Miracle-dz/UniFAR-FTUs huggingface dataset:
Transcriptome changes associated with instructed learning in the barn owl auditory localization pathway

Owls reared wearing prismatic spectacles learn to make adaptive orienting movements. This instructed learning depends on re‐calibration of the midbrain auditory space map, which in turn involves the formation of new synapses. Here we investigated whether these processes are associated with differential gene expression, using longSAGE. Newly fledged owls were reared for 8–36 days with prism or control lenses at which time the extent of learning was quantified by electrophysiological mapping. Transciptome profiles were obtained from the inferior colliculus (IC), the major site of synaptic plasticity, and the optic tectum (OT), which provides an instructive signal that controls the direction and extent of plasticity. Twenty‐two differentially expressed sequence tags were identified in IC and 36 in OT, out of more than 35,000 unique tags. Of these, only four were regulated in both structures. These results indicate that regulation of two largely independent gene clusters is associated with synaptic remodeling (in IC) and generation of the instructive signal (in OT). Real‐time PCR data confirmed the changes for two transcripts, ubiquitin/polyubiquitin and tyrosine 3‐monooxgenase/tryotophan 5‐monooxygenase activation protein, theta subunit (YWHAQ; also referred to as 14‐3‐3 protein). Ubiquitin was downregulated in IC, consistent with a model in which protein degradation pathways act as an inhibitory constraint on synaptogenesis. YWHAQ was up‐regulated in OT, indicating a role in the synthesis or delivery of instructive information. In total, our results provide a path towards unraveling molecular cascades that link naturalistic experience with synaptic remodeling and, ultimately, with the expression of learned behavior. © 2007 Wiley Periodicals, Inc. Develop Neurobiol, 2007.
Think globally, act locally: the role of local demographics and vaccination coverage in the dynamic response of measles infection to control

The global reduction of the burden of morbidity and mortality owing to measles has been a major triumph of public health. However, the continued persistence of measles infection probably not only reflects local variation in progress towards vaccination target goals, but may also reflect local variation in dynamic processes of transmission, susceptible replenishment through births and stochastic local extinction. Dynamic models predict that vaccination should increase the mean age of infection and increase inter-annual variability in incidence. Through a comparative approach, we assess national-level patterns in the mean age of infection and measles persistence. We find that while the classic predictions do hold in general, the impact of vaccination on the age distribution of cases and stochastic fadeout are mediated by local birth rate. Thus, broad-scale vaccine coverage goals are unlikely to have the same impact on the interruption of measles transmission in all demographic settings. Indeed, these results suggest that the achievement of further measles reduction or elimination goals is likely to require programmatic and vaccine coverage goals that are tailored to local demographic conditions.
On hard and fuzzy c-means clustering with conditionally positive definite kernel

In this paper, we investigate three types of c-means clustering algorithms with a conditionally positive definite kernel. One is based on hard c-means, and the others are based on standard and entropy-regularized fuzzy c-means. First, based on a conditionally positive definite kernel describing a squared Euclidean distance between data in the feature space, these algorithms are derived from revised optimization problems of the conventional kernel c-means. Next, based on the relationship between the positive definite kernel and conditionally positive definite kernel, the revised dissimilarity between a datum and a cluster center in the feature space is shown. Finally, it is shown that a conditionally positive definite kernel c-means algorithm and a kernel c-means algorithm with a positive definite kernel derived from the conditionally positive definite kernel are essentially identical to each other. An explicit mapping for a conditionally positive definite kernel is also described geometrically.
Lean and Efficient Business Tier for Performance Scaling

Large mission critical real-time legacy OLTP systems supporting the service sectors like banking, telecom, and financial services are monolithic in nature and thereby not flexible to enable business transformation which is the need of the hour due to emerging dynamic changes to business ecosystem. Broadly speaking, these large mission critical applications can be classified into three stages of activities: pre-processing, core business processing and post processing activities. This paper focuses on making the Business processing activities tier lean and efficient. By leveraging recent advances in technologies, a methodology is described by which the OLTP applications can be successfully transformed into agile systems. The methodology enables a view of the Business Tier in five dimensions. The first dimension is identifying the business‟s core critical path and how to make it lean. The second dimension is how to enhance concurrency of the activities in the critical path. The third dimension is to improve the parallelism in execution of concurrency. The fourth is to separate I/O operations off the critical path. The fifth being how to minimize contentions for shared resources to ensure higher efficiencies. The paper also presents, the results of the experiments carried out by applying the above recommendation and the performance improvements to decide the optimal setup for an environment for given workload. Addressing the five dimensions of Business Tier, this paper demonstrates the transformation that can be achieved which will enable the business to be agile and respond to market ecosystem demands in a very efficient and effective manner.
A new method for the design of multi-sine excitations for the assessment of non-linear devices

