Miracle-dz/UniFAR-FTUs huggingface dataset:
Postnatal development of cerebellar zones revealed by neurofilament heavy chain protein expression

The cerebellum is organized into parasagittal zones that control sensory-motor behavior. Although the architecture of adult zones is well understood, very little is known about how zones emerge during development. Understanding the process of zone formation is an essential step toward unraveling how circuits are constructed to support specific behaviors. Therefore, we focused this study on postnatal development to determine the spatial and temporal changes that establish zonal patterns during circuit formation. We used a combination of wholemount and tissue section immunohistochemistry in mice to show that the cytoskeletal protein neurofilament heavy chain (NFH) is a robust marker for postnatal cerebellar zonal patterning. The patterned expression of NFH is initiated shortly after birth, and compared to the domains of several known zonal markers such as zebrin II, HSP25, neurogranin, and phospholipase Cβ4 (PLCβ4), NFH does not exhibit transient expression patterns that are typically remodeled between stages, and the adult zones do not emerge after a period of uniform expression in all lobules. Instead, we found that throughout postnatal development NFH gradually reveals distinct zones in each cerebellar lobule. The boundaries of individual NFH zones sharpen over time, as zones are refined during the second and third weeks after birth. Double labeling with neurogranin and PLCβ4 further revealed that although the postnatal expression of NFH is spatially and temporally unique, its pattern of zones respects a fundamental and well-known molecular topography in the cerebellum. The dynamics of NFH expression support the hypothesis that adult circuits are derived from an embryonic map that is refined into zones during the first 3-weeks of life.
Querypoint: moving backwards on wrong values in the buggy execution

As developers debug, they often have to seek the origins of wrong values they see in their debugger. This search must be performed backwards in time since the code causing the wrong value is executed before the wrong value appears. Therefore, locating the origin of wrong values with breakpoint- or log- based debuggers demands persistence and significant experience. Querypoint, is a Firefox plugin that enhances the popular Firebug JavaScript debugger with a new, practical feature called lastChange. lastChange automatically locates the last point at which a variable or an object property has been changed. Starting from a program suspended on a breakpoint, the lastChange algorithm applies queries to the live program during re-execution, recording the call stack and limited program state each time the property value changes. When the program halts again on the breakpoint, it shows the call stack and program state at the last change point. To evaluate the usability and effectiveness of Querypoint we studied four experienced JavaScript developers applying the tool to two test cases.
Molecular Genetic Analysis of the APP, PSEN1, and PSEN2 Genes in Finnish Patients With Early-onset Alzheimer Disease and Frontotemporal Lobar Degeneration

Mutations in 3 genes, amyloid precursor protein (APP), presenilin 1 (PSEN1), and presenilin 2 (PSEN2), have been identified as causing a proportion of early-onset Alzheimer disease (eoAD) cases. A few PSEN mutations have also been previously detected in patients with frontotemporal lobar degeneration (FTLD). In order to evaluate the role of these genes in a clinical series of Finnish eoAD and FTLD patients, we sequenced exons 16 and 17 of the APP gene and the coding regions of the PSEN1 and PSEN2 genes in 140 eoAD and 66 FTLD patients. No pathogenic mutations were identified in the cohort. The E318G variant was detected with similar frequencies in the cases with eoAD and FTLD and the healthy controls, therefore, showing no association between E318G and eoAD. Furthermore, the PSEN2 R71W variant seems to be nonpathogenic, because it was present in our healthy controls. Mutations in the PSEN1, PSEN2, and APP genes seem to be rare in this population, as these genes exhibited no pathogenic mutations in our cohort of eoAD and FTLD patients even though about 40% of the cases were familial ones. This suggests the involvement of other, still unknown genetic factors in the pathogenesis of these diseases.
Telomere Dynamics in Keloids

