Miracle-dz/UniFAR-FTUs huggingface dataset:
Intellicount: High-Throughput Quantification of Fluorescent Synaptic Protein Puncta by Machine Learning

Abstract Synapse formation analyses can be performed by imaging and quantifying fluorescent signals of synaptic markers. Traditionally, these analyses are done using simple or multiple thresholding and segmentation approaches or by labor-intensive manual analysis by a human observer. Here, we describe Intellicount, a high-throughput, fully-automated synapse quantification program which applies a novel machine learning (ML)-based image processing algorithm to systematically improve region of interest (ROI) identification over simple thresholding techniques. Through processing large datasets from both human and mouse neurons, we demonstrate that this approach allows image processing to proceed independently of carefully set thresholds, thus reducing the need for human intervention. As a result, this method can efficiently and accurately process large image datasets with minimal interaction by the experimenter, making it less prone to bias and less liable to human error. Furthermore, Intellicount is integrated into an intuitive graphical user interface (GUI) that provides a set of valuable features, including automated and multifunctional figure generation, routine statistical analyses, and the ability to run full datasets through nested folders, greatly expediting the data analysis process.
A CMOS Q-Enhancement Bandpass-Filter For Use In Paging Receivers

Paging receivers often have to work in a dense signal environment. This poses high demands on the preselection filter. One of the most difficult aspects is the large image rejection demand, which only can be satisfied by use of a narrow-band or high-Q filter. The practical restrictions for possible filter implementations are the low cost, low power and the small size of the pager. By use of positive feedback around a cheap off-chip low-Q inductor we obtain an enhanced quality factor. We are therefore able to construct selective filters using cheap small-size inductors. The price paid for Q-enhancement is a larger noise and higher sensitivity to component variations. The higher noise influence is eliminated using a high gain in the preceding LNA-stage, which is considered a part of the filter. Simulated results are: Q enhanced from 30 to 100, Image-rejection = 48dB, f0 = 280MHz, Voltage-gain = 20dB, Noise- figure = 2.4dB, IMFDR = 66dB, IDD = 1mA, VDD = 2V. The original contribution of this work is the application of the enhancement principle to off-chip components, which benefits the minimization of size and cost.
Structural basis and distal effects of Gag substrate coevolution in drug resistance to HIV-1 protease

Significance Drug resistance is a major health problem, especially in quickly evolving disease targets including HIV-1 protease. Treatment regimens including HIV-1 protease inhibitors select for viral variants carrying mutations both in the protease and the substrates to confer drug resistance. We report the molecular mechanisms of this protease–substrate coevolution based on complex crystal structures of protease–substrate variants, complemented with molecular dynamics simulations. Specific interactions with I50V/A71V protease are observed to be lost or formed in response to coevolution mutations in the p1-p6 substrate cleavage site. Our structural analysis provides insights into how coevolution in HIV-1 may contribute to thwarting the effectiveness of available drug regimens. Drug resistance mutations in response to HIV-1 protease inhibitors are selected not only in the drug target but elsewhere in the viral genome, especially at the protease cleavage sites in the precursor protein Gag. To understand the molecular basis of this protease–substrate coevolution, we solved the crystal structures of drug resistant I50V/A71V HIV-1 protease with p1-p6 substrates bearing coevolved mutations. Analyses of the protease–substrate interactions reveal that compensatory coevolved mutations in the substrate do not restore interactions lost due to protease mutations, but instead establish other interactions that are not restricted to the site of mutation. Mutation of a substrate residue has distal effects on other residues’ interactions as well, including through the induction of a conformational change in the protease. Additionally, molecular dynamics simulations suggest that restoration of active site dynamics is an additional constraint in the selection of coevolved mutations. Hence, protease–substrate coevolution permits mutational, structural, and dynamic changes via molecular mechanisms that involve distal effects contributing to drug resistance.
Operation of diode-clamped FET-SEED optical receivers with low-contrast single-ended signals

