Miracle-dz/UniFAR-FTUs huggingface dataset:
Analyses of multiple-site and concurrent Chlamydia trachomatis serovar infections, and serovar tissue tropism for urogenital versus rectal specimens in male and female patients

Objectives The aims of this study were: to determine the incidence of concurrent infections on a serovar level; to determine the incidence of multiple anatomical infected sites on a detection and genotyping level and analyse site-specific serovar distribution; to identify tissue tropism in urogenital versus rectal specimens. Methods Chlamydia trachomatis-infected patients in two populations were analysed: 75 visiting the outpatient department of obstetrics and gynaecology of the MC Haaglanden, and 358 visiting the outpatient sexually transmitted disease clinic, The Hague, The Netherlands. The PACE 2 assay (Gen-Probe) was used to detect C trachomatis from urethral, cervical, vaginal, oropharyngeal and anorectal swabs. C trachomatis genotyping was performed on all C trachomatis positive samples, using the CT-DT genotyping assay. Results Samples from 433 patients (256 female and 177 male) with confirmed C trachomatis infection were analysed. In 11 patients (2.6%), concurrent serovars in one anatomical sample site were present. In 62 (34.1%) female and four (9.3%) male patients, multiple sample site infections were found. A substantial percentage of women tested at the cervical/vaginal and rectal site were found to be positive at both sites (36.1%, 22/61). In men, D/Da and G/Ga serovars were more prevalent in rectal than urogenital specimens (p=0.0081 and p=0.0033, respectively), while serovar E was more prevalent in urogenital specimens (p=0.0012). Conclusions The prevalence of multiple serovar infections is relatively low. Significant differences in serovar distribution are found in rectal specimens from men, with serovar G/Ga being the most prominent, suggesting tissue tropism.
Towards in silico design of epitope-based vaccines

Background: Epitope-based vaccines (EVs) make use of immunogenic peptides (epitopes) to trigger an immune response. Due to their manifold advantages, EVs have recently been attracting growing interest. The success of an EV is determined by the choice of epitopes used as a basis. However, the experimental discovery of candidate epitopes is expensive in terms of time and money. Furthermore, for the final choice of epitopes various immunological requirements have to be considered. Methods: Numerous in silico approaches exist that can guide the design of EVs. In particular, computational methods for MHC binding prediction have already become standard tools in immunology. Apart from binding prediction and prediction of antigen processing, methods for epitope design and selection have been suggested. We review these in silico approaches for epitope discovery and selection along with their strengths and weaknesses. Finally, we discuss some of the obvious problems in the design of EVs. Conclusion: State-of-the-art in silico approaches to MHC binding prediction yield high accuracies. However, a more thorough understanding of the underlying biological processes and significant amounts of experimental data will be required for the validation and improvement of in silico approaches to the remaining aspects of EV design.
Esthetic Color Training in Dentistry

Part I: Color and Appearance 1. Color The Nature of Color The Physical Specification of Object Color The Human Color Vision System Color Perception 2. Colorimetry Color Specification Color Difference Evaluation Color Measuring Instruments 3. Other Appearance Attributes Translucency and Opacity Gloss Surface Roughness Opalescence Iridescence Fluorescence Phosphorescence Part II: Natural Teeth And Esthetic Dental Materials 4. Natural Teeth Anatomy And Histology Of Teeth Optical Properties Of Human Teeth 5. Esthetic Dental Materials Dental Ceramics Resin Composites Denture Teeth And Prefabricated Teeth Denture Base Materials Tooth Bleachig Materials Glass Ionomer Restorative Materials Hybrid Ionomer Restorative Materials Maxillofacial Materials Orthodontic Materials Pediatric Dentistry Materials Interim Restorative Materials Standardization Of Color And Appearance Of Dental Materials Part III: Color And Appearance -Matching, Communication & Reproduction 6. The Foundation Of Color Education Color Vision And Dentistry Education In Color And Appearance Color Training 7. Color Matching Shade Guides Color Matching Conditions Color Matching Method Instruments For Color Maching In Dentistry Color Formulation In Dentistry 8. Communication Of Color And Appearance Verbal/Written Instructions Custom Made Or Modified Shade Guides/Tabs Traditional Film Photograhy Slide Films Digital Images Additional Considerations 9. Reproduction Of Color And Appearance Indirect Restorative Materials Direct Restorative Materials (Resin Composites) Color Correction Of Indirect Restorations Part IV: DVD Instruction Manual Installing The Program Program Description Color Training Method Tips Conclusion
Bacon : A GPU Programming Language With Just in Time Specialization ( Draft )

