Miracle-dz/UniFAR-FTUs huggingface dataset:
High-throughput DNA synthesis in a multichannel format.

We describe an approach to high-throughput parallel DNA synthesis in which a multiwell format is used. The reactions are carried out in open wells using an argon ambient atmosphere to prevent reagent contamination. The controlled-pore glass beads which form the substrate for synthesis are held in individual wells with high-density polyethylene filter bottoms through which reagents are drawn into a vacuum manifold. The synthesis is carried out using direct reagent dispensing into the individual reaction wells. A computer controls the sequence in which reagents are dispensed and the timing of the periodic vacuum pulses required to synthesize the desired sequence. Experiments to date have demonstrated the viability of the approach for a variety of test sequences. Results obtained with HPLC analysis demonstrate coupling efficiencies as high as 99.5% under optimized conditions. Use of the oligomers for DNA sequencing templates and as PCR primers has been demonstrated in production applications. The current instrument design consists of a series of discrete reaction chambers in a 12 channel module which can be multiplexed in a 12 x n format where n can be 1-8, i.e. 96 wells. A projected time interval for 12 parallel syntheses is 2.5 h, with 96 syntheses in 3.5 h. Because of the reduced volume of reagents required in the open well format, significant cost savings are projected.
A camera-based calibration for automotive augmented reality Head-Up-Displays

Using Head-up-Displays (HUD) for Augmented Reality requires to have an accurate internal model of the image generation process, so that 3D content can be visualized perspectively correct from the viewpoint of the user. We present a generic and cost-effective camera-based calibration for an automotive HUD which uses the windshield as a combiner. Our proposed calibration model encompasses the view-independent spatial geometry, i.e. the exact location, orientation and scaling of the virtual plane, and a view-dependent image warping transformation for correcting the distortions caused by the optics and the irregularly curved windshield. View-dependency is achieved by extending the classical polynomial distortion model for cameras and projectors to a generic five-variate mapping with the head position of the viewer as additional input. The calibration involves the capturing of an image sequence from varying viewpoints, while displaying a known target pattern on the HUD. The accurate registration of the camera path is retrieved with state-of-the-art vision-based tracking. As all necessary data is acquired directly from the images, no external tracking equipment needs to be installed. After calibration, the HUD can be used together with a head-tracker to form a head-coupled display which ensures a perspectively correct rendering of any 3D object in vehicle coordinates from a large range of possible viewpoints. We evaluate the accuracy of our model quantitatively and qualitatively.
Restructuring Personality Disorders: A Short-Term Dynamic Approach

Part 1 The framework: quantum change for personality disordered patients the STRP model - process, theory, and constructs assessment and treatment planning how to formulate core issues techniques of STRP the use of anxiety and maximizing the therapeutic alliance comprehensive restructuring of the personality overview of the treatment process. Part 2 Process and technique in treatment of personality disorders the cluster C disorders - the treatment-responsive group the cluster B disorders - the mixed-results groups the cluster A disorders - the treatment-refractory group treatment pitfalls termination and follow- up measuring therapeutic effectiveness future challenges.
Novel and Efficient Cellular Automata Based Symmetric Key Encryption Algorithm for Wireless Sensor Networks

Our proposed method L2D-CASKE, the lightweight 2-dimensional (2-D) Cellular Automata (CA) based symmetric key encryption algorithm is a 128 bit length that allows a key length of 128 bits. It is designed as a lightweight encryption algorithm. As being light weight, it can be easily applied on small devices such as wireless sensor motes, smart cards and other PDAs. An encryption algorithm having simple loop operations, based on iterative parameters is used in this work. A number of sequences and operations are used for this purpose. In this paper, the well designed algorithm was verified using MATLAB 7.7 (R2008) tool and the hardware synthesized on Field Programmable Gate Arrays (FPGAs). To achieve this, our algorithm uses loop design based on iterations and the same is realized on FPGA. Advantages of our algorithm can be listed in terms of its flexibility for a set of given constraints, less complexity involved in its performance. This is achieved through the usage of generic VHDL coding. Virtex-4 XC4VL25 -10ff668 is used as a test device in Xilinx 9.1 for realizing our algorithm.
Safe controller optimization for quadrotors with Gaussian processes