We report an experimental study of the contrast ratio needed for single-ended operation of diode-clamped optical receivers. These receivers, realized in field-effect-transistor-self-electrooptic-effect device (FET-SEED) technology, are high impedance FET-based receivers designed to operate with two optical beams in prototype smart-pixel systems. Single-ended data can be supplied to these devices by operating them, with a clock beam on one detector and a signal beam on the other detector in a return-to-zero (RZ) format. We find that with the use of this clock beam, the receiver can operate successfully with optical data having contrast ratios less than 2 at rates as high as 300 Mb/s, or at sensitivities as high as 20 fJ at 300 Mb/s. Simple models of the thresholding behavior of the circuit explain this result.
Constructing Virtual Ar chitectureson a Tiled Processor

Astheamountof availablesilicon resourcesononechip increases,wehaveseentheadventof ever increasingparallel resourcesintegratedon-chip. Manyarchitecturesuse theseresourcesas individually controllable, parallel processingelements.While such architecturesexcel at parallel applications,they seldomsupportlegacysingle-threaded applications. In this work, we proposeusing parallel resourcesto facilitate executionof legacycodeswith acceptable performanceon parallel architectures containing a drasticallydifferent instructionsetthroughtheuseof anall software parallel dynamicbinary translationengine. This enginespatially implementsdifferent portions of a superscalar processoracrossdistinct parallel elementsthusexploiting the pipelineparallelism inherent in a superscalar. This virtual microarchitecture facilitates changing the allocationof silicon resourcesbetweendifferent superscalar unitsin softwarewhich is notpossiblewhenspecialpurpose physicalresourcesare built. We proposebuilding dynamically recon gurable architectures that inspectthe current virtual machine con guration along with the dynamicinstructionstreamand change the con guration to bestsuit the program’s needsat runtime. An x86 to Raw parallel translationenginewasbuilt in which tiles dedicatedto translationcanbe tradedfor tiles dedicatedto thememory systemasanexampleof dynamicrecon guration.
Input-Output Triggered Control via the Small Gain Theorem and Switched Systems Modeling

SUMMARY This paper investigates stability of nonlinear control systems under intermittent information. Following recent results in the literature, we replace the traditional periodic paradigm, where the up-to-date information is transmitted and control laws are executed in a periodic fashion, with the event-triggered paradigm. Building on the small gain theorem, we develop input-output triggered control algorithms yielding stable closed-loop systems. In other words, based on the currently available (but outdated) measurements of the outputs and external inputs of a plant, a mechanism triggering when to obtain new measurements and update the control inputs is provided. Depending on the noise environment, the developed algorithm yields stable, asymptotically stable, and L p -stable (with bias) closed-loop systems. Control loops are modeled as interconnections of hybrid systems for which novel results on L p -stability are presented. The prediction of a triggering event is achieved by employing L p -gains over a ﬁnite horizon. By resorting to convex programming, a method to compute L p -gains over a ﬁnite horizon is devised. Finally, our approach is successfully applied to a trajectory tracking problem for unicycles. Copyright c (cid:13) 2014 John Wiley & Sons, Ltd.
Risk Factors Associated With Chronic Hepatitis C Virus Infection: Limited Frequency of an Unidentified Source of Transmission

Objective:Risk factors have been studied in patients with acute non-A, non-B hepatitis, and approximately 40–50% have no known risk factor for viral acquisition. A significant undefined source of viral transmission has been suggested. We sought to clearly delineate the risk factors in a population of patients with documented chronic hepatitis C virus (HCV) infection to assess the magnitude of HCV transmission without known risk factors.Methods:Risk factor profiles were carefully assessed in 301 consecutive patients with chronic HCV infection. Patients were classified by gender and age. Overall risk factor distributions were calculated and comparisons were made between groups to detect differences in mode of HCV acquisition.Results:One hundred ninety-six men and 105 women were studied; 223 were age ≤ 45 yr and 78 were > 45 yr. Overall, 25% of patients had a history of transfusion and 49% had a history of intravenous drug use (IVDU). Only 12% had no history of risk factor exposure. Men were more likely to have a history of IVDU and less likely to have a history of blood transfusion or sexual exposure/household contact. Younger patients were more likely to have a history of IVDU and older patients were more likely to have a history of blood transfusion and to deny all risk factor exposure. Conclusions: A careful history delineated a potential risk factor for HCV acquisition in 88% of patients with chronic HCV infection. Men and younger patients had different risk factor profiles than women and older patients, respectively. It is likely that an important unknown mode of HCV transmission occurs in a significant minority of patients.
A Comparison of Mid-Level Frontogenesis to Radar-Indicated Heavy Snowbands