Objective: Little is known about telomere dynamics in keloids. As keloid formation is dependent on cell replication, in theory telomeres should be shorter in keloids than in normal skin. We examined this concept in the present study. Methods: We measured by Southern blot analysis telomere length in keloids and in adjacent normal skin of 16 individuals. When available, we also measured telomere length in blood (leukocytes) and subcutaneous fat. Results: Telomere length was highly variable among individuals but highly correlated among tissues (cells) within the individual. The mean telomere length in the keloids was longer than that in the adjacent normal skin and displayed a length gradient, with the mean length of telomeres shorter just below the epidermis and longer at the base of the keloids. No apparent telomerase activity was detected in the keloids. Conclusions: Our findings suggest a transient activation of telomerase, the reverse transcriptase that prevents telomere shortening, probably during the early phase of keloid formation. The activation of telomerase serves to maintain (or even elongate) telomere length in the keloid. However, telomerase activity is repressed in the fully developed keloid.
[ROC analysis of image quality in digital luminescence radiography in comparison with current film-screen systems in mammography].

AIM To compare in mammography the image quality of digital luminescence radiography (DLR) to that of usual film screen mammography and xeromammography. MATERIALS AND METHODS Three single emulsion film-screen combinations, one double coated high resolution film and xeroradiography, were tested for this purpose. In our phantom study the detectability of microcalcifications, fibrils and low contrast details were first of all studied separately. Image processing techniques were, for example, contrast variation by grey scale level windowing, "unsharp mask" filtering and regulatable edge enhancement. Phantom images were made and then the image quality was evaluated by observer performance study using a receiver operating characteristic (ROC analysis). RESULTS Best results in respect of detection of microcalcifications and fibrils were found in xeroradiography, luminescent image plate and double-coated film-screen combination. These systems showed more favourable ROC curves than the single emulsion film-screen combinations. CONCLUSIONS Our results indicate that image quality of digital images in the field of image processing is equal to that of conventional mammographic techniques and partially superior to detection of low contrast details.
A three level strategy for the design and performance evaluation of Hospital Departments: A case study

The increased demand for hospital services has saturated the capacity of Hospital Departments (HDs) that require suitable tools for the efficient management of resources and of flows of patients, staff, and drugs. The paper proposes a model based on a three level strategy to design at the tactical level a HD. The first module employs a Unified Modeling Language tool and a timed Petri net model to describe the flow of patients. The optimization module employs the fluid relaxation to concisely approximate in a continuous Petri net framework the HD model and optimize suitable performance indices. The simulation module verifies that the optimized parameters allow an effective workflow organization while maximizing the patient flow. A real case study on the pulmonology department of the general hospital of Bari (Italy) shows the efficiency of the proposed method.
Dispatching Agents in Electronic Institutions

In Electronic Institutions [1], agents may be prevented from achieving their goals if other participants are not present in a given scene. In order to overcome this situation we propose the addition of an institutional agent in charge of dispatching agents to scenes through a participation request protocol. We further propose to endow this agent with the capability of instantiating new agents, thus providing grounds for a self-optimization of the system. Advantages of our proposal are illustrated with the implementation of an information auditing process.
The Annual Cycle of Northern Hemisphere Storm Tracks. Part II: Regional Detail