One of the most fundamental problems when designing controllers for dynamic systems is the tuning of the controller parameters. Typically, a model of the system is used to obtain an initial controller, but ultimately the controller parameters must be tuned manually on the real system to achieve the best performance. To avoid this manual tuning step, methods from machine learning, such as Bayesian optimization, have been used. However, as these methods evaluate different controller parameters on the real system, safety-critical system failures may happen. In this paper, we overcome this problem by applying, for the first time, a recently developed safe optimization algorithm, SafeOpt, to the problem of automatic controller parameter tuning. Given an initial, low-performance controller, SafeOpt automatically optimizes the parameters of a control law while guaranteeing safety. It models the underlying performance measure as a Gaussian process and only explores new controller parameters whose performance lies above a safe performance threshold with high probability. Experimental results on a quadrotor vehicle indicate that the proposed method enables fast, automatic, and safe optimization of controller parameters without human intervention.
Coding of neuronal differentiation by calcium transients

Excitability has long been recognized as the basis for rapid signaling in the mature nervous system, but roles of channels and receptors in controlling slower processes of differentiation have been identified only more recently. Voltage‐dependent and transmitter‐activated channels are often expressed at early stages of development prior to synaptogenesis, and allow influx of Ca2+. Here we examine the functions of spontaneous transient elevations of intracellular Ca2+ in embryonic neurons. These Ca2+ transients abruptly raise levels of Ca2+ as much as tenfold, for brief periods, repeatedly, and can be highly localized. Like cloudbursts on the developing landscape, Ca2+ transients modulate growth and stimulate differentiation, in a frequency‐dependent manner, probably by changes in phosphorylation or proteolysis of regulatory and structural proteins in local regions. We review the mechanisms by which Ca2+ transients are generated and their effects in regulating motility via the cytoskeleton and differentiation via transcription. BioEssays 22:811–817, 2000. © 2000 John Wiley & Sons, Inc.
A method and a tool for rapid prototyping of large-scale business information systems

This paper presents a method and concepts of a supporting tool for rapid prototyping of large-scale business information systems. Our method is based on the following guidelines: (1) small team of highly skilled members with combined skills, (2) prototype-based development of subsystems and the system as a whole, (3) brainstorming sessions always involving system analysts database and application designers, and user representatives (if needed), and (4) application generator providing for efficient prototype development by maximum automation of all design phases. The also presented application generator (AppGen) is based on standardization of functional and visual characteristics of an application, a library of high-level, coarse grained components, and a set of rules for model-to-application mapping enabling automatic application reconfiguration in case of changes in the data model.
Chaos Theory and Epilepsy

Recently, interest has turned to the mathematical concept of chaos as an explanation for a variety of complex processes in nature. Chaotic systems, among other characteristics, can produce what appears to be random output. Another property of chaotic systems is that they may exhibit abrupt intermittent transitions between highly ordered and disordered states. Because of this property, it is hypothesized that epilepsy may be an example of chaos. In this review, some of our basic concepts of nonlinear dynamics and chaos are illustrated. Mathematical techniques developed to study the properties of nonlinear dynamical systems are outlined. Finally, the results of applying these techniques to the study of human epilepsy are discussed. The application of these powerful and novel mathematical techniques to analysis of the electroencephalogram has provided now insights into the epileptogenic process and may have considerable utility in the diagnosis and treatment of epilepsy. The Neuroscientist 2:118-126, 1996
Role of purine-rich exonic splicing enhancers in nuclear retention of pre-mRNAs

