uniform uniaxial strain, spin-orbit coupling, exchange field, and smooth staggered potential. We show that the direction of applied strain can efficiently tune strain-strength induced oscillation of band-gap of armchair graphene nanoribbon (AGNR). It is also found that electronic conductance in both AGNR and zigzag graphene nanoribbon (ZGNR) oscillates with Rashba spin-orbit coupling akin to the Datta-Das field effect transistor. Two distinct strain response regimes of electronic conductance as function of spin-orbit couplings magnitude are found. In the regime of small strain, conductance of ZGNR presents stronger strain dependence along the longitudinal direction of strain. Whereas for high values of strain shows larger effect for the transversal direction. Furthermore, the local density of states shows that depending on the smoothness of the staggered potential, the edge states of AGNR can either emerge or be suppressed. These emerging states can be determined experimentally by either spatially scanning tunneling microscope or by scanning tunneling spectroscopy. Our findings open up new paradigms of manipulation and control of strained graphene based nanostructure for application on novel topological quantum devices.
Au-gated SrTiO3 field-effect transistors with large electron concentration and current modulation
Authors: Verma Amit , Raghavan Santosh , Stemmer Susanne , Jena Debdeep
Published: September 2014

We report the fabrication of low-leakage rectifying Pt and Au Schottky diodes and Au-gated metal-semiconductor field effect transistors (MESFETs) on n-type SrTiO3 thin films grown by hybrid molecular beam epitaxy. In agreement with previous studies, we find that compared to Pt, Au provides a higher Schottky barrier height with SrTiO3. As a result of the large dielectric constant of SrTiO3 and the large Schottky barrier height of Au, the Au-gated MESFETs are able to modulate ∼1.6 × 1014 cm−2 electron density, the highest modulation yet achieved using metal gates in any material system. These MESFETs modulate current densities up to ∼68 mA/mm, ∼20× times larger than the best demonstrated SrTiO3 MESFETs. We also discuss the roles of the interfacial layer, and the field-dependent dielectric constant of SrTiO3 in increasing the pinch off voltage of the MESFET.
Frequency selectivity without resonance in a fluid waveguide
Authors: van der Heijden Marcel
Published: September 2014

Significance

This work describes a simple waveguide that not only carries fluid waves, but also performs a spectral analysis. When driven by a complex input that contains several frequency components, it will spatially separate those components, in analogy to the separation of white light by a prism. The frequency tuning of the waveguide is not based on resonance, but on wave dispersion: Each wave has its own region in which it undergoes a steep deceleration, causing it to focus its energy and deliver it. This method of spectral analysis has not been described before. The waveguide bears a striking resemblance to the inner ear of mammals, both in terms of structure and behavior.
Evaluation of a New Monochloramine Generation System for ControllingLegionellain Building Hot Water Systems
Authors: Duda Scott , Kandiah Sheena , Stout Janet E. , Baron Julianne L. , Yassin Mohamed , Fabrizio Marie , Ferrelli Juliet , Hariri Rahman , Wagener Marilyn M. , Goepfert John , Bond James , Hannigan Joseph , Rogers Denzil
Published: September 2014

Objective.

To evaluate the efficacy of a new monochloramine generation system for control ofLegionellain a hospital hot water distribution system

Setting.

A 495-bed tertiary care hospital in Pittsburgh, Pennsylvania. The hospital has 12 floors covering approximately 78,000 m2.

Methods.

The hospital hot water system was monitored for a total of 29 months, including a 5-month baseline sampling period prior to installation of the monochloramine system and 24 months of surveillance after system installation (postdisinfection period). Water samples were collected for microbiological analysis (Legionellaspecies,Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Acinetobacterspecies, nitrifying bacteria, heterotrophic plate count [HPC] bacteria, and nontuberculous mycobacteria). Chemical parameters monitored during the investigation included monochloramine, chlorine (free and total), nitrate, nitrite, total ammonia, copper, silver, lead, and pH.

Results.

A significant reduction inLegionelladistal site positivity was observed between the pre- and postdisinfection periods, with positivity decreasing from an average of 53% (baseline) to an average of 9% after monochloramine application (P> .05). Although geometric mean HPC concentrations decreased by approximately 2 log colony-forming units per milliliter during monochloramine treatment, we did not observe significant changes in other microbial populations.

Conclusions.

This is the first evaluation in the United States of a commercially available monochloramine system installed on a hospital hot water system forLegionelladisinfection, and it demonstrated a significant reduction inLegionellacolonization. Significant increases in microbial populations or other negative effects previously associated with monochloramine use in large municipal cold water systems were not observed.