This paper presents a novel way of generating multi-sine signals for the representation of modern communication signals. The multi-sine signals are in very good agreement with the original signals with regards to their statistical characteristic (CCDF) and spectrum and have shown to accurately predict the ACPR response for non-linear systems. Investigations of the novel approach on IS-95 and WCDMA signals have shown that it could be used to simulate different types of communication signals. The presented approach is based on spot correlation to compute the difference between the target communication signal and multi-sine signals. Consequently, this new approach determines the phases and amplitudes of the original communication signal and further optimises the initial values according to statistical properties of the target signal.
Redesigning Data Structures for Non-Volatile Byte-Addressable Memory

Recent architecture trends show that DRAM density scaling is facing significant challenges and will hit a scalability wall at 40nm [4, 5]. Additionally, power constraints will also limit the amount of DRAM installed in future systems [3]. To support next generation systems, technologies such as Phase Change Memory (PCM) and Memristor are being developed as DRAM replacements. These memories offer latencies that are orders of magnitude lower than either disk or flash and are comparable to DRAM. Not only are they byte-addressable like DRAM but, in addition, they are non-volatile. Projected cost analysis [3] and power-efficiency characteristics of Non-Volatile Byte-addressable Memory (NVBM) lead us to believe that it can replace both disk and memory in data stores (e.g., databases, NoSQL systems, etc.) but not through legacy block or file systems interfaces. The overhead of these interfaces will dominate NVBM’s nanosecond access latencies and furthermore, these interfaces impose a two-level logical separation of data, differentiating between in-memory vs. on-disk copies of data. Traditional data stores have to both update the in-memory data and, for durability, sync the data to disk with the help of a write-ahead log. Not only does this data movement use extra power and reduce performance for low latency NVBM, the logical separation also reduces the capacity of an NVBM system. Instead, we propose a single-level NVBM hierarchy where no distinction is made between a volatile and a persistent copy of data. With a single-level NVBM store, we need to ensure that data structures will never be left in an inconsistent state. Unfortunately, processors today do not provide the necessary extensions to prevent writes from being flushed from cache to memory and given that the memory controller can reorder cache line writes, current mechanisms for updating data structures are likely to cause corruption in the face of failures. To address the above requirements for NVBM, we propose the use of Consistent and Durable Data Structures (CDDSs), a design that allows for the creation of log-less storage systems on non-volatile memory without processor modifications. These data structures allow mutations to be safely performed directly (using loads and stores) on the single copy of data. Instead of using write-ahead logging or shadow paging, we have architected CDDSs to use 10 [6,-) 20 [6,-) 99 [6,-)
Biometria testicular, características seminais, libido e concentração de testosterona em ovinos da raça Santa Inês, criados a campo, na microrregião de Campo Maior, Piauí

The aim of this study was to characterize and correlate reproductive parameters of sheep of the Santa Ines breed, maintained on pasture field, mimoso (Axonopus sp), in the microrregion of Campo Maior, Piaui. A total of 76 sheep with ages and weight averages of 27.85±3.85months and 46.57±7.51kg, respectively, during the drought period and little availability of food in the area. The testicular values obtained were: circumference 31.91±2.33cm; length 8.85±0.85cm; width 6.06±0.61cm; thickness 5.91±0.57cm; consistence 3.98±0.54 points and volume 349.11±11. 59cm³. The body weight and testicular measures presented correlation between one another. The average values of the seminal parameters (volume 1.48±0.32mL; aspect 4.50 ±0.45points; massal motility 4.77±0.30points; progressive individual motility 84.47±1.72%; vigor 4.59±0.21points; concentration 1.54±0.32x109sptz/mm³; larger defects 3.06±1.27%; total defects 7.88±0.91%); libi-do (4.46±0.23points) and testosterone concentration (11.56±2.26ng/mL), did not correlate to the other studied characteristics. In sheep of Santa Ines breed, maintained on field native pasture with predominance of mimoso (Axonopus sp), it was found animal growth limitation but it has not affected seminal parameters, libido and testosterone concentration. There was no relation found between body and testicular values, however, testicular values were correlated with testosterone levels.
Research Statement

The last decade has seen a proliferation of software systems for storing and managing large collections of data. These different systems are targeted at different types of data, or different data access patterns; examples include: transactional applications, such as banking (OLTP), analytical and reporting applications, such as finding the most popular items that have sold in a retail store (OLAP), as well as systems specialized for streaming (real-time), social networks and other graphs, and data archives. This is a sharp change from just a few decades ago where all applications were supported by monolithic data management systems (e.g., Oracle, or DB2). This proliferation of systems has occurred because it delivers significantly better performance. However, end users now need to pick the right data management system for their query workloads. Furthermore, modern enterprises typically see a variety of query workloads. For instance, a banking enterprise uses a transactional system for customer banking transactions, an analytical system for business intelligence, a streaming system for stock trading, and an archival system to meet regulatory requirements for data retention. As a consequence, today’s companies have to manage and integrate several types of data management systems, which is tedious, expensive, and counter-productive for their business. So rather than making the world of data management easier, the zoo of systems sometimes has the opposite effect: it makes the life of the end users harder and more costly.
Behavioral abnormalities and Parkinson’s-like histological changes resulting from Id2 inactivation in mice