Frontogenesis and conditional symmetric instability have been researched extensively, becoming widely used as a means of predicting small scale heavy snow events. The secondary ageostrophic circulation induced by frontogenesis has been shown to produce narrow bands of precipitation, sustained for periods of time by the continual release of moist symmetric instability. This study analyzes six levels of frontogenesis to determine if a specific level is consistently in close proximity to the radar-indicated snowband detected at the same time. The closest level for three cases was examined in greater detail to emphasize a relationship between frontogenesis and moist symmetric instability. Results show frontogenesis in the 700mb to 750mb layer was close to the snowband location within reasonable accuracy, but is shown to vary. In addition, two conceptual models of frontogenesis in relation to saturated equivalent potential vorticity are verified.
THE PAST AND PRESENT DISTRIBUTION AND STATUS OF SEA LIONS AND FUR SEALS IN WESTERN AUSTRALIA

A comparison of the distribution and abundance of seals in Western Australia, according to accounts by early navigators and colonists with surveys made in 1974-7 shows that the Fur seal Arctocephalus jorsteri (Lesson) has contracted in both distribution and abundance, whereas the Sea lion Neophoca cinerea (Peron) has declined only in abundance. The largest known Sea lion populations now occur on Beagle, Buller, Fisherman, Carnac, Middle Doubtful, Wedge and Daw Islands. The largest known Fur seal populations are on Eclipse and Middle Doubtful Islands, and on several islands in the Archipelago of the Recherche. The total size of Western Australian populations is about 700 Sea lions and about 400-500 Fur seals. The abundance of the Sea lion on Carnac I. was monitored over three years, and was found to range from 25-32 animals. On Middle Doubtful Island both species of seal were present but were ecologically segregated. All Fur seals were found around the rocky shores, whereas Sea lions ascended as far as the summit (80m).
Environmental drivers of soil phosphorus composition in natural ecosystems

Abstract. Soil organic and inorganic phosphorus (P) compounds can be influenced by distinctive environmental properties. This study aims to analyze soil P composition in natural ecosystems, relating organic (inositol hexakisphosphate, DNA and phosphonates) and inorganic (orthophosphate, polyphosphate and pyrophosphate) compounds with major temporal (weathering), edaphic and climatic characteristics. A dataset including 88 sites was assembled from published papers that determined soil P composition using one-dimensional liquid state 31P nuclear magnetic resonance spectroscopy of NaOH-EDTA extracts of soils. Bivariate and multivariate regression models were used to better understand the environmental properties influencing soil P. In bivariate relationships, trends for soil P compounds were similar for mineral and organic layers but with different slopes. Independent and combined effects of weathering, edaphic and climatic properties of ecosystems explained up to 78 % (inositol hexakisphosphates) and 89 % (orthophosphate) of variations in organic and inorganic P compounds across the ecosystems, likely deriving from parent material differences. Soil properties, particularly pH, total carbon, and carbon-to-phosphorus ratios, over climate and weathering mainly explained the P variation. We conclude that edaphic and climatic drivers regulate key ecological processes that determine the soil P composition in natural ecosystems. These processes are related to the source of P inputs, primarily determined by the parent material and soil forming factors, plant and microbe P cycling, the bio-physico-chemical properties governing soil phosphatase activity, soil solid surface specific reactivity, and P losses through leaching, and finally the P persistence induced by the increasing complexity of organic and inorganic P compounds as the pedogenesis evolves. Soil organic and inorganic P compounds respond differently to combinations of environmental drivers, which likely indicates that each P compound has specific factors governing its presence in natural ecosystems.
How does wearing a lumbar orthosis interfere with gait initiation?