Infect Control Hosp Epidemiol2014;35(11):1356–1363
Translating bioinformatics in oncology: guilt-by-profiling analysis and identification of KIF18B and CDCA3 as novel driver genes in carcinogenesis
Authors: Itzel Timo , Scholz Peter , Maass Thorsten , Krupp Markus , Marquardt Jens U. , Strand Susanne , Becker Diana , Staib Frank , Binder Harald , Roessler Stephanie , Wang Xin Wei , Thorgeirsson Snorri , Müller Martina , Galle Peter R. , Teufel Andreas
Published: September 2014

Motivation : Co-regulated genes are not identified in traditional microarray analyses, but may theoretically be closely functionally linked [guilt-by-association (GBA), guilt-by-profiling]. Thus, bioinformatics procedures for guilt-by-profiling/association analysis have yet to be applied to large-scale cancer biology.

We analyzed 2158 full cancer transcriptomes from 163 diverse cancer entities in regard of their similarity of gene expression, using Pearson’s correlation coefficient (CC). Subsequently, 428 highly co-regulated genes (|CC| ≥ 0.8) were clustered unsupervised to obtain small co-regulated networks. A major subnetwork containing 61 closely co-regulated genes showed highly significant enrichment of cancer bio-functions. All genes except kinesin family member 18B (KIF18B) and cell division cycle associated 3 (CDCA3) were of confirmed relevance for tumor biology. Therefore, we independently analyzed their differential regulation in multiple tumors and found severe deregulation in liver, breast, lung, ovarian and kidney cancers, thus proving our GBA hypothesis. Overexpression of KIF18B and CDCA3 in hepatoma cells and subsequent microarray analysis revealed significant deregulation of central cell cycle regulatory genes. Consistently, RT-PCR and proliferation assay confirmed the role of both genes in cell cycle progression.

Finally, the prognostic significance of the identified KIF18B- and CDCA3-dependent predictors ( P = 0.01, P = 0.04) was demonstrated in three independent HCC cohorts and several other tumors.

In summary, we proved the efficacy of large-scale guilt-by-profiling/association strategies in oncology. We identified two novel oncogenes and functionally characterized them. The strong prognostic importance of downstream predictors for HCC and many other tumors indicates the clinical relevance of our findings.

Contact : andreas.teufel@ukr.de

Supplementary information:  Supplementary data are available at Bioinformatics online.
The Ensembl REST API: Ensembl Data for Any Language
Authors: Yates Andrew , Beal Kathryn , Keenan Stephen , McLaren William , Pignatelli Miguel , Ritchie Graham R. S. , Ruffier Magali , Taylor Kieron , Vullo Alessandro , Flicek Paul
Published: September 2014

Motivation: We present a Web service to access Ensembl data using Representational State Transfer (REST). The Ensembl REST server enables the easy retrieval of a wide range of Ensembl data by most programming languages, using standard formats such as JSON and FASTA while minimizing client work. We also introduce bindings to the popular Ensembl Variant Effect Predictor tool permitting large-scale programmatic variant analysis independent of any specific programming language.

Availability and implementation: The Ensembl REST API can be accessed at http://rest.ensembl.org and source code is freely available under an Apache 2.0 license from http://github.com/Ensembl/ensembl-rest .

Contact:  ayates@ebi.ac.uk or flicek@ebi.ac.uk

Supplementary information:  Supplementary data are available at Bioinformatics online.
Clinical Practice Guideline for the Management of Chronic Kidney Disease in Patients Infected With HIV: 2014 Update by the HIV Medicine Association of the Infectious Diseases Society of America
Authors: Lucas Gregory M. , Ross Michael J. , Stock Peter G. , Shlipak Michael G. , Wyatt Christina M. , Gupta Samir K. , Atta Mohamed G. , Wools-Kaloustian Kara K. , Pham Paul A. , Bruggeman Leslie A. , Lennox Jeffrey L. , Ray Patricio E. , Kalayjian Robert C.
Published: September 2014

It is important to realize that guidelines cannot always account for individual variation among patients. They are not intended to supplant physician judgment with respect to particular patients or special clinical situations. IDSA considers adherence to these guidelines to be voluntary, with the ultimate determination regarding their application to be made by the physician in the light of each patient's individual circumstances.
Hadronic gamma-rays from RX J1713.7−3946?
Authors: Gabici S. , Aharonian F. A.
Published: September 2014

