Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of phylogenetic methods for inferring the direction of HIV transmission: HPTN 052.

BACKGROUND Phylogenetic analysis can be used to assess HIV transmission in populations. We inferred the direction of HIV transmission using whole-genome HIV sequences from couples with known linked infection and known transmission direction. METHODS Complete next generation sequencing (NGS) data were obtained for 105 unique index-partner sample pairs from 32 couples enrolled in the HIV Prevention Trials Network (HPTN) 052 trial (up to two samples/person). Index samples were obtained up to 5.5 years before partner infection; partner samples were obtained near the time of seroconversion. The bioinformatics method, phyloscanner, was used to infer transmission direction. Analyses were performed using samples from individual sample pairs, samples from all couples (one sample/person; group analysis) and all available samples (multi-sample group analysis). Analysis was also performed using NGS data from defined regions of the HIV genome (gag, pol, env). RESULTS Using whole-genome NGS data, transmission direction was inferred correctly (index to partner) for 98/105 (93.3%) of the individual sample pairs, 99/105 (94.3%) sample pairs using group analysis, and 31 (96.9%) of the 32 couples using multi-sample group analysis. There were no cases where the incorrect transmission direction (partner to index) was inferred. The accuracy of the method was higher with greater time between index and partner sample collection. Pol region sequences performed better than env or gag sequences for inferring transmission direction. CONCLUSIONS We demonstrate the potential of a phylogenetic method to infer the direction of HIV transmission between two individuals using whole-genome and pol NGS data.
Modelling of the human tongue

Biomechanical modelling of the human tongue This project aims at building a 3D biomechanical model of the human tongue, including all the muscles which are embedded into tongue tissues. A non-linear hyperelastic Finite Element model has been built and inserted into geometrical models of the upper airways. This dynamical model is now used to study the complex speech production process. In the future, we plan to use it to assist the surgeries of tongue cancers, trying to give a prediction of (.)
Über Desoxyribonucleinsäure-Molekeln in Protein-Mischfilme

A nucleoprotein of a vitrous consistency was extracted from the gonads of the coalfish (Gadus virens). The preparation of deoxyribonucleic acid (DNA) from this nucleoprotein and from staphylococci is described. Both of these different kinds of DNA have been mixed with bovine serum albumin or cytochrom c respectively to produce solutions which subsequently were spread onto the Langmuir trough under defined conditions. After transfer of aliquots from the surface monolayers to carbon support films the preparations were examined with the electron microscope. The micrographs show threads of various lengths, partly stretched, partly folded in loops, consisting of DNA molecules embedded in a protein envelope. Measurements and calculations of 5900 particles of the complex of Gadus virens-DNA-Albumin, with relatively short threads show a distribution of discontinuous character. If length is plotted against number then it occurs that there are maxima of different lengths of threads. The abscissae of these maxima obey the ratio 1 : 2 : 4 : 8. This holds for longer threads too the maxima of which, however, have smaller ordinate values.
Peridigm summary report : lessons learned in development with agile components.

This report details efforts to deploy Agile Components for rapid development of a peridynamics code, Peridigm. The goal of Agile Components is to enable the efficient development of production-quality software by providing a well-defined, unifying interface to a powerful set of component-based software. Specifically, Agile Components facilitate interoperability among packages within the Trilinos Project, including data management, time integration, uncertainty quantification, and optimization. Development of the Peridigm code served as a testbed for Agile Components and resulted in a number of recommendations for future development. Agile Components successfully enabled rapid integration of Trilinos packages into Peridigm. A cost of this approach, however, was a set of restrictions on Peridigm's architecture which impacted the ability to track history-dependent material data, dynamically modify the model discretization, and interject user-defined routines into the time integration algorithm. These restrictions resulted in modifications to the Agile Components approach, as implemented in Peridigm, and in a set of recommendations for future Agile Components development. Specific recommendations include improved handling of material states, a more flexible flow control model, and improved documentation. A demonstration mini-application, SimpleODE, was developed at the onset of this project and is offered as a potential supplement to Agile Components documentation.
Intelligent Resource Operational Network (IRON) for Cultural Modeling

In this poster session, we describe a framework for developing human, social, and cultural behavior models. The goal of this framework is take a hybrid approach to intelligence and behavior modeling. This hybrid model, called the Intelligent Resource Operational Network (IRON), attempts to combine multiple modeling and machine learning resources which include, but are not limited to: rule-based and expert systems, neural networks, genetic algorithms, and cognitive models, etc.
Bury Me in a Pot Bunker: Golf Through the Eyes of the Game's Most Challenging Course Designer