SUMMARY Characterizing dopaminergic neuronal development and function in novel genetic animal models might uncover strategies for researchers to develop disease-modifying treatments for neurologic disorders. Id2 is a transcription factor expressed in the developing central nervous system. Id2−/− mice have fewer dopaminergic neurons in the olfactory bulb and reduced olfactory discrimination, a pre-clinical marker of Parkinson’s disease. Here, we summarize behavioral, histological and in vitro molecular biological analyses to determine whether midbrain dopaminergic neurons are affected by Id2 loss. Id2−/− mice were hyperactive at 1 and 3 months of age, but by 6 months showed reduced activity. Id2−/− mice showed age-dependent histological alterations in dopaminergic neurons of the substantia nigra pars compacta (SNpC) associated with changes in locomotor activity. Reduced dopamine transporter (DAT) expression was observed at early ages in Id2−/− mice and DAT expression was dependent on Id2 expression in an in vitro dopaminergic differentiation model. Evidence of neurodegeneration, including activated caspase-3 and glial infiltration, were noted in the SNpC of older Id2−/− mice. These findings document a novel role for Id2 in the maintenance of midbrain dopamine neurons. The Id2−/− mouse should provide unique opportunities to study the progression of neurodegenerative disorders involving the dopamine system.
The life cycle of submesoscale eddies generated by topographic
interactions

Abstract. The Persian Gulf Water and Red Sea Water are salty and dense waters recirculating at subsurface in the Gulf of Oman and the Gulf of Aden respectively, under the influence of mesoscale eddies which dominate the surface flow in both semi-enclosed basins. In situ measurements combined with altimetry indicate that the Persian Gulf Water is driven by mesoscale eddies in the form of filaments and submesoscale structures. In this paper, we study the formation and the life cycle of intense submesoscale vortices and their impact on the spread of Persian Gulf Water and Red Sea Water. We use a three-dimensional hydrostatic model with submesoscale-resolving resolution to study the evolution of submesoscale vortices. Our configuration is an idealized version of the Gulf of Oman and Aden: a zonal row of mesoscale vortices interacting with north and south topographic slopes. Intense submesoscale vortices are generated in the simulations along the continental slopes due to two different mechanisms. The first mechanism is due to frictional generation of vorticity in the bottom boundary layer, which detaches from the topography, forms an unstable vorticity filament, and undergoes horizontal shear instability that leads to the formation of submesoscale coherent vortices. The second mechanism is inviscid and implies arrested topographic Rossby waves breaking and forming submesoscale coherent vortices where a mesoscale anticyclone interacts with the topographic slope. Submesoscale vortices subsequently drift away, merge and form larger vortices. They can also pair with opposite signed vortices and travel across the domain. They can weaken or disappear via several mechanisms, in particular fusion into the larger eddies or erosion on the topography. Particle patches are advected and sheared by vortices and are entrained into filaments. Their size first grows as the square root of time, a signature of the merging processes, then it increases linearly with time, corresponding to their ballistic advection by submesoscale eddies. On the contrary, witout intense submesoscale eddies, particles are mainly advected by mesoscale eddies; this implies a weaker dispersion of particles than in the previous case. This shows the important role of submesoscale eddies in spreading Persian Gulf Water and Red Sea Water.
Improving Mobile Infrastructure for Pervasive Personal Computing

Abstract : The emergence of pervasive computing systems such as Internet Suspend/Resume has facilitated ubiquitous access to a user's personalized computing environment by layering virtual machine technology on top of distributed storage. This usage model poses several new challenges, such as establishing trust in unmanaged hardware that a user may access, and efficiently migrating virtual machine "VM" state across low-bandwidth networks. This document describes Trust-Sniffer, a tool that reduces the security risks associated with transient use by helping a user to gain confidence in software on an untrusted machine. The root of trust is a small, user carried device such as a USB memory stick. Trust-Sniffer verifies the on-disk boot image of the target machine and incrementally expands the zone of trust by validating applications, including dynamically linked libraries, before they are executed. An application is validated by comparing its checksum to a list of known good checksums. If a binary cannot be validated, its execution is blocked. This staged approach to establishing confidence in an untrusted machine strikes a good balance between the needs of security and ease-of-use, and facilitates rapid transient use of hardware. This document also describes a solution to optimize the transfer of large amounts disk and memory state for VM migration, based on opportunistic replay of user actions. The term opportunistic means that replay need not be perfect to be useful. In contrast to other replay techniques, opportunistic replay captures user interactions with applications at the GUI level, resulting in very small replay logs that economize network utilization. Replay of user interactions on a VM at the migration target site can result in divergent VM state. Cryptographic hashing techniques are used to identify and transmit only the differences.
Specific circulating immune complexes in acute Chagas' disease.