RX J1713.7−3946 is a key object to check the supernova remnant paradigm of the origin of Galactic cosmic rays. While the origin of its gamma-ray emission (hadronic versus leptonic) is still debated, the hard spectrum at GeV energies reported by the Fermi collaboration is generally interpreted as a strong argument in favour of a leptonic scenario. On the contrary, we show that hadronic interactions can naturally explain the gamma-ray spectrum if gas clumps are present in the supernova remnant shell. The absence of thermal X-rays from the remnant fits well within this scenario.
Direct entry by RNase E is a major pathway for the degradation and processing of RNA in Escherichia coli
Authors: Clarke Justin E. , Kime Louise , Romero A. David , McDowall Kenneth J.
Published: September 2014

Escherichia coli endoribonuclease E has a major influence on gene expression. It is essential for the maturation of ribosomal and transfer RNA as well as the rapid degradation of messenger RNA. The latter ensures that translation closely follows programming at the level of transcription. Recently, one of the hallmarks of RNase E, i.e. its ability to bind via a 5′-monophosphorylated end, was shown to be unnecessary for the initial cleavage of some polycistronic tRNA precursors. Here we show using RNA-seq analyses of ribonuclease-deficient strains in vivo and a 5′-sensor mutant of RNase E in vitro that, contrary to current models, 5′-monophosphate-independent, ‘direct entry’ cleavage is a major pathway for degrading and processing RNA. Moreover, we present further evidence that direct entry is facilitated by RNase E binding simultaneously to multiple unpaired regions. These simple requirements may maximize the rate of degradation and processing by permitting multiple sites to be surveyed directly without being constrained by 5′-end tethering. Cleavage was detected at a multitude of sites previously undescribed for RNase E, including ones that regulate the activity and specificity of ribosomes. A potentially broad role for RNase G, an RNase E paralogue, in the trimming of 5′-monophosphorylated ends was also revealed.
Anatomy-Based Eligibility Measure for Robotic-Assisted Bypass Surgery
Authors: Escoto Abelardo , Trejos Ana Luisa , Patel Rajni V. , Goela Aashish , Kiaii Bob
Published: September 2014

Objective

Robotic-assisted endoscopic single-vessel small thoracotomy allows clinicians to perform coronary artery bypass grafting surgery in a minimally invasive manner using the da Vinci Surgical System. Not all patients are suitable for this technique, and the lack of an appropriate method for patient eligibility avoids completion of the procedure robotically. The objective of this study was to develop a patient eligibility method based on the anatomy of the chest of the patient.

Methods

Preoperative computed tomography thorax scans of 110 patients were analyzed. Two-dimensional measurements taken on the axial images were used with the goal of finding a relation between the anatomy of the patient and the completion of the procedure robotically.

Results

Patients with a distance from the left anterior descending coronary artery to the anterior chest wall of smaller than 15 mm have a 20% probability of requiring conversion of the procedure to open surgery. This probability increases if the chest of the patient is very elliptical, having an anterior-posterior dimension of less than 45% of the transverse dimension.

Conclusions

The smaller the distance is from the left anterior descending artery to the anterior chest wall, the lower the chances are of completing the procedure robotically.
Intraoperative Near-Infrared Fluorescence Imaging as an Adjunct to Robotic-Assisted Minimally Invasive Esophagectomy
Authors: Sarkaria Inderpal S. , Bains Manjit S. , Finley David J. , Adusumilli Prasad S. , Huang James , Rusch Valerie W. , Jones David R. , Rizk Nabil P.
Published: September 2014

During esophagectomy, identification and preservation of the right gastroepiploic vascular arcade are critical and may be challenging with minimally invasive approaches. We assessed the use of near-infrared fluorescence imaging fluorescence angiography (NIFI-FA) during robotic-assisted minimally invasive esophagectomy (RAMIE) as an aid to visualize the gastric vasculature with mobilization. After intravenous administration of 10 mg of indocyanine green, a robotic platform with near-infrared optical fluorescence capability was used to examine the gastric vasculature in patients undergoing RAMIE. Thirty (71%) of 42 patients undergoing RAMIE were assessed using NIFI-FA during mobilization of the greater gastric curve and fundus; 11 were excluded because the system was not available, and 1 was excluded because of documented allergy to iodinated contrast. The median time from indocyanine green administration to detectable fluorescence was 37.5 seconds (range, 20–105 seconds). Near-infrared fluorescence imaging FA identified or confirmed termination of the vascular arcade in all 30 cases. Subjectively, NIFI-FA often identified otherwise unvisualized small transverse vessels between the termination of the vascular arcade and the first short gastric artery, as well as between the short gastric arteries. Identification and/or confirmation of the vascular arcade position during mobilization of the greater curve/omentum were also aided by NIFI-FA. Although there are limitations to the current technology, NIFI-FA may be a useful adjunct to confirm and identify the position of gastroepiploic vessels, allow for safer and more confident dissections during gastric mobilization, as well as potentially decrease serious intraoperative vascular misadventures.
Robotic Repair of Sinus Venosus Atrial Septal Defect with Partial Anomalous Pulmonary Venous Return and Persistent Left Superior Vena Cava
Authors: Lewis Clifton T.P. , Bethencourt Daniel M. , Stephens Richard L. , Cline Jennifer L. , Tyndal Charles M.
Published: September 2014