Intron-containing pre-mRNAs are normally retained in the nucleus until they are spliced to produce mature mRNAs that are exported to the cytoplasm. Although the detailed mechanism is not well understood, the formation of splicing-related complexes on pre-mRNAs is thought to be responsible for the nuclear retention. Therefore, pre-mRNAs containing suboptimal splice sites should tend to leak out to the cytoplasm. Such pre-mRNAs often contain purine-rich exonic splicing enhancers (ESEs) that stimulate splicing of the adjacent intron. Here, we show that ESEs per se possess an activity to retain RNAs in the nucleus through a saturable nuclear retention factor. Cross-competition experiments revealed that intron-containing pre-mRNAs (without ESEs) used the same saturable nuclear retention factor as ESEs. Interestingly, although intronless mRNAs containing ESEs were also poorly exported, spliced mRNAs produced from ESE-containing pre-mRNAs were efficiently exported to the cytoplasm. Thus, the splicing reaction can reset the nuclear retention state caused by ESEs, allowing nuclear export of mature mRNAs. Our results reveal a novel aspect of ESE activity that should contribute to gene expression and RNA quality control.
Lion (Panthera leo) populations are declining rapidly across Africa, except in intensively managed areas

Significance At a regional scale, lion populations in West, Central, and East Africa are likely to suffer a projected 50% decline over the next two decades, whereas lion populations are only increasing in southern Africa. Many lion populations are either now gone or expected to disappear within the next few decades to the extent that the intensively managed populations in southern Africa may soon supersede the iconic savannah landscapes in East Africa as the most successful sites for lion conservation. The rapid disappearance of lions suggests a major trophic downgrading of African ecosystems with the lion no longer playing a pivotal role as apex predator. We compiled all credible repeated lion surveys and present time series data for 47 lion (Panthera leo) populations. We used a Bayesian state space model to estimate growth rate-λ for each population and summed these into three regional sets to provide conservation-relevant estimates of trends since 1990. We found a striking geographical pattern: African lion populations are declining everywhere, except in four southern countries (Botswana, Namibia, South Africa, and Zimbabwe). Population models indicate a 67% chance that lions in West and Central Africa decline by one-half, while estimating a 37% chance that lions in East Africa also decline by one-half over two decades. We recommend separate regional assessments of the lion in the World Conservation Union (IUCN) Red List of Threatened Species: already recognized as critically endangered in West Africa, our analysis supports listing as regionally endangered in Central and East Africa and least concern in southern Africa. Almost all lion populations that historically exceeded ∼500 individuals are declining, but lion conservation is successful in southern Africa, in part because of the proliferation of reintroduced lions in small, fenced, intensively managed, and funded reserves. If management budgets for wild lands cannot keep pace with mounting levels of threat, the species may rely increasingly on these southern African areas and may no longer be a flagship species of the once vast natural ecosystems across the rest of the continent.
SEMIPARAMETRIC STRUCTURAL MODELS OF BINARY RESPONSE: SHAPE RESTRICTIONS AND PARTIAL IDENTIFICATION

I study the partial identifying power of structural single-equation threshold-crossing models for binary responses when explanatory variables may be endogenous. The sharp identified set of threshold functions is derived for the case in which explanatory variables are discrete, and I provide a constructive proof of sharpness. There is special attention to a widely employed semiparametric shape restriction, which requires the threshold-crossing function to be a monotone function of a linear index involving the observable explanatory variables. The restriction brings great computational benefits, allowing calculation of the identified set of index coefficients without calculating the nonparametrically specified threshold function. With the restriction in place, the methods of the paper can be applied to produce identified sets in a class of binary response models with mismeasured explanatory variables.
Mutational neighbourhood and mutation supply rate constrain adaptation in Pseudomonas aeruginosa