Abstract The interaction between medical devices and the human body must be evaluated in standardised laboratory tests. Since wearing a lumbar orthosis is assumed to reduce lower back mobility and reinforce trunk movement control through imposed lordosis, this device is expected to affect gait initiation which requires trunk and pelvic rotations. Thirteen healthy subjects were asked to initiate gait without orthosis (control) and orthosis with or without lordosis constraints. The biomechanical parameters usually reported for gait initiation were studied and no statistically significant effects were found. Indeed, the duration of the anticipation, and execution phases and maximal instantaneous velocity of centre of gravity at the end of the first step were not modified by the experimental conditions. The lack of interference underlines the robustness of the gait initiation parameters, which therefore may lead subjects to adopt adaptive strategies to retain this invariance. Future experiments should be conducted to highlight these strategies. Practitioner Summary: The aim of this study was to investigate the effect of various lumbar orthosis characteristics on gait initiation organisation. The results, based on a dynamic analysis of balance strategies, showed that the medical device had no repercussions on movement control. Several explanations are proposed, which should be validated by future studies.
The pig X and Y Chromosomes: structure, sequence, and evolution

We have generated an improved assembly and gene annotation of the pig X chromosome, and a first draft assembly of the pig Y chromosome, by sequencing BAC and fosmid clones, and incorporating information from optical mapping and fibre-FISH. The X chromosome carries 1,014 annotated genes, 689 of which are protein-coding. Gene order closely matches that found in Primates (including humans) and Carnivores (including cats and dogs), which is inferred to be ancestral. Nevertheless, several protein-coding genes present on the human X chromosome were absent from the pig (e.g. the cancer/testis antigen family) or inactive (e.g. AWAT1), and 38 pig-specific X-chromosomal genes were annotated, 22 of which were olfactory receptors. The pig Y chromosome assembly focussed on two clusters of male-specific low-copy number genes, separated by an ampliconic region including the HSFY gene family, which together make up most of the short arm. Both clusters contain palindromes with high sequence identity, presumably maintained by gene conversion. The long arm of the chromosome is almost entirely repetitive, containing previously characterised sequences. Many of the ancestral X-related genes previously reported in at least one mammalian Y chromosome are represented either as active genes or partial sequences. This sequencing project has allowed us to identify genes - both single copy and amplified - on the pig Y, to compare the pig X and Y chromosomes for homologous sequences, and thereby to reveal mechanisms underlying pig X and Y chromosome evolution.
Referral practice among Swiss and non-Swiss walk-in patients in an urban surgical emergency department.

AIM To assess the relationship between nationality, gender and age and use of health services among patients visiting an urban university hospital emergency department (ED). INTRODUCTION ED crowding is an increasingly significant national and international problem. Overcrowding has many potential detrimental effects, including frustration for patients and ED personnel and greater risk of poor outcomes. This is partially caused by the growing numbers of visits by so called "walk-in patients" with minor problems. METHODS From May 1, 2007 to May 31, 2008, sociodemographic information was collected prospectively from 6955 male and 4303 female patients at Inselspital, University Hospital Bern, Switzerland, who had requested our emergency services for non-urgent problems. A stratified sample of 1173 patients was taken for further analysis of referral by a general practitioner (GP) and having a GP at all. RESULTS In all, 26% of visits were by foreign nationals. Only 57% of these were registered with a GP, compared to 83% of Swiss nationals (p <0.0001). Swiss patients referred themselves to us in 87%, compared to 97% self-referrals among foreigners (p <0.0001). Between 7:00 pm and 7:00 am, our ED was significantly more often visited by non-Swiss patients (p <0.0001). Foreign patients were significantly younger than Swiss patients (median age 45, range 1-98 years versus age 35, range 2-89 years, p <0.0001). CONCLUSION Nationality is associated with greater use of ED services for non-urgent problems. Several explanations are conceivable for this. Clinical and policy efforts must address barriers to GP care, since in the long term the GP provides better and more cost-effective care for patients with minor complaints.
Root exudates mediate kin recognition in plants