To the millions of golfers who have played his world-famous courses, Pete Dye is either a creative genius or a demonic tormentor. To play well on Pete's courses, or on any of those influenced by his ideas, you have to know Pete. Bury Me in a Pot Bunker is his own story of how he revolutionised his favourite game by designing courses that both delight and bedevil golfers.
Design of high frequency circuits for a gigabit per second data transmission system with isolation transformers and improved electrostatic protection

The focus of this dissertation is the design of a 10 Gbit/s wireline data communication system. The data is sent from the driver chip to the receiver chip on a printed circuit board (PCB). In the GHz frequency range, the parasitic effect of various circuits along the signal path affect the quality of the signal sent. Electrostatic Discharge (ESD) protection, PCB traces and packaging increase the signal loss and distortion. The parasitic effect of ESD protection circuits limits the maximum bandwidth for data transmission. The current high speed driver architectures have the driver circuit directly connected to the chip pads and PCB traces. This causes the chip to be prone to ESD discharge effects. Placing large ESD devices that shunt the output driver to ground, results in their parasitic capacitances acting as low pass filters that severely limit the data transmission rate. The packaging and PCB material are investigated in this project too. An electrical model of the bonding wire is developed through MATLAB® and HSPICE®. In order to increase the data rate, changes in the architecture are performed. The con­ tribution of this project is the introduction of on chip monolithic 4 port RF transformers at the driver and receiver front-end circuits. The transformers act as ESD isolation devices be­ cause they filter the low frequency components of the ESD signals before they damage the driver. The driver is physically isolated from the chip exterior. The signal in the driver is conveyed to the traces outside the chip by transformer induction behavior. Spark gap devices are added as ESD discharge paths too. Through investigating several transformer architec­ tures, planar interleaved transformers are fabricated and characterized to have a bandwidth beyond 5GHz needed for suitable data transmission. A design and characterization method of RF transformers by geometric scaling is presented.
Dynamic Reliability, Preventive Maintenance, Control of the Risk in Real Time

SUMMARY This article presents a concept of dynamic reliability based on the calculation of the probability of residual survival as evaluated in real time. This probability is calculated by taking into consideration the knowledge of the past operations scenario, revealed by means of the records of the stress sustained. This stress is evaluated with the help of the in-car information sources, sensors, measuring chains, and recorders. The whole of the information is used to define the parameters of our calculation model. In this model two methods of data processing are presented. If the first one memorizes the history of the operation’s real conditions, the other one – based on the system’s state function – naturally considers the past using the failure rate derivative. These approaches make it possible to make more realistic and precise decisions concerning the preventive change, which consequently leads to the following advantages: the extension of the period preceding the change, and a better control over the risk.
Gun Tube/Charge/Projectile Interactions and Gun Tube Wear

Abstract : During initial testing of the first US stick propellant charge for howitzer applications, the M203A1, an unusual asymmetric wear pattern developed. Virtually all wear which occurred during the 3000 round test was located in the top quadrant (10-2 o'clock) of the tube near the origin of rifling. Further complicating the analysis was the use of a 'simulator projectile', the PXR6325, in lieu of the fielded M549A1 projectile for the wear study. This study was initiated to determine if the PXR6325 projectile had unduly influenced the wear results and to determine how stick propellants differ from their granular counterparts in the processes producing gun tube wear. These questions were addressed in a three-pronged attack in which: a) historical US and NATO stick propellant wear data were analyzed; b) the two projectiles under study were compared using physical properties and finite element modeling; c) a matrix of test firings in a highly instrumented gun tube was conducted to measure properties such as heat transfer and gun tube strain at various circumferentially separated points of interest. As a result of these efforts, the contributions of the stick charges and different projectile designs on asymmetric gun wear were discerned. Using these data, the results of a subsequent stick charge wear retest using a new gun tube and a different projectile were accurately predicted. Keywords: Howitzer gun tube wear; Propelling charges; 155-mm Howitzers; Asymmetric wear; Thermocouple data; M203A1 Propelling charge.
Assessment of Driver Yielding Rates Pre- and Post-RRFB Installation, Bend, Oregon