Se investigo la presencia de complejos inmunes circulantes formados por IgM e IgG (CIC-IgM y CIC-IgG), utilizando enzimoinmu-noensayos ELISA) antigeno-especificos, en 30 pacientes con enfermedad de Chagas aguda que presentaban parasitemia y chagoma de inocu-lacion. La poblacion control estaba formada por pacientes con infeccion cronica por T. cruzi (30), toxoplasmosis aguda (10), leishmaniasis (8), artritis reumatoidea (3) e individuos sanos con serologia negativa para Chagas (30). Los pacientes chagasicos agudos fueron 100% CIC-IgG y 96,66% CIC-IgM positivos, mientras que Ias pruebas de inmunofluorescencia para anti-cuerpos especificos de tipo IgG e IgM mostra-ron 90% y 86,66% de positividad, respectivamente. Los pacientes cronicos fueron 68% CIC-IgG y 0% CIC-IgM positivos. El resto de los controles arrojaron resultados negativos por ELISA CIC-IgM y CIC-IgG). La alta sensibilidad dei ELISA permitiria un diagnostico inmunologico temprano, como asi tambien un tra-tamiento inmediato, de la infeccin aguda por T. cruzi, eliminando asi el problema de resultados falsos-positivos y falsos-negativos que afecta a los metodos tradicionales para deteccion de anticuerpos circulantes.
Observations and lessons learned from automated testing

This report addresses some of our observations made in a dozen of projects in the area of software testing, and more specifically, in automated testing. It documents, analyzes and consolidates what we consider to be of interest to the community. The major findings can be summarized in a number of lessons learned, covering test strategy, testability, daily integration, and best practices. The report starts with a brief description of five sample projects. Then, we discuss our observations and experiences and illustrate them with the sample projects. The report concludes with a synopsis of these experiences and with suggestions for future test automation endeavors.
Introduction and evaluation of a Weibull hydraulic conductivity‐pressure head relationship for unsaturated soils

Analytical and numerical solutions for flow through partially saturated soils typically require functional relationships between water content, pressure, and hydraulic conductivity. Here we propose a Weibull‐type function to describe the hydraulic conductivity‐pressure head function. We show that this is a more flexible function that has the ability to address air entry pressure, while retaining the ease of integration and differentiation that facilitates many important computations which have to this point favored the Gardner exponential function (which is a special case of the proposed function). The ability to fit measured values is shown to be better than commonly employed functions of similar simplicity. Strong relationships were found between the parameters of the proposed function and the corresponding soil water retention curve, thus providing predictive capability. A simple relationship was also found between the parameters of the function and the wetting front pressure, ψf. Applying the proposed function to estimate ψf improves the accuracy of predictions for infiltration using the Green and Ampt model.
Vegetation Response After Invasive Tamarix Spp. Removal in the Riparian Zone and Semi-arid Rangeland Ecosystems

Removal of Tamarix spp. (a.k.a. tamarisk, saltcedar, Athel) invasion is often involved in restoration of Western, riparian habitat; however monitoring of vegetation after removal is often neglected and thus opportunity for adaptive management lost. To address this need, I have conducted three and half years of monitoring vegetation response after invasive Tamarix removal in twenty-five sites on the East and Western Colorado, starting fall 2009. I am also comparing six different methodologies: Point intercept, line transect, nearest neighbor, metersquare quadrats, nested Whittaker plots, and densitometer with the objective of developing monitoring protocols that can be used by scientists and land managers alike. This project is in collaboration with Branson Trinchera Conservation District (BTCD), The Nature Conservancy (TNC), the Colorado Water Conservation Board (CWCB), US Fish and Wildlife Service (USFWS), and the Bureau of Land Management (BLM).
A new unbiased equation error algorithm for IIR ADF and its application to ALE

A new online algorithm for updating equation error IIR ADF is proposed. The proposed algorithm, which involves maintaining a constant power of the desired signal, is independent of the white disturbance signal, and hence there is no bias in the coefficient's estimate of the ADF. We also provide the analysis and simulation results which verify this kind of performance. Application of the proposed algorithm to an adaptive line enhancer (ALE) is also provided. When compared with the method which uses a cascaded notch filter, we observe a considerable improvement in performance due to the complete elimination of the effect of white noise under mean sense condition.