Though recent work has demonstrated that plants can recognize species, kin versus strangers, and self/non-self roots, no mechanism for identity recognition in plants has yet been found. Here we examined the role of soluble chemicals in signaling among roots. Utilizing Arabidopsis thaliana, we exposed young seedlings to liquid media containing exudates from siblings, strangers (non-siblings), or only their own exudates. In one experiment, root secretions were inhibited by sodium orthovanadate and root length and number of lateral roots were measured. In a second experiment, responses to siblings, strangers, and their own exudates were measured for several accessions (genotypes), and the traits of length of the longest lateral root and hypocotyl length were also measured. The exposure of plants to the root exudates of strangers induced greater lateral root formation than exposure of plants to sibling exudates. Stranger recognition was abolished upon treatment with the secretion inhibitor. In one experiment, plants exposed to sibling or stranger exudates have shorter roots than plants only exposed to their own exudates. This self/non-self recognition response was not affected by the secretion inhibitor. The results demonstrate that that kin recognition and self/non-self are two separate identity recognition systems involving soluble chemicals. Kin recognition requires active secretion by roots.
Specializing continuations a model for dynamic join points

By modeling dynamic join points, pointcuts, and advice in a defunctionalized continuation-passing style interpreter, we provide a fundamental account of these AOP mechanisms. Dynamic join points develop in a principled and natural way as activations of continuation frames. Pointcuts arise directly in the semantic specification as predicates identifying continuation frames. Advice models procedures operating on continuations, specializing the behaviour of continuation frames. In this way, an essential form of AOP is seen, neither as meta-programming nor as an ad hoc extension, but as an intrinsic feature of programming languages.
A New Element within the T-Cell Receptor α Locus Required for Tissue-Specific Locus Control Region Activity

ABSTRACT Locus control regions (LCRs) are cis-acting regulatory elements thought to provide a tissue-specific open chromatin domain for genes to which they are linked. The gene for T-cell receptor α chain (TCRα) is exclusively expressed in T cells, and the chromatin at its locus displays differentially open configurations in expressing and nonexpressing tissues. Mouse TCRα exists in a complex locus containing three differentially regulated genes. We previously described an LCR in this locus that confers T-lineage-specific expression upon linked transgenes. The 3′ portion of this LCR contains an unrestricted chromatin opening activity while the 5′ portion contains elements restricting this activity to T cells. This tissue-specificity region contains four known DNase I hypersensitive sites, two located near transcriptional silencers, one at the TCRα enhancer, and another located 3′ of the enhancer in a 1-kb region of unknown function. Analysis of this region using transgenic mice reveals that the silencer regions contribute negligibly to LCR activity. While the enhancer is required for complete LCR function, its removal has surprisingly little effect on chromatin structure or expression outside the thymus. Rather, the region 3′ of the enhancer appears responsible for the tissue-differential chromatin configurations observed at the TCRα locus. This region, herein termed the “HS1′ element,” also increases lymphoid transgene expression while suppressing ectopic transgene activity. Thus, this previously undescribed element is an integral part of the TCRαLCR, which influences tissue-specific chromatin structure and gene expression.
Antialiased parameterized solid texturing simplified for consumer-level hardware implementation

Procedural solid texturing was introduced fourteen years ago, but has yet to find its way into consumer level graphics hardware for real-time operation. To this end, a new model is introduced that yields a parameterized function capable of synthesizing the most common procedural solid textures, specifically wood, marble, clouds and fire. This model is simple enough to be implemented in hardware, and can be realized in VLSI with as little as 100,000 gates. The new model also yields a new method for antialiasing synthesized textures. An expression for the necessary box filter width is derived as a function of the texturing parameters, the texture coordinates and the rasterization variables. Given this filter width, a technique for efficiently box filtering the synthesized texture by either mip mapping the color table or using a summed area color table are presented. Examples of the antialiased results are shown.