The presence of partial anomalous pulmonary venous return and/or persistent left superior vena cava (LSVC) is usually viewed as a contraindication for robotic repair of complex atrial septal defects, such as those of the sinus venosus type. Three patients, aged 29, 73, and 23 years, successfully underwent totally endoscopic, robotic-assisted repair of sinus venosus-type atrial septal defect with partial anomalous pulmonary venous return and persistent LSVC. Two different techniques—direct cannulation or placement of a sump sucker—were successfully used to manage venous return from the persistent LSVC.
Robotically Assisted, Completely Endoscopic Transmyocardial Revascularization is Feasible
Authors: Brunsting Louis A. , Snyder Averel B. , Espinal Eric A. , Srivastava Sudhir P.
Published: September 2014

Objective

The purpose of this study was to assess the feasibility of an endoscopic, optical-fiber-based, laser delivery system (LDS) developed to perform sole-therapy transmyocardial revascularization (TMR) in a totally endoscopic, robotically assisted operation.

Methods

Forty-two patients were enrolled in a multicenter, prospective, single-arm clinical trial conducted at four US centers between 2005 and 2007. Transmyocardial revascularization was performed completely endoscopically with robotic assistance, introducing the Holmium:Yttrium aluminum garnet (YAG) LDS via a 5-mm port. Completion of the operation endoscopically defined procedural success. Clinical data were recorded before, during, and at least 30 days after the procedure.

Results

All patients had Canadian Cardiovascular Score angina class IV at baseline. The mean ejection fraction was 49% (range [R], 28–71), the mean age was 59.1 years (R, 36–80), 71% (30/42) were men, 86% (36/42) underwent previous coronary artery bypass grafting surgery, and 76% (32/42) underwent prior coronary stenting. Procedural success was accomplished in 93% (39/42). For the procedural successes, the mean number of TMR channels was 32 (R, 16–50), the median operative time was 88 minutes (R, 48–250 minutes), and the median length of stay postoperatively was 2.5 days (R, 1–10). There was no operative or 30-day mortality, and no patient received any transfusion. At 30 days, freedom from major adverse cardiac events was 95% (two patients had transient congestive heart failure). At the median 6-month follow-up (single-center data, n = 12), the mean (SD) Canadian Cardiovascular Score angina score was 1.3 (0.05) ( P < 0.001 vs baseline).

Conclusions

Robotically assisted TMR can be performed using an endoscopic, optical-fiber-based LDS, with high procedural success, avoidance of early adverse clinical events, and potential for successful angina relief.
Robotic Coronary Artery Bypass Grafting Decreases 30-Day Complication Rate, Length of Stay, and Acute Care Facility Discharge Rate Compared with Conventional Surgery
Authors: Leyvi Galina , Forest Stephen J. , Srinivas Vankeepuram S. , Greenberg Mark , Wang Nan , Mais Alec , Snyder Max J. , DeRose Joseph J.
Published: September 2014

Objective

The objective of this study was to compare the short-term outcomes of robotic with conventional on-pump coronary artery bypass grafting (CABG).

Methods

The study population included 2091 consecutive patients who underwent either conventional or robotic CABG from January 2007 to March 2012. Preoperative, intraoperative, and 30-day postoperative variables were collected for each group. To compare the incidence of rapid recovery between conventional and robotic CABG, the surrogate variables of early discharge and discharge to home (vs rehabilitation or acute care facility) were evaluated. A multivariate logistic regression analysis was used.

Results

One hundred fifty robotic and 1619 conventional CABG cases were analyzed. Multivariate logistic regression analysis demonstrated that robotic surgery was astrongpredictoroflower30-day complications [odds ratio (OR), 0.24; P =0.005], short length of stay (OR, 3.31; P < 0.001), and decreased need for an acute care facility (OR, 0.55; P = 0.032). In the presence of complications (New York State Complication Composite), the robotic technique was not associated with a change in discharge status.