This paper describes Bacon, a data-parallel programming system targeting OpenCL-compatible graphics processors. This system is built upon the existing OpenCL standard in order to make it easier for programmers to write high performance kernels for GPU accelerated applications. The OpenCL C syntax is extended into a new language, Bacon C, intended to make development significantly more convenient and enabling pre-optimizations based on just-in-time specialization as this code is compiled via OpenCL at runtime. Benchmarks are provided for matrix multiplication comparing a Bacon implementation to versions using OpenCL directly. Speedups are demonstrated both for naive implementations and when comparing a Bacon implementation of generalized block decomposed matrix multiplication to a hand-vectorized OpenCL kernel. This latter result demonstrates the benefit of the total loop unrolling enabled by just-in-time specialization. Additionally, a Bacon implementation of a more complex computation, stereo disparity, is considered.
Viral Etiology of Chronic Obstructive Pulmonary Disease Exacerbations during the A/H1N1pdm09 Pandemic and Postpandemic Period

Viral infections are one of the main causes of acute exacerbations of chronic obstructive pulmonary disease (AE-COPD). Emergence of A/H1N1pdm influenza virus in the 2009 pandemic changed the viral etiology of exacerbations that were reported before the pandemic. The aim of this study was to describe the etiology of respiratory viruses in 195 Spanish patients affected by AE-COPD from the pandemic until the 2011-12 influenza epidemic. During the study period (2009–2012), respiratory viruses were identified in 48.7% of samples, and the proportion of viral detections in AE-COPD was higher in patients aged 30–64 years than ≥65 years. Influenza A viruses were the pathogens most often detected during the pandemic and the following two influenza epidemics in contradistinction to human rhino/enteroviruses that were the main viruses causing AE-COPD before the pandemic. The probability of influenza virus detection was 2.78-fold higher in patients who are 30–64 years old than those ≥65. Most respiratory samples were obtained during the pandemic, but the influenza detection rate was higher during the 2011-12 epidemic. There is a need for more accurate AE-COPD diagnosis, emphasizing the role of respiratory viruses. Furthermore, diagnosis requires increased attention to patient age and the characteristics of each influenza epidemic.
Polynomial Interpolation

In practice, often we can measure a physical process or quantity (e.g., temperature) at a number of points (e.g., time instants for temperature), but we do not have an analytic expression for the process that would let us calculate its value at an arbitrary point. Interpolation provides a simple and good way of estimating the analytic expression, essentially a function, over the range spanned by the measured points.1 Consider a family of functions of a single variable x:
Compiler-supported simulation of highly scalable parallel applications

In this paper, we propose and evaluate practical, automatic techniques that exploit compiler analysis to facilitate simulation of very large message-passing systems. We use a compiler-synthesized static task graph model to identify the control-flow and the subset of the computations that determine the parallelism, communication and synchronization of the code, and to generate symbolic estimates of sequential task execution times. This information allows us to avoid executing or simulating large portions of the computational code during the simulation. We have used these techniques to integrate the MPI-Sim parallel simulator at UCLA with the Rice dHPF compiler infrastructure. The integrated system can simulate unmodified High Performance Fortran (HPF) programs compiled to the Message-Passing Interface standard (MPI) by the dHPF compiler, and we expect to simulate MPI programs as well. We evaluate the accuracy and benefits of these techniques for three standard benchmarks on a wide range of problem and system sizes. Our results show that the optimized simulator has errors of less than 17% compared with direct program measurement in all the cases we studied, and typically much smaller errors. Furthermore, it requires factors of 5 to 2000 less memory and up to a factor of 10 less time to execute than the original simulator. These dramatic savings allow us to simulate systems and problem sizes 10 to 100 times larger than is possible with the original simulator.
Improving adhesion between thin chromium film and polyimide substrate by Ar+ irradiation