The Oregon Department of Transportation improved two crosswalks on US 97 (Bend Parkway) near Bend, Oregon by installing Rectangular Rapid Flashing Beacons (RRFB), replacing signs, and enhancing pavement markings. At the location of the intersections where the RRFBs were installed the highway is a four-lane facility with a center median, bike lanes, and sidewalks. The posted speed is 45 miles per hour. At about the same time that the improvements were made at the two crosswalks on the Bend Parkway, RRFBs were installed at another nearby location in the City of Bend. As the use of RRFBs is considered experimental, particularly at locations with posted speeds in excess of 35 mph, an evaluation of driver compliance rates and conflicts at the three intersections was undertaken. Driver yielding rates increased significantly at all three intersections where RRFBs were installed. Prior to the installation of RRFBs, data was collected on a total of 159 crossings at the three intersections; following RRFB installation data was collected on a total of 211 crossings. The average yielding rate was 17.8%; following installation the average yielding rate more than tripled to 79.9%. The conclusion of the study was that RRFBs should be considered for installation on high-speed facilities where there are posted speeds greater than 35 miles per hour if there are pedestrians and bicyclists using the facility and a history of crashes or the potential for them. The design of an RRFB installation needs to include features to improve the visibility of the crossing.
Effect of search window size on search and rescue call-around performance

Abstract : The Fixed Wing Search and Rescue (FWSAR) project tasked Defence Research and Development Canada (DRDC) to provide guidance on the primary search window requirements for a new SAR aircraft. At issue was the effect of the size and location of the SAR technician's window on the SAR technician's ability to verbally guide a pilot to fly the aircraft over a search object. An answer was obtained through a two-stage approach. First, data were collected using a simulation of the call-around. In the synthetic environment, six SAR technicians performed a large number of call-arounds where the search window size and observer position in a simulated aircraft were adjusted on a trial-by-trial basis. Then, a live flying trial at CFB Comox involving two SAR technicians was conducted to validate the results obtained from the synthetic environment. Three recommendations emerged. First, the primary search window should provide a field of view of at least 160 . Second, performance is not affected by the visual effect of placing the window ahead of, or behind, the wing. Third, to obtain the full benefit of the field of view afforded by the window, the observer must be provided with an ergonomically sound work station.
Influence of some EPB operation parameters on ground movements

Some of the details of EPB tunnelling are difficult to introduce in conventional numerical models, nevertheless there are some parameters that can be included in the analyses in a fairly easy way. The EPB operating pressures are examples of these parameters. In this paper, the influence of such pressures on the ground movements and volume losses is examined. The construction of one of Barcelona Line 9 tunnels is taken as the reference case study. It is a 9.40 m diameter tunnel excavated in soft deltaic materials, below the ground water level
A robust confidence–accuracy dissociation via criterion attraction

Abstract Many studies have shown that confidence and accuracy can be dissociated in a variety of tasks. However, most of these dissociations involve small effect sizes, occur only in a subset of participants, and include a reaction time (RT) confound. Here, I develop a new method for inducing confidence–accuracy dissociations that overcomes these limitations. The method uses an external noise manipulation and relies on the phenomenon of criterion attraction where criteria for different tasks become attracted to each other. Subjects judged the identity of stimuli generated with either low or high external noise. The results showed that the two conditions were matched on accuracy and RT but produced a large difference in confidence (effect appeared for 25 of 26 participants, effect size: Cohen’s d = 1.9). Computational modeling confirmed that these results are consistent with a mechanism of criterion attraction. These findings establish a new method for creating conditions with large differences in confidence without differences in accuracy or RT. Unlike many previous studies, however, the current method does not lead to differences in subjective experience and instead produces robust confidence–accuracy dissociations by exploiting limitations in post-perceptual, cognitive processes.
Providing bandwidth on demand services using optical network design and the silo network architecture

This research concerns the issue of providing applications with direct access to bandwidth on demand services in cloud computing environments. Computationally intensive applications like scientific computing, data visualization and financial trading, require large amounts of network bandwidth and cannot tolerate variations in network performance. A cloud provider can address these concerns by reserving bandwidth of varying magnitude for application flows while minimizing network cost. We use a two-pronged strategy to address this issue. First, we design a provider network that satisfies long-term estimated traffic demands using traffic engineering approaches, minimizing the network deployment cost. Second, we accommodate application bandwidth requests of varying magnitude without exposing the details of the provider's network to the application. Cloud providers use optical networks to connect their infrastructure that is distributed over geographically diverse locations. We design an optical network to accommodate a given set of traffic demands with the objective of minimizing the number of wavelength interfaces or optical ports used by the nodes. Advances in optical communications enable grouping of wavelengths into wavebands and augment the communication devices, like optical cross connects, to switch wavebands. We propose a hierarchical approach which uses waveband technology to establish optical connections for the considered set of traffic demands. Simulations indicate that the hierarchical approach produces scalable solutions in terms of different waveband and cluster sizes. Customers of cloud providers pay only for the services and infrastructure they use; hence, cloud providers need to use customizable architectures to offer customer applications differentiated services. We augment the Services Integration and controL Optimization (SILO) network architecture to provide applications with bandwidth on demand services. The SILO architecture allows network stacks to be customized per application flow and enables easy service deployment for cloud providers. High bandwidth application flows are accommodated over multiple virtual circuits set up between the source and destination; multiple flow bandwidth application flows are groomed into a single virtual circuit. Each virtual circuit operates at network link speed and uses the optical connections established during network design.
Stirring: Theory and Practice

