Miracle-dz/UniFAR-FTUs huggingface dataset:
A Systematic Screen for Tube Morphogenesis and Branching Genes in the Drosophila Tracheal System

Many signaling proteins and transcription factors that induce and pattern organs have been identified, but relatively few of the downstream effectors that execute morphogenesis programs. Because such morphogenesis genes may function in many organs and developmental processes, mutations in them are expected to be pleiotropic and hence ignored or discarded in most standard genetic screens. Here we describe a systematic screen designed to identify all Drosophila third chromosome genes (∼40% of the genome) that function in development of the tracheal system, a tubular respiratory organ that provides a paradigm for branching morphogenesis. To identify potentially pleiotropic morphogenesis genes, the screen included analysis of marked clones of homozygous mutant tracheal cells in heterozygous animals, plus a secondary screen to exclude mutations in general “house-keeping” genes. From a collection including more than 5,000 lethal mutations, we identified 133 mutations representing ∼70 or more genes that subdivide the tracheal terminal branching program into six genetically separable steps, a previously established cell specification step plus five major morphogenesis and maturation steps: branching, growth, tubulogenesis, gas-filling, and maintenance. Molecular identification of 14 of the 70 genes demonstrates that they include six previously known tracheal genes, each with a novel function revealed by clonal analysis, and two well-known growth suppressors that establish an integral role for cell growth control in branching morphogenesis. The rest are new tracheal genes that function in morphogenesis and maturation, many through cytoskeletal and secretory pathways. The results suggest systematic genetic screens that include clonal analysis can elucidate the full organogenesis program and that over 200 patterning and morphogenesis genes are required to build even a relatively simple organ such as the Drosophila tracheal system.
Jaywalking Your Dog: Computing the Fréchet Distance with Shortcuts

The similarity of two polygonal curves can be measured using the Frechet distance. We introduce the notion of a more robust Frechet distance, where one is allowed to shortcut between vertices of one of the curves. This is a natural approach for handling noise, in particular batched outliers. We compute a $(3+\varepsilon)$-approximation to the minimum Frechet distance over all possible such shortcuts, in near linear time, if the curve is $c$-packed and the number of shortcuts is either small or unbounded. To facilitate the new algorithm we develop several new tools: (a) a data structure for preprocessing a curve (not necessarily $c$-packed) that supports $(1+\varepsilon)$-approximate Frechet distance queries between a subcurve (of the original curve) and a line segment; (b) a near linear time algorithm that computes a permutation of the vertices of a curve, such that any prefix of $2k-1$ vertices of this permutation forms an optimal approximation (up to a constant factor) to the original curve compared to .
The results of a third Gamma Knife procedure for recurrent trigeminal neuralgia.

OBJECT Gamma Knife radiosurgery (GKRS) is the least invasive treatment option for medically refractory, intractable trigeminal neuralgia (TN) and is especially valuable for treating elderly, infirm patients or those on anticoagulation therapy. The authors reviewed pain outcomes and complications in TN patients who required 3 radiosurgical procedures for recurrent or persistent pain. METHODS A retrospective review of all patients who underwent 3 GKRS procedures for TN at 4 participating centers of the North American Gamma Knife Consortium from 1995 to 2012 was performed. The Barrow Neurological Institute (BNI) pain score was used to evaluate pain outcomes. RESULTS Seventeen patients were identified; 7 were male and 10 were female. The mean age at the time of last GKRS was 79.6 years (range 51.2-95.6 years). The TN was Type I in 16 patients and Type II in 1 patient. No patient suffered from multiple sclerosis. Eight patients (47.1%) reported initial complete pain relief (BNI Score I) following their third GKRS and 8 others (47.1%) experienced at least partial relief (BNI Scores II-IIIb). The average time to initial response was 2.9 months following the third GKRS. Although 3 patients (17.6%) developed new facial sensory dysfunction following primary GKRS and 2 patients (11.8%) experienced new or worsening sensory disturbance following the second GKRS, no patient sustained additional sensory disturbances after the third procedure. At a mean follow-up of 22.9 months following the third GKRS, 6 patients (35.3%) reported continued Score I complete pain relief, while 7 others (41.2%) reported pain improvement (BNI Scores II-IIIb). Four patients (23.5%) suffered recurrent TN following the third procedure at a mean interval of 19.1 months. CONCLUSIONS A third GKRS resulted in pain reduction with a low risk of additional complications in most patients with medically refractory and recurrent, intractable TN. In patients unsuitable for other microsurgical or percutaneous strategies, especially those receiving long-term oral anticoagulation or antiplatelet agents, GKRS repeated for a third time was a satisfactory, low risk option.
Procedure for assessing myeloperoxidase and inflammatory mediator responses in hairless mouse skin †