Ar+ irradiation and annealing at an elevated temperature are used to improve the adhesion of deposited Cr thin films by vacuum evaporation onto polyimide (PI) substrates. The Ar+ ions of 50 and 200 keV and various Ar+ doses ranging from 1 × 1013 to 2 × 1016 ions/cm2 are chosen for the experiments, after many preliminary trials. The surface analyses are conducted employing Rutherford Backscattering Spectroscopy (RBS), Fourier transform infrared spectrometry (FTIR), X-ray photoelectron spectroscopy (XPS), and Scanning electron microscopy (SEM). Ar+ irradiation produces an interfacial layer of about 100 A (10 nm) thick in which Cr particles and PI molecules are physically mixed and chemically bonded. The chemical bonds of CrO and a trace of CrC are observed by XPS and FTIR. Impact-wear tests are also conducted in order to determine the effects of the Ar+ irradiation on the wear property of a Cr/PI system. A significant increase in the property is observed and the increase appears to be a function of the degree of adhesion of the Cr film to the PI substrate.
Differential Sodium and Potassium Transport Selectivities of the Rice OsHKT2;1 and OsHKT2;2 Transporters in Plant Cells1[C][OA]

Na+ and K+ homeostasis are crucial for plant growth and development. Two HKT transporter/channel classes have been characterized that mediate either Na+ transport or Na+ and K+ transport when expressed in Xenopus laevis oocytes and yeast. However, the Na+/K+ selectivities of the K+-permeable HKT transporters have not yet been studied in plant cells. One study expressing 5′ untranslated region-modified HKT constructs in yeast has questioned the relevance of cation selectivities found in heterologous systems for selectivity predictions in plant cells. Therefore, here we analyze two highly homologous rice (Oryza sativa) HKT transporters in plant cells, OsHKT2;1 and OsHKT2;2, that show differential K+ permeabilities in heterologous systems. Upon stable expression in cultured tobacco (Nicotiana tabacum) Bright-Yellow 2 cells, OsHKT2;1 mediated Na+ uptake, but little Rb+ uptake, consistent with earlier studies and new findings presented here in oocytes. In contrast, OsHKT2;2 mediated Na+-K+ cotransport in plant cells such that extracellular K+ stimulated OsHKT2;2-mediated Na+ influx and vice versa. Furthermore, at millimolar Na+ concentrations, OsHKT2;2 mediated Na+ influx into plant cells without adding extracellular K+. This study shows that the Na+/K+ selectivities of these HKT transporters in plant cells coincide closely with the selectivities in oocytes and yeast. In addition, the presence of external K+ and Ca2+ down-regulated OsHKT2;1-mediated Na+ influx in two plant systems, Bright-Yellow 2 cells and intact rice roots, and also in Xenopus oocytes. Moreover, OsHKT transporter selectivities in plant cells are shown to depend on the imposed cationic conditions, supporting the model that HKT transporters are multi-ion pores.
Proceedings of the 1997 IEEE International Conference on Robotics and Automation Structural Design Optimization and Comparative Analysis of a New High-Performance Robot Arm via Finite Element Analysis

This paper reports the structural design of a new highperformance robot arm. Design objectives for the new arm include large (1-2 meter) workspace, low weight, 5 kg payload capacity, high sti ness, high structural vibration frequencies, precise joint-level torque control, a total of three degrees-offreedom, and mechanical simplicity. A comparative analysis is reported for four very di erent two degree-of-freedom linkage candidates using the nite element method.
A 1.8 GHz CMOS VCO with reduced phase noise

A 2 V, 6 mA, 15% tuning range, 1.8 GHz VCO implemented in a standard 0.35 /spl mu/m CMOS process is presented. The phase noise of the VCO has been greatly reduced by means of on-chip filters and one off-chip low frequency inductor. The phase noise measured at 3 MHz offset from the carrier is between -141.5 dBc/Hz and -138.5 dBc/Hz over the whole tuning range.
What does bonding to modified wood tell us about adhesion