In Part I of this study, the annual cycle of the Northern Hemisphere storm tracks was investigated using feature tracking and Eulerian variance-based diagnostics applied to both the vorticity and meridional wind fields. Results were presented and discussed for the four seasons at both upper- (250 hPa) and lower- (850 hPa) tropospheric levels. Here, using the meridional wind diagnostics, the annual cycles of the North Pacific and North Atlantic storm tracks are examined in detail. This is done using monthly and 20° longitudinal sector averages. Many sectors have been considered, but the focus is on sectors equally spaced in the two main oceanic storm tracks situated at their western, central, and eastern regions, with the western ones being mainly over the upstream continents. The annual cycles of the upper- and lower-tropospheric storm tracks in the central and eastern Pacific, as well as in the western and central Atlantic sectors, all have rather similar structures. In amplitude, each sector at both levels has a summer minimum and a relatively uniform strength from October to April, despite the strong winter maxima in the westerly jets. However, high-intensity storms occur over a much wider latitudinal band in winter. The storm track in each sector moves poleward from May to August and returns equatorward from October to December, and there is a marked asymmetry between spring and autumn. There are many differences between the North Pacific and North Atlantic storm tracks, and some of these seem to have their origin in the behavior over the upstream East Asian and North American continents, suggesting the importance of seeding from these regions. The East Asian storm track near 48°N has marked spring and autumn maxima and weak amplitude in winter and summer. The 33°N track is strong only in the first half of the year. In contrast, the eastern North American storm track is well organized throughout the year, around the baroclinicity that moves latitudinally with the seasons. The signatures associated with these features are found to gradually decrease downstream in each case. In particular, there is very little latitudinal movement in the storm track in the eastern Atlantic.
Efficacy and Longevity of Nitenpyram Against Adult Cat Fleas (Siphonaptera: Pulicidae)

Abstract Nitenpyram (Capstar) is a fast acting, orally administered flea treatment that is absorbed into the blood of the host animal and is readily available for uptake by feeding fleas. We examined the efficacy of a single dose of nitenpyram against adult cat fleas, Ctenocephalides felis (Bouché), over several days. We recorded adult flea mortality and flea egg production on treated and untreated cats. Nitenpyram provided 100% kill of all fleas on the host at the time of treatment and for up to 24 h after treatment. Between 24 and 48 h after treatment, there was a 98.6% reduction in adult flea numbers. From 48 to 72 h, there was a 5% reduction in adult fleas. There was a 97% reduction and 95.2% reduction in the number of flea eggs collected from treated versus untreated animals during the first 48 h and from 48 to 72 h, respectively. In addition, we quantified three distinct behavioral responses of infested adult cats treated with nitenpyram to determine the extent of any immediate, overt behavioral responses in treated animals. A significant increase in scratching, biting, licking, and twitching occurred for 5 h. The biting and licking continued for 7 h after treatment. Administration of nitenpyram provides an effective mechanism to eliminate adult fleas from hosts for up to 48 h after treatment.
Distribution of E. coli Levels and Recreation Use as Factor of Stream Order in the Central Great Plains, Central Oklahoma-Texas Plains, and South Central Plains Ecoregions

II ACKNOWLEDGEMENTS . III NOMENCLATURE . IV TABLE OF CONTENTS . V LIST OF FIGURES . VI LIST OF TABLES . VII Need for Study . 1 Stream Order Theory . 4 Microbial Transport in Surface Waters . 7 Objectives . 8 Introduction . 10 Description of Study Area . 11 Data Sources . 14 GIS Methods . 16 Stream delineation and stream order calculation . 16 Watershed and urban area calculation . 17 Unimpacted watersheds . 18 Materials and Methods . 20 Results and Discussion . 25 Analysis of median E. coli by Strahler stream order . 25 Analysis of median E. coli by modified Shreve stream order . 36 Analysis of median E. coli by Shreve stream order and watershed area . 46 Discussion of results . 53 REFERENCES . 64
Activation of acetylcholine receptors on clonal mammalian BC3H‐1 cells by low concentrations of agonist.