Stirring is one of the most important operations in process technology. No chemical exists that has non been submitted to a mixing process during its synthesis. Furthermore, stirring is important for the pharmaceutical and food industries, too. The most important mixing operations are applied to homogenize miscible liquids, to intensify the heat transfer between a liquid and the heat exchanger, and to perform mass transfer in multiphase systems, to whirl up solid particles in fluids and to disperse immiscible liquids. This book discusses in detail the above listed operations, taking into consideration also different rheological behaviour of the system treated (Newtonian and non-Newtonian). For each stirring task reliable scale-up rules are presented. In addition, mixing in pipes is discussed in great detail. Since there are so many aspects it is almost impossible for the user to get and keep an overview. Therefore, this book presents more than 730 references and covers publications until the end of the year 2000 for everybody who needs to know more details.
Stop Bullying at Work: Strategies and Tools for HR and Legal Professionals

The nature and impact of workplace bullying is addressed in this comprehensive overview. From the perspective of the human resources (HR) department, this practical guide provides the tools to both investigate interpersonal conflict and eliminate the problem. Policy models that not only tackle harassment issues but also implement strategies that comply with legislation are also presented. HR practitioners will learn to handle harassment at all levels of employment and, as a result, create productive work environments.
Computer-supported collaboration using Pick-and-Drop interaction on handheld computers

This study investigates a new interaction technique for collaboration on handheld computers called Pick-and-Drop. The technique is an extension of the popular Drag-and-Drop method used in many graphical interfaces today, but with Pick-and-Drop on-screen objects can be picked from one screen with a pen and dropped onto another. The aim of the study is to answer whether Pick-and-Drop promote collaboration among children by letting them focus more on other users and the task at hand than on the computer interaction. The study also investigates in what way collaborative situations can benefit from Pick-and-Drop. A prototype Pick-and-Drop system was implemented on four customized handheld computers equipped with wireless network communication. The prototype allowed spontaneous collaboration using ad-hoc networks and peer-to-peer communication. Radio Frequency Identification (RFID) tags were used to identify the pens when picking and dropping objects from the screen. Ten children aged 6-7 years old participated in the study at an after- school recreational centre. They tried Pick-and-Drop by playing a collaborative game of buying and selling apples using golden coins represented as icons on the screen. The test was video filmed for later analysis. The study showed that Pick-and-Drop offers effective collaborative interaction based on a mix of turn taking and concurrent interaction. Users do not have to switch focus when using an application or sharing data as the interaction style stays the same. There was an interesting difference in control over the interaction when users shared objects by “giving” or by “taking”. Users stayed in better control when they shared objects through giving.
Restoration of clipped sound signals -a weighted Fourier series and AR approach

Sound signals can be distorted in many dierent ways, one of them is calledclipping. A clipped sound signal diers from a non-clipped signal in the waythat the amplitudes of the sound wave that are higher than a certain amplitudethreshold has been partially lowered or completely lowered to the threshold,the latter is called hard clipping. Since data is lost when a signal is clipped,there is an interest in restoring the signal. For a hard clipped signal, it is oftenimpossible to perfectly restore the signal.In this thesis two dierent methods for partially restoring a symmetrically hardclipped signal are suggested. The two methods considered are a weighted Fourierseries (WFS) t and an autoregressive (AR) model approach. Both methodsattempt to restore the signal by solving optimization problems designed to min-imize the errors of the respective model.Evaluation and comparison of the two methods showed that the AR methodtypically performed better than the WFS method. The AR method was eec-tive at restoring the signal, while the WFS method stuck close to the clippedsignal, which might be due to dierences in their optimization problems.