Determining adhesive bond performance for chemically modified wood is important not only in relation to its commercial utility but also because this information helps in understanding wood bond durability. Although wood modification is usually used to improve anti-swell efficiency, the modification can alter adhesive bond performance. Generally, modification is expected to diminish adhesion by making the wood surface less polar and less porous, resulting in poorer adhesive wetting of the wood and fewer chemical bonds between the two surfaces. On the other hand, chemical modification can help the wood bonds to pass water exposure durability tests because modified wood will swell less. Given the great variety of wood adhesives, species, and modification methods, a simple theory does not explain bonding behaviour. However, our model that takes into account the mechanism for dissipating stress induced by moisture-driven dimensional change, as well as general adhesion theories and adhesive-wood interactions, is useful for explaining our observations. Our model is evaluated in relation to bond strengths and percentage wood failure for dry and water-soaked compressive shear blocks of yellow poplar sapwood. The wood was modified with acetic anhydride, butylene oxide, or propylene oxide to provide different polar characteristics for the wood and then bonded with adhesives that belong to both of the main groups in our model, the flexible and the reinforcing adhesives. Thus, we were able to evaluate the validity of this model for explaining our experimental results, and this knowledge should lead to a more systematic design of improved adhesives for bonding wood.
A lab-on-chip approach for monitoring the electrochemical activity of biorealistic cell cultures

The objective of any cell culturing platform is to decipher the in vivo functionality of native tissue in order to deliver reliable cell models for disease and pharmacological studies and eventually in patient-specific tissue engineering. We present a new perspective in lab-on-chip implementations for cell culturing, emphasizing on a versatile technology for cell micropatterning that can integrate electrical and pH monitoring modalities to record extracellular activity. We employ Parylene C, a highly biocompatible material, as a flexible culture substrate that controls the cellular microtopography and promotes a more in vivo-like morphology of neonatal rat ventricular myocytes. Moreover, we transfer the patterning technology on commercially available Multi-Electrode arrays to highlight the potential of integration with products customly used for extracellular electrical recordings. Finally, we implement flexible Parylene sensors for spatiotemporal pH monitoring, using the material both as a support medium and as a sensing membrane. Integration of these three attributes may deliver a compact solution with high scientific and commercial impact.
Biodiversity-Based Identification and Functional Characterization of the Mannose-Specific Adhesin of Lactobacillus plantarum

ABSTRACT Lactobacillus plantarum is a frequently encountered inhabitant of the human intestinal tract, and some strains are marketed as probiotics. Their ability to adhere to mannose residues is a potentially interesting characteristic with regard to proposed probiotic features such as colonization of the intestinal surface and competitive exclusion of pathogens. In this study, the variable capacity of 14 L. plantarum strains to agglutinate Saccharomyces cerevisiae in a mannose-specific manner was determined and subsequently correlated with an L. plantarum WCFS1-based genome-wide genotype database. This led to the identification of four candidate mannose adhesin-encoding genes. Two genes primarily predicted to code for sortase-dependent cell surface proteins displayed a complete gene-trait match. Their involvement in mannose adhesion was corroborated by the finding that a sortase (srtA) mutant of L. plantarum WCFS1 lost the capacity to agglutinate S. cerevisiae. The postulated role of these two candidate genes was investigated by gene-specific deletion and overexpression in L. plantarum WCFS1. Subsequent evaluation of the mannose adhesion capacity of the resulting mutant strains showed that inactivation of one candidate gene (lp_0373) did not affect mannose adhesion properties. In contrast, deletion of the other gene (lp_1229) resulted in a complete loss of yeast agglutination ability, while its overexpression quantitatively enhanced this phenotype. Therefore, this gene was designated to encode the mannose-specific adhesin (Msa; gene name, msa) of L. plantarum. Domain homology analysis of the predicted 1,000-residue Msa protein identified known carbohydrate-binding domains, further supporting its role as a mannose adhesin that is likely to be involved in the interaction of L. plantarum with its host in the intestinal tract.
Microstructured polymer optical fiber-based surface plasmon resonance sensor