A preparation procedure for making multiple inflammatory biomarker measurements from the same skin tissue was assessed. The backs of euthymic hairless mice were exposed to sulfur mustard (HD) vapor for 6 min. Animals were euthanized 24 h following exposure, dorsal skin tissue was excised and 12‐mm, full‐thickness biopsy punches of the exposed skin sites were taken. Specimens were snap‐frozen, crushed to a powder using a biopulverizer unit, solubilized in buffer and centrifuged. Supernatant was assayed for pro‐inflammatory cytokines and the acute‐phase reactive protein, serum amyloid P (SAP). Myeloperoxidase (MPX), which is indicative of neutrophil infiltration into the skin, was associated with the pellet fraction. Results indicate an elevation of interleukin‐6, SAP and MPX in mouse skin tissue specimens 24 h following HD vapor exposure. The tissue preparation procedure allows the use of a single skin specimen to make multiple inflammatory endpoint measurements requiring different preparation processes, and it will be used in subsequent studies to characterize further the inflammatory nature of HD‐exposed skin tissue. Copyright © 2000 John Wiley & Sons, Ltd.
Outdoor Scene Image Segmentation Based on Background Recognition and Perceptual Organization

In this paper, we propose a novel outdoor scene image segmentation algorithm based on background recognition and perceptual organization. We recognize the background objects such as the sky, the ground, and vegetation based on the color and texture information. For the structurally challenging objects, which usually consist of multiple constituent parts, we developed a perceptual organization model that can capture the nonaccidental structural relationships among the constituent parts of the structured objects and, hence, group them together accordingly without depending on a priori knowledge of the specific objects. Our experimental results show that our proposed method outperformed two state-of-the-art image segmentation approaches on two challenging outdoor databases (Gould data set and Berkeley segmentation data set) and achieved accurate segmentation quality on various outdoor natural scene environments.
Topology-varying 3D shape creation via structural blending

We introduce an algorithm for generating novel 3D models via topology-varying shape blending. Given a source and a target shape, our method blends them topologically and geometrically, producing continuous series of in-betweens as new shape creations. The blending operations are defined on a spatio-structural graph composed of medial curves and sheets. Such a shape abstraction is structure-oriented, part-aware, and facilitates topology manipulations. Fundamental topological operations including split and merge are realized by allowing one-to-many correspondences between the source and the target. Multiple blending paths are sampled and presented in an interactive, exploratory tool for creative 3D modeling. We show a variety of topology-varying 3D shapes generated via continuous structural blending between man-made shapes exhibiting complex topological differences, in real time.
Upscaling of Dynamic Capillary Pressure of Two‐Phase Flow in Sandstone