Understanding adaptation by natural selection requires understanding the genetic factors that determine which beneficial mutations are available for selection. Here, using experimental evolution of rifampicin-resistant Pseudomonas aeruginosa, we show that different genotypes vary in their capacity for adaptation to the cost of antibiotic resistance. We then use sequence data to show that the beneficial mutations associated with fitness recovery were specific to particular genetic backgrounds, suggesting that genotypes had access to different sets of beneficial mutations. When we manipulated the supply rate of beneficial mutations, by altering effective population size during evolution, we found that it constrained adaptation in some selection lines by restricting access to rare beneficial mutations, but that the effect varied among the genotypes in our experiment. These results suggest that mutational neighbourhood varies even among genotypes that differ by a single amino acid change, and this determines their capacity for adaptation as well as the influence of population biology processes that alter mutation supply rate.
Histogram-Based Ratio Mismatch Calibration for Bridge-DAC in 12-bit 120 MS/s SAR ADC

This brief reports a 120 MS/s 12-bit successive approximation register analog-to-digital converter (ADC). The conversion nonlinearity in a bridge digital-to-analog converter is analyzed, and its corresponding histogram-based ratio mismatch (HBRM) calibration is presented in detail. Verified by behavioral simulations as well as measured results, the solution improves both the dynamic performance and the static performance of the ADC. The measurement results demonstrate that the HBRM calibration effectively improves the signal-to-noise distortion ratio from 56.9 to 63.7 dB at dc input, with a sampling frequency of 120 MS/s.
Endoglin – a marker of vascular endothelial cell proliferation in cancer

Endoglin (CD105) is an accessory receptor of transforming growth factor B. The highest synthesis, as well as expression, of endoglin has been found in vascular endothelial cells. The involvement of endoglin in angiogenesis and in angiogenesis-dependent processes has been observed. Endoglin promotes angiogenesis not only by activation of vascular endothelial cell proliferation but also by induction of the antiapoptotic pathway in hypoxic endothelial cells. The potential application of endoglin as a tumour angiogenesis marker, useful for cancer diagnostics and clinical application, is anticipated. Endoglin expression may be useful as an indicator of disease progression and helpful for estimation of recurrence and metastasis risk.
Janus-faced Enzymes Yeast Tgl3p and Tgl5p Catalyze Lipase and Acyltransferase Reactions

The yeast triacylglycerol (TAG) lipases Tgl3p and Tgl5p not only contain a TAG lipase, but also an acyltransferase motif. We show that purified Tgl3p and Tgl5p indeed exhibit lysophospholipid acyltransferase activity. Both Tgl3p and Tgl5p affect the level of glycerophospholipids, and Tgl3p is also important for efficient sporulation of yeast.
Serious Games for education and training

Serious Games (SGs) are gaining an ever increasing interest for education and traning. Exploiting the latest simulation and visualization technologies, SGs are able to contextualize the player’s experience in challenging, realistic environments, supporting situated cognition. However, we still miss methods and tools for effectively and deeply infusing pedagogy and instruction inside digital games. After presenting an overview of the state of the art of the SG taxonomies, the paper introduces the pedagogical theories and models most relevant to SGs and their implications on SG design. We also present a schema for a proper integration of games in education, supporting different goals in different steps of a formal education process. By analyzing a set of well-established SGs and formats, the paper presents the main mechanics and models that are being used in SG designs, with a particular focus on assessment, feedback and learning analytics. An overview of tools and models for SG design is also presented. Finally, based on the performed analysis, indications for future research in the field are provided.
Optical camera tracking in virtual studios: Degenerate cases

Over the past few years, virtual studios applications have significantly attracted the attention of the entertainment industry. Optical tracking systems for virtual sets production have become particularly popular tending to substitute electro-mechanical ones. In this work, an existing optical tracking system is revisited, in order to tackle with inherent degenerate cases; namely, reduction of the perspective projection model to the orthographic one and blurring of the blue screen. In this context, we propose a simple algorithm for 3D motion estimation under orthography using 3D-to-2D line correspondences. In addition, the watershed algorithm is employed for successful feature extraction in the presence of defocus or motion blur.
Antigen-Retrieval Procedure for Bromodeoxyuridine Immunolabeling with Concurrent Labeling of Nuclear DNA and Antigens Damaged by HCl Pretreatment