The patch‐clamp technique was used to examine the activation of single acetylcholine receptor channels of clonal BC3H‐1 mouse muscle cells. Single‐channel currents were activated by low concentrations of the strong agonists acetylcholine (ACh, 50‐100 nM), carbamylcholine (1‐2 microM), and suberyldicholine (30‐50 nM). At low agonist concentrations channel openings occur as isolated short‐duration openings and as bursts of longer duration openings separated by brief closed periods. Two distinct types of brief closed periods separate long duration openings: brief closures (mean duration, 50 microseconds) and intermediate closures (mean duration, 0.5‐1.0 ms). The kinetic properties of intermediate closures depend on the agonist, suggesting that they reflect receptor reopening from the closed state leading to the open state. Properties of brief closures, in contrast, are independent of the agonist, indicating that they result from an additional closed state leading away from the pathway producing the open state. A receptor activation scheme is proposed which accounts for the observed closed states, and transition rate estimates are presented for steps within the proposed scheme. The channel opening rate, beta, differs several‐fold for the agonists studied (200‐1400 s‐1) and is comparable to the dissociation rate, k‐2 (900 s‐1). The dissociation rate is similar for the three agonists studied. The channel closing rate, alpha, is much slower than the opening rate (20‐60 s‐1). The probability is high that a doubly liganded channel is in the open state and depends on the agonist (0.75‐0.97). Beta increases and alpha decreases at more negative membrane potentials, whereas k‐2 shows little potential dependence.
Generic method for intensity standardization of medical images using multiscale curvelet representation

Most computer-aided diagnosis (CAD) methods in medical imaging are finely tuned for the settings of training data, i.e., the acquisition protocol and machine settings. Therefore, they may fail to perform optimally on images acquired under a different protocol. Intensity standardization, or mapping the acquired data to a predefined intensity profile, can alleviate this challenge. In this work, we present a generic method for intensity standardization of 2D/3D medical images using localized subband energy scaling of the multi-scale curvelet transform. During the training phase, reference data are first decomposed into scale and orientation localized subbands using the multiscale curvelet transform, followed by calculating a reference energy value for each subband. During the testing stage, the localized energy of each subband is scaled to the reference localized energy value from the training stage through an iterative process. We validated our generic standardization method on 2D chest X-rays (CXR) and 3D T1-weighted MRI sequences acquired using different scanners on a group of both healthy and diseased subjects. A significant improvement (Dice coefficient of 0.91±0.05 versus 0.68 ± 0.13, p-value< 0.001) was obtained in the whole brain segmentation accuracy after standardization. Similarly, for air-trapping quantification, the standardization improved the correlation with the expert visual assessment of air-trapping from CXR from R = 0.32 to R = 0.93. The proposed intensity standardization technique could be adopted as a pre-processing step for 2D and 3D data to improve the accuracy of CAD on data obtained from variable sources.
Optimal Phasor Data Compression Unit Installation for Wide-Area Measurement Systems—An Integer Linear Programming Approach

Phasor measurement units (PMUs) are time-synchronous measuring devices that acquire highly accurate phasor data at high frequency. They are the core components in wide-area measurement systems for smart grid monitoring, protection, and control. However, they do generate much data and create a heavy burden on the communication network. One of the most practical ways of alleviating this problem is to install phasor data compression units (PDCUs) across the power system to concentrate PMU data and reduce total data traffic. These PDCUs implement hardware-based compression algorithms and, therefore, will incur minimum communication delays while significantly reducing the overall traffic generated by PMU. Since these PDCUs are pieces of hardware to be installed, given a target traffic reduction rate, it is economical to decide the optimal deployment of PDCUs. We will call this the optimal PDCU installation (OPI) problem. In this paper, we first introduce the functionality of PDCU and then give a generalized OPI formulation. We also provide an extra OPI formulation that fits under the integer linear programming framework and introduce a binary search algorithm to efficiently solve it. The OPI solutions for the IEEE 30-bus, 57-bus, 118-bus, and 300-bus systems are provided in this paper.
A low input, low-power dissipation CMOS ADC

This paper presents the design of a low input (0.75 to 1.75V) and low power dissipation pipelined CMOS ADC. The 8 bits ADC consumes 78.3mW power at 2.5V supply voltage. The DNL and INL are 0.6LSB and 0.7LSB respectively, and SFDR is 51.259dB at 195kHz input frequency. The chip area is 1.023 mm times 0.795 mm with TSMC0.25mum CMOS technology
Hybrid rate control for IEEE 802.11