Conclusions

In this retrospective review, robotic CABG was associated with a lower 30-day complication rate, a shorter length of stay, and a lower incidence of acute care facility discharge than conventional on-pump CABG. It may suggest a more rapid recovery to preoperative status after robotic surgery; however, only a randomized prospective study could confirm the advantages of a robotic approach.
Mini-invasive Aortic Surgery: Personal Experience
Authors: Spinelli Francesco , Stilo Francesco , La Spada Michele , Benedetto Filippo , De Caridi Giovanni , Barillà David , Giardina Massimiliano , David Antonio
Published: September 2014

Objective

In this study, we retrospectively evaluated our experience in minilaparotomy (MINI) and compared the results with conventional open repair (OPEN).

Methods

From January 2005 to December 2012, we surgically treated 234 consecutive patients with elective infrarenal abdominal aortic aneurysms, 195 men and 39 women, with a mean age of 74 years. Inclusion criteria for MINI were not ruptured abdominal aortic aneurysm, increased surgical risk, anatomical limits for endovascular repair, no previous surgical invasion of the abdominal cavity, and no requirement for concomitant abdominal surgical invasion. Surgical treatment was OPEN in 113 patients (48.3%) and MINI through an 8- to 14-cm incision in 121 patients (51.7%). Epidural anesthesia has been added in 26.5% and in 19.3% of the MINI and OPEN patients, respectively. Mortality, complications, aortic clamping time, operative time, need for postoperative morphine therapy, time to solid diet, and length of hospital stay were registered.

Results

The MINI has been performed in all patients selected, with 72 aortoaortic grafts and 49 aortobisiliac grafts. Early mortality was 1.6% versus 3.5% ( P > 0.5); 1-, 3-, and 5-year mortality were 7% versus 9%, 19% versus 22%, and 29% versus 34% ( P > 0.5); complications were 12.2% versus 26.6% ( P > 0.05); mean (SD) clamping time was 48 (12) versus 44 (14) minutes ( P > 0.5); mean (SD) operative time was 218.72 (41.95) versus 191.44 (21.73) minutes ( P > 0.025); mean (SD) estimated intraoperative blood loss was 425.64 (85.95) versus 385.30 (72.41) mL ( P > 0.1); mean (SD) morphine consumption in the group given epidural and the group not given epidural was 0 (2) and 2 (2) mg intravenously (IV) versus 2 (4) ( P < 0.5) and 4 (3) mg IV ( P > 0.1); mean (SD) ambulation was 2.1 (0.6) versus 4.1 (2.7) ( P < 0.5); mean (SD) time to solid diet was 2.1 (0.4) versus 3.5 (1.6) ( P < 0.5); and mean (SD) length of hospital stay was 4.9 (1.64) versus 7.35 (1.95) days ( P > 0.05), in the MINI and OPEN groups, respectively. Postoperative hernia at 3 years was 18% versus 23% in the MINI and OPEN groups ( P < 0.5), respectively.

Conclusions

The MINI gives the patients a significantly shorter period of recovery with the quality and safety of the OPEN. This experience suggested extending the indication to all surgical candidates without local limitations.
Reduction in Pain and Inflammation Associated With Chronic Low Back Pain With the Use of the Medical Food Theramine
Authors: Shell William E. , Pavlik Stephanie , Roth Brandon , Silver Michael , Breitstein Mira L. , May Lawrence , Silver David
Published: September 2014