Visualizing the proliferation marker bromodeoxyuridine (BrdU) requires pretreatment of tissue, typically with dilute hydrochloric acid (HCl). We report here that pretreatment by steam heating of paraformaldehyde-fixed tissue sections covered with citrate buffer yields much brighter labeling of BrdU
Switching-wavelength pulse source constructed from a dispersion-managed SOA fiber ring laser

A new approach to generate switching-wavelength picosecond pulses is developed based on a dispersion-managed semiconductor optical amplifier (SOA) fiber laser cavity. Gain modulation on a 1.55-/spl mu/m SOA is used together with subharmonic gating of pulses in the cavity. An 8-GHz, eight-wavelength output is obtained with a constant spacing of 0.91 nm between neighboring wavelengths. The wavelength channels have nearly identical peak powers. The total amplitude and time jitter of the output is measured to be smaller than 0.4 ps. The spacing and the number of output wavelengths can be easily tuned by changing the operating frequency and the subharmonic ratio without modifying the optical cavity.
Increased Arterial Stiffness Is Independently Related to Cerebrovascular Disease and Aneurysms of the Abdominal Aorta: The Second Manifestations of Arterial Disease (SMART) Study

Background— Arterial stiffness is a risk factor for stroke and myocardial infarction. We investigated whether carotid arterial stiffness is related to other localizations of manifest arterial disease. Methods— Carotid artery stiffness was measured by ultrasonography as the change in diameter in systole relative to the diastolic diameter in patients enrolled in the Second Manifestations of Arterial Disease (SMART) Study, a cohort study among patients with manifest cardiovascular disease or cardiovascular risk factors. The first consecutive 1561 patients with manifest cardiovascular disease were classified in 4 categories: cerebrovascular disease, coronary artery disease, peripheral artery disease, or aneurysm of the abdominal aorta (AAA). Differences in arterial stiffness among the categories were studied by linear regression analyses. Patients with coronary artery disease as single diagnosis (n=482) served as reference group. Results— Patients with cerebrovascular disease (arterial distension −42.0 μm [95% CI, −57.2 to −26.8]) and those with an AAA (−64.4 μm [95% CI, −84.8 to −44.0]) had an increased carotid stiffness compared with the reference group. Adjustment for confounders attenuated the relations, which remained statistically significant (−34.2 μm [95% CI, −47.8 to −20.7] and −33.2 μm [95% CI, −51.8 to −14.6], respectively). Conclusion— Our study suggests that increased arterial stiffness is important in the pathophysiology of especially cerebrovascular disease and AAA. That the differences in arterial stiffness between disease categories attenuated after adjustment for important risk factors but remained significant suggests that besides being an element in the causal pathway, arterial stiffness is also a risk factor for cardiovascular disease itself.
scMRI Reveals Large-Scale Brain Network Abnormalities in Autism

Autism is a complex neurological condition characterized by childhood onset of dysfunction in multiple cognitive domains including socio-emotional function, speech and language, and processing of internally versus externally directed stimuli. Although gross brain anatomic differences in autism are well established, recent studies investigating regional differences in brain structure and function have yielded divergent and seemingly contradictory results. How regional abnormalities relate to the autistic phenotype remains unclear. We hypothesized that autism exhibits distinct perturbations in network-level brain architecture, and that cognitive dysfunction may be reflected by abnormal network structure. Network-level anatomic abnormalities in autism have not been previously described. We used structural covariance MRI to investigate network-level differences in gray matter structure within two large-scale networks strongly implicated in autism, the salience network and the default mode network, in autistic subjects and age-, gender-, and IQ-matched controls. We report specific perturbations in brain network architecture in the salience and default-mode networks consistent with clinical manifestations of autism. Extent and distribution of the salience network, involved in social-emotional regulation of environmental stimuli, is restricted in autism. In contrast, posterior elements of the default mode network have increased spatial distribution, suggesting a ‘posteriorization’ of this network. These findings are consistent with a network-based model of autism, and suggest a unifying interpretation of previous work. Moreover, we provide evidence of specific abnormalities in brain network architecture underlying autism that are quantifiable using standard clinical MRI.