We propose a surface plasmon resonance sensor based on microstructured polymer optical fiber (mPOF) made of polymethyl methacrylate (PMMA) with the cladding having only one layer of air holes near the edge of the fiber. In such sensor, the nanoscale silver metal film can be deposited on the outer side of the fiber, which is easily realized. Numerical simulation results show that spectral and intensity sensitivity are in the range of 8.3×10-5~9.4×10-5RIU.
Multiple presynaptic metabotropic glutamate receptors modulate excitatory and inhibitory synaptic transmission in hippocampal area CA1

The metabotropic glutamate receptors (mGluRs) have many important roles in regulation of neuronal excitability and synaptic transmission. In hippocampal area CA1, activation of mGluRs can reduce both excitatory and inhibitory synaptic transmission. The conventional view is that the presynaptic effects are mediated by L-2-amino-4-phosphonobutyric acid (L-AP4)-sensitive, or group III mGluRs (mGluR4, mGluR6, mGluR7, mGluR8). However, some studies suggest that other mGluR subtypes may also be involved in regulation of excitatory and inhibitory synaptic transmission in area CA1. We have found that two pharmacologically distinct presynaptic receptors are involved in the depression of excitatory transmission at the Schaffer collateral--CA1 synapse. Consistent with previous studies, one receptor subtype is an L-AP4- sensitive receptor that is pharmacologically similar to mGluR4 or mGluR7. However, we have found that a second mGluR subtype, which is pharmacologically similar to mGluR1 and mGluR5 (group I mGluRs), can also reduce excitatory synaptic transmission in area CA1. Analysis of effects of agonists of these two receptors on miniature EPSCs and paired-pulse facilitation suggest that both receptors are localized presynaptically. It is also shown that the mGluR that reduces transmission at inhibitory synapses in area CA1 is presynaptically localized, is insensitive to L-AP4, and is sensitive to agonists selective for mGluR1 and mGluR5.
‘SGoFicance Trace’: Assessing Significance in High Dimensional Testing Problems

Recently, an exact binomial test called SGoF (Sequential Goodness-of-Fit) has been introduced as a new method for handling high dimensional testing problems. SGoF looks for statistical significance when comparing the amount of null hypotheses individually rejected at level γ = 0.05 with the expected amount under the intersection null, and then proceeds to declare a number of effects accordingly. SGoF detects an increasing proportion of true effects with the number of tests, unlike other methods for which the opposite is true. It is worth mentioning that the choice γ = 0.05 is not essential to the SGoF procedure, and more power may be reached at other values of γ depending on the situation. In this paper we enhance the possibilities of SGoF by letting the γ vary on the whole interval (0,1). In this way, we introduce the ‘SGoFicance Trace’ (from SGoF's significance trace), a graphical complement to SGoF which can help to make decisions in multiple-testing problems. A script has been written for the computation in R of the SGoFicance Trace. This script is available from the web site http://webs.uvigo. es/acraaj/SGoFicance.htm.
The uncommon roles of common gene regulatory factors in the genomes of differentiating cells

Viewed through the lens of comparative regulatory mechanisms in developmental processes, the article of Calero‐Nieto et al (2014, this issue) is of particular interest. This work uncovers the causal combinatorial subtleties of the distinct enhancer occupancy profiles displayed by ten different transcription factors, which are expressed in common in two hematopoietic cell types, a stem cell‐like precursor and primary mast cells.
Unified multi-antenna code design for fading channels with spatio-temporal/spectral correlations

A unified framework for coherent multiple antenna communications is presented leading to a general space-time code design criterion valid for arbitrary spatial and temporal fading correlations. This framework provides insights into the effect of each of spatial and temporal correlations on space-time code design. The single code design expression applies to quasi-static, fast fading and multiple block fading channels and more generally also to channels with arbitrary correlations in the temporal dimension as well as in the spatial dimension with arbitrary rank. The general coding strategy proposed consists of precoding a space-time code with its size determined by the rank of transmit correlation, the structure determined by the Cholesky factorization of the temporal correlation, and the precoding matrix obtained from the eigenvectors of the transmit correlation matrix