Management of chronic back pain is a challenge for physicians. Although standard treatments exert a modest effect, they are associated with narcotic addiction and serious side effects from nonsteroidal antiinflammatory agents. Moreover, neurotransmitter depletion from both the pain syndrome and therapy may contribute to a poor treatment outcome. Neurotransmitter deficiency may be related both to increased turnover rate and inadequate neurotransmitter precursors from the diet, particularly for essential and semi-essential amino acids. Theramine, an amino acid blend 68405-1 (AAB), is a physician-prescribed only medical food. It contains neurotransmitter precursors and systems for increasing production and preventing attenuation of neurotransmitters. A double-blind controlled study of AAB, low-dose ibuprofen, and the coadministration of the 2 agents were performed. The primary end points included the Roland Morris index and Oswestry disability scale. The cohort included 122 patients aged between 18 and 75 years. The patients were randomized to 1 of 3 groups: AAB alone, ibuprofen alone, and the coadministration of the 2 agents. In addition, C-reactive protein, interleukin 6, and plasma amino acid concentrations were measured at baseline and 28 days time points. After treatment, the Oswestry Disability Index worsened by 4.52% in the ibuprofen group, improved 41.91% in the AAB group, and improved 62.15% in the combination group. The Roland Morris Index worsened by 0.73% in the ibuprofen group, improved by 50.3% in the AAB group, and improved 63.1% in the combination group. C-reactive protein in the ibuprofen group increased by 60.1%, decreased by 47.1% in the AAB group, and decreased by 36% in the combination group. Similar changes were seen in interleukin 6. Arginine, serine, histidine, and tryptophan levels were substantially reduced before treatment in the chronic pain syndrome and increased toward normal during treatment. There was a direct correlation between improvement in amino acid concentration and treatment response. Treatment with amino acid precursors was associated with substantial improvement in chronic back pain, reduction in inflammation, and improvement in back pain correlated with increased amino acid precursors to neurotransmitters in blood.
The importance of the magnesium transporter MgtB for virulence of Yersinia pseudotuberculosis and Yersinia pestis
Authors: Ford Donna C. , Joshua George W. P. , Wren Brendan W. , Oyston Petra C. F.
Published: September 2014

Mg2+has been shown to be an important signal controlling gene regulation via the PhoPQ two-component regulatory system for a range of Gram-negative bacteria, includingYersinia pestisandYersinia pseudotuberculosis. The magnesium ion transporter MgtB is part of the complex PhoPQ regulon, being upregulated in response to low Mg2+. Despite the presence of other Mg2+transport systems inYersinia, inactivation ofmgtBhad a significant effect on the ability of the bacteria to scavenge this crucial ion. Whereas inactivation of PhoPQ is reported to adversely affect intracellular survival, we show thatY. pestisandY. pseudotuberculosisΔmgtBmutants survived equally as well as the respective parent strain within macrophages, although they were more sensitive to killing in theGalleriamodel of infection. Surprisingly, despite MgtB being only one member of the Mg2+stimulon and PhoPQ controlling the expression levels of a range of genes includingmgtB, theYersiniaΔmgtBmutants were more highly attenuated than the equivalentYersiniaΔphoPmutants in mouse models of infection. MgtB may be a suitable target for development of novel antimicrobials, and investigation of its role may help elucidate the contribution of this component of the PhoPQ regulon to pathogenesis.
mInDel: an efficient pipeline for high-throughput InDel marker discovery
Authors: Lv Yuanda , Liu Yuhe , Zhang Xiaolin , Zhao Han
Published: September 2014

Background

Next-Generation Sequencing (NGS) technologies have emerged as a powerful tool to reveal nucleotide polymorphisms in a high-throughput and cost-effective manner. However, it remains a daunting task to proficiently analyze the enormous volume of data generated from NGS and to identify length polymorphisms for molecular marker discovery. The development of insertion-deletion polymorphism (InDel) markers is in particular computationally intensive, calling for integrated high performance methods to identify InDels with high sensitivity and specificity, which would directly benefit areas from genomic studies to molecular breeding.

Results

We present here a NGS-based tool for InDel marker discovery (mInDel), a high-performance computing pipeline for the development of InDel markers between any two genotypes. The mInDel pipeline proficiently develops InDel markers by comparing shared region size using sliding alignments between assembled contigs or reference genomes. mInDel has successfully designed thousands of InDel markers from maize NGS data locally and genome-wide. The program needs less than 2 hours to run when using 20 threads on a high-performance computing server to implement 40G data.

Conclusions

mInDel is an efficient, integrated pipeline for a high-throughput design of InDel markers between genotypes. It will be particularly applicable to the crop species which require a sufficient amount of DNA markers for molecular breeding selection. mInDel is freely available for downloading atwww.github.com/lyd0527/mInDelwebsite.
MyGene.info: gene annotation query as a service
Authors: Wu Chunlei , Mark Adam , Su Andrew I.
Published: September 2014