Streaming multimedia content in real-time over a wireless link is a challenging task because of the rapid fluctuations in link conditions that can occur due to movement, interference, and so on. The popular IEEE 802.11 standard includes low-level tuning parameters like the transmission rate. Standard device drivers for today's wireless products are based on gathering statistics, and consequently, adapt rather slowly to changes in conditions. To meet the strict latency requirements of streaming applications, we designed and implemented an advanced control algorithm that uses signal-strength (SNR) information to achieve fast responses. Since SNR readings are quite noisy we do not use that information to directly control the rate setting, but rather as a safeguard limiting the range of feasible settings to choose from. We report on real-time experiments involving two laptops equipped with IEEE 802.11a wireless interface cards. The results show that using SNR information greatly enhances responsiveness in comparison to statistics-based rate controllers.
Scrapie and cellular prion proteins differ in their kinetics of synthesis and topology in cultured cells

Both the cellular and scrapie isoforms of the prion protein (PrP) designated PrPc and PrPSc are encoded by a single-copy chromosomal gene and appear to be translated from the same 2.1-kb mRNA. PrPC can be distinguished from PrPSc by limited proteolysis under conditions where PrPC is hydrolyzed and PrPSc is resistant. We report here that PrPC can be released from the surface of both normal-control and scrapie- infected murine neuroblastoma (N2a) cells by phosphatidylinositol- specific phospholipase C (PIPLC) digestion and it can be selectively labeled with sulfo-NHS-biotin, a membrane impermeant reagent. In contrast, PrPSc was neither released by PIPLC nor labeled with sulfo- NHS-biotin. Pulse-chase experiments showed that [35S]methionine was incorporated almost immediately into PrPC while incorporation into PrPSc molecules was observed only during the chase period. While PrPC is synthesized and degraded relatively rapidly (t1/2 approximately 5 h), PrPSc is synthesized slowly (t1/2 approximately 15 h) and appears to accumulate. These results are consistent with several observations previously made on rodent brains where PrP mRNA and PrPC levels did not change throughout the course of scrapie infection, yet PrPSc accumulated to levels exceeding that of PrPC. Our kinetic studies demonstrate that PrPSc is derived from a protease-sensitive precursor and that the acquisition of proteinase K resistance results from a posttranslational event. Whether or not prolonged incubation periods, which are a cardinal feature of prion diseases, reflect the slow synthesis of PrPSc remains to be established.
Nine Hundred Years of Weekly Streamflows: Stochastic Downscaling of Ensemble Tree‐Ring Reconstructions

We combined the methods and advantages of stochastic hydrology and paleohydrology to estimate 900 years of weekly flows for the North and South Saskatchewan Rivers at Edmonton and Medicine Hat, Alberta, respectively. Regression models of water‐year streamflow were constructed using historical naturalized flow data and a pool of 196 tree‐ring (earlywood, latewood, and annual) ring‐width chronologies from 76 sites. The tree‐ring models accounted for up to 80% of the interannual variability in historical naturalized flows. We developed a new algorithm for generating stochastic time series of weekly flows constrained by the statistical properties of both the historical record and proxy streamflow data, and by the necessary condition that weekly flows correlate between the end of a year and the start of the next. A second innovation, enabled by the density of our tree‐ring network, is to derive the paleohydrology from an ensemble of 100 statistically significant reconstructions at each gauge. Using paleoclimatic data to generate long series of weekly flow estimates augments the short historical record with an expanded range of hydrologic variability, including sequences of wet and dry years of greater length and severity. This unique hydrometric time series will enable evaluation of the reliability of current water supply and management systems given the range of hydroclimatic variability and extremes contained in the stochastic paleohydrology. It also could inform evaluation of the uncertainty in climate model projections, given that internal hydroclimatic variability is the dominant source of uncertainty.