Biomedical knowledge is often represented as annotations of biological entities such as genes, genetic variants, diseases, and drugs. For gene annotations, they are fragmented across data repositories like NCBI Entrez, Ensembl, UniProt, and hundreds (or more) of other specialized databases. While the volume and breadth of annotations is valuable, their fragmentation across many data silos is often frustrating and inefficient. Bioinformaticians everywhere must continuously and repetitively engage in data wrangling in an effort to comprehensively integrate knowledge from all these resources, and these uncoordinated efforts represent an enormous duplication of work. We previously released MyGene.info (http://mygene.info) to enable bioinformatics developers to gain programmatic access to gene annotation data through our high-performance web services. This article focuses on the updates to MyGene.info since our last paper (2013 database issue). With the completely re-factored system, MyGene.info now expands the support from the original nine species to over 14K species, covering >17M genes with >50 gene-specific annotation types. Two simple web service endpoints provides high-performance query access to all these aggregated gene annotations. The infrastructure underlying MyGene.info is highly scalable, which offers both high-performance and high-concurrency, and makes MyGene.info particularly suitable for the use cases of real-time applications and analysis pipelines.
Genome-Wide Mapping In A House Mouse Hybrid Zone Reveals Hybrid Sterility Loci And Dobzhansky-Muller Interactions
Authors: Turner Leslie M. , Harr Bettina
Published: September 2014

Mapping hybrid defects in contact zones between incipient species can identify genomic regions contributing to reproductive isolation and reveal genetic mechanisms of speciation. The house mouse features a rare combination of sophisticated genetic tools and natural hybrid zones between subspecies. Male hybrids often show reduced fertility, a common reproductive barrier between incipient species. Laboratory crosses have identified sterility loci, but each encompasses hundreds of genes. We map genetic determinants of testis weight and testis gene expression using offspring of mice captured in a hybrid zone betweenM. musculus musculusandM. m. domesticus. Many generations of admixture enables high-resolution mapping of loci contributing to these sterility-related phenotypes. We identify complex interactions among sterility loci, suggesting multiple, non-independent genetic incompatibilities contribute to barriers to gene flow in the hybrid zone.
Crystal structure of 6-(4-chlorophenyl)-6a-nitro-6,6a,6b,7,9,11a-hexahydrospiro[chromeno[3′,4′:3,4]pyrrolo[1,2-c]thiazole-11,11′-indeno[1,2-b]quinoxaline] chloroform monosolvate
Authors: Sivakumar Nithya , Viswanathan Vijayan , Rao Jonnalagadda Naga Siva , Raghunathan Raghavachary , Velmurugan Devadasan
Published: September 2014

In the title compound, C33H23ClN4O3S·CHCl3, the thiazole ring adopts an envelope conformation with the N atom as the flap, and the pyrrolidine ring adopts a half-chair conformation. The thiazole ring mean plane makes a dihedral angle of 59.31 (1)° with the pyrrolidine ring mean plane, 71.67 (1)° with the chromene ring and 82.59 (1)° with the chlorobenzene ring. An intramolecular C—H...N hydrogen bond occurs. In the crystal, a second C—H...N hydrogen bond links the main and solvent molecules. The solvent chloroform molecule is disordered about two positions with an occupancy ratio of 0.508 (14):0.492 (14).
Crystal structure of tolylfluanid
Authors: Cho Seonghwa , Kim Jineun , Kang Gihaeng , Kim Tae Ho
Published: September 2014

The title compound, C10H13Cl2FN2O2S2{systematic name:N-[(dichlorofluoromethyl)sulfanyl]-N′,N′-dimethyl-N-p-tolylsulfamide}, is a well known fungicide. The dihedral angle between the mean plane of the dimethylamino group and that of the benzene ring is 32.3 (3)°. One Cl atom and one F atom of the dichlorofluoromethylthio group are disordered over two sets of sites with an occupancy ratio of 0.605 (9):0.395 (9). In the crystal structure, two C—H...Cl hydrogen bonds link adjacent molecules, forming dimers withR22(14) loops. C—H...O hydrogen bonds link pairs of dimers into chains along theb-axis direction. These chains are joined by an additional C—H...O contact, generating a sheet in theabplane.
Crystal structure of 3-[4-(benzyloxy)phenyl]-2,3-dihydro-1H-benzo[f]chromen-1-one
Authors: Vasanthi R. , Reuben Jonathan D. , Ezhilarasi K. S. , Sathya S. , Usha G.
Published: September 2014

In the title compound, C26H20O3, the pyran ring has a distorted half-chair conformation and its mean plane is inclined to the naphthalene ring system, to which it is fused, by 10.79 (9)°. The dihedral angles between the napthalene unit and the benzene and phenyl rings are 54.39 (9) and 52.65 (12)°, respectively, while the benzene and phenyl rings are inclined to one another by 74.80 (14)°. There is a short C—H...O contact in the chromen-1-one unit. In the crystal, molecules are linked by two pairs of C—H...O hydrogen bonds, forming inversion dimers described by graph set motifsR22(8) andR22(10), giving rise to chains running parallel to (101). The chains are linkedviaC—H...π interactions, forming sheets lying parallel to (010).
Specular neutron reflection at the mica/water interface – irreversible adsorption of a cationic dichain surfactant
Authors: Browning Kathryn Louise , Griffin Lucy Rachael , Gutfreund Philipp , Barker Robert David , Clifton Luke Ashley , Hughes Arwel , Clarke Stuart Matthew
Published: September 2014

Neutron reflection from the important mineral mica at the solid/liquid interface is presented here using a new approach – a very thin mica crystal supported on a silicon substrate. This approach avoids the problems of crystal defects and surface undulations that have hindered previous work. The use of mica as a reflectivity substrate is important as it is a model surface, which is atomically smooth with a high structural charge. In this work the mica/water interface is fully characterized. In particular, a characteristic double critical edge is observed, arising from the higher scattering length densities of the mica and D2O subphase relative to the silicon support. The experimental data are modelled using a combined approach: conventional amplitude summation (matrix method) for the thin layers and reflected intensity summation with attenuation terms for the thick layers of mica and hydrocarbon adhesive. Reflection data from the adsorption of the dichain cationic surfactant didodecyldimethylammonium bromide (DDAB) to the surface of muscovite mica from aqueous solution are also presented. It is found that, at twice the critical micelle concentration, a bilayer of DDAB with a thickness of 24 Å is observed, containing essentially no water. Its partial removal by washing and ion exchange is also presented.
Investigation of orthorhombic–tetragonal structural crossover in (Ba0.92Ca0.08)(Zr0.05Ti0.95)O3
Authors: Singh G. , Upadhaya A. , Sinha A. K. , Tiwari V. S.
Published: September 2014

The orthorhombic to tetragonal phase transition in (Ba0.92Ca0.08)(Zr0.05Ti0.95)O3was investigated using high-temperature X-ray diffraction between 260 and 333 K. The results established the presence of tetragonal (P4mm) and orthorhombic (Amm2) phase co-existence in the temperature range of 293 ≤T≤ 313 K. The tetragonal phase was found to increase from 27% at 293 K to 76% at 313 K. The structural refinement and line-profile analysis ruled out the presence of an intermediate monoclinic structure duringP4mm→Amm2 crossover. The analysis shows a pure orthorhombic (Amm2) structure forT< 293 K and tetragonal forT> 313 K.
Nanocrystallite model for amorphous calcium carbonate
Authors: Rez P. , Sinha S. , Gal A.
Published: September 2014

Amorphous calcium carbonate phases, either synthesized artificially or generated biogenically, can be identified from broadened peaks in X-ray or electron diffraction profiles. It is conceivable that randomly oriented nanocrystals, approximately 1 nm in size, could give rise to coherent diffraction profiles that are characterized as amorphous. The coherent diffraction profiles for 200 keV electrons, as might be used in an electron microscope, and Cu Kα X-rays were calculated for needle-shaped calcite crystals bounded by \{ {11\overline 21}\} facets and rhomb-shaped crystals bounded by \{ {10\overline 14} \} facets. Crystals of about 1.0 nm in size gave a profile that is consistent with the X-ray measurements of amorphous calcium carbonate. The relative intensity of high-angle broadened peaks and changes in the IR spectrum are best explained by disorder in the nanocrystallites. The presence of randomly oriented nanocrystallites also explains the lack of optical birefringence.
Crystal chemistry of clinker relicts from aged cementitious materials
Authors: Secco Michele , Peruzzo Luca , Palasse Laurie , Artioli Gilberto , Viani Alberto , Gualtieri Alessandro Francesco
Published: September 2014

Despite the general tendency to consider Portland cement virtually fully hydrated within a few years, the occurrence of non-reacted clinker phases in cementitious materials that are several decades old is rather common. In this work, the integration of microstructural analysis by scanning electron microscopy and quantitative microchemical and micromineralogical characterization techniques, such as electron microprobe analysis and electron backscatter diffraction, allowed the definition of the crystal-chemical properties of partially hydrated cement residuals within different types of aged cementitious materials. The results on several clinker relicts show that the calcium silicate phases are transformed systematically and pervasively by hydration reactions, whereas the aluminate and ferrite phases do frequently persist in the anhydrous state. These relict phases may be distinguished through their peculiar chemical, mineralogical and textural features. These observations raise interesting questions concerning the long-term hydration kinetics of clinker phases and the durability behaviour of cementitious materials in operating conditions.