Dynamic capillary pressure (DCP) is the capillary pressure defined under transient flow condition during displacement, and it is vital for predicting two‐phase behavior in porous media. This article studies the effect of pore scale force and interfacial area by using captivating Lattice Boltzmann method based on a pseudo‐potential model developed for simulating incompressible multiphase flow in porous media. We analyze the relationship between pore scale forces and DCP based on the energy conservation law and define DCP as a function of energy rate of pressure and viscosity of each phase. We present two‐phase displacement simulations on a computed tomography (CT) image‐based porous model and analyze the effects of injection rate and wettability on DCP based on the proposed upscaling method, where the wettability is defined as the contact angle of the nonwetting phase. The primary results show that (1) the DCP curves are higher than that of the quasi‐static capillary pressure, and a higher injection rate leads to a larger DCP and a faster saturation change. (2) Significant effects of wettability on DCP and the DCP coefficients are observed, where the DCP coefficient is defined as the ratio of the difference between DCP and static capillary pressure over the rate of change of saturation. A larger contact angle results in a higher DCP and a lower change rate of saturation, and consequently induces a larger DCP coefficient. The average DCP coefficient is found to vary from 4.56 × 106 to 3.55 × 105Pa · ms when the nonwetting phase contact angle changes from 140° to 105° in the saturation range of 0.3 to 0.8. This study indicates that the proposed upscaling method is valid to investigate the DCP of two‐phase flow in sandstone.
An Efficient Authorship Protection Scheme for Shared Multimedia Content

Many electronic content providers today like Flickr and Google, offer space to users to publish their electronic media(e.g. photos and videos) in their cloud infrastructures so that they can be publicly accessed. Features like including other information, such as keywords or owner information into the digital material is already offered by existing providers. Despite the useful features made available to users by such infrastructures, the authorship of the published content is not protected against various attacks such as compression. In this paper we propose a robust scheme that uses digital invisible watermarking and hashing to protect the authorship of the digital content and provide resistance against malicious manipulation of multimedia content. The scheme is enhanced by an algorithm called MMBEC, that is an extension of an established scheme MBEC towards higher resistance.
Chromatic properties of neurons in macaque area V2

Abstract We recorded from single cells in area V2 of cynomolgus monkeys using standard acute recording techniques. After measuring each cell's spatial and temporal properties, we performed several tests of its chromatic properties using sine-wave gratings modulated around a mean gray background. Most cells behaved like neurons in area V1 and their responses were adequately described by a model that assumes a linear combination of cone signals. Unlike in V1, we found a subpopulation of cells whose activity was increased or inhibited by stimuli within a narrow range of color combinations. No particular color directions were preferentially represented. V2 cells showing color specificity, including cells showing narrow chromatic tuning, were present in any of the stripe compartments, as defined by cytochrome-oxidase (CO) staining. An addition of chromatic contrast facilitated the responses of most neurons to gratings with various luminance contrasts. Neurons in all three CO compartments gave significant responses to isoluminant gratings. Receptive-field properties of cells were generally similar for luminance and chromatically defined stimuli. We found only a small number of cells with a clearly identifiable double-opponent receptive-field organization.
Antennas and Propagation for Body-Centric Wireless Communications

Now in a newly updated and revised edition, this timely resource provides you with complete and current details on the theory, design, and applications of wireless antennas for on-body electronic systems. The Second Edition offers readers brand new material on advances in physical phantom design and production, recent developments in simulation methods and numerical phantoms, descriptions of methods for simulation of moving bodies, and the use of the body as a transmission channel. You also find a completely revised chapter on channel characterization and antenna design at microwave frequencies.This cutting-edge volume brings you the state-of-the-art in existing applications like Bluetooth headsets together with detailed treatment of techniques, tools, and challenges in developing on-body antennas for an array of medical, emergency response, law enforcement, personal entertainment, and military applications on the horizon. The book briefs you on energy propagation around and into the body and how to estimate performance of on-body wireless links, and then dives into the nuts-and-bolts of designing antenna systems that deliver the goods. It covers on-body communication channels at microwave frequency bands and at low frequency bands, as well as ultra wideband systems for WPANs and WBANs. You get details on body-centric UWB antennas and channels, as well as advances in wearable mobile, EBG, and smart fabric antennas for cellular and WLAN communications. Chapters on telemedicine applications, such as remote diagnoses, and implantable medical devices cover crucial propagation issues and other obstacles that need to be addressed. Rounding out the coverage is a section on antenna design for body-sensor networks and their emerging military and space applications. Packed with hands-on guidance from noted experts, this volume will be indispensable for your efforts in designing and improving body-centric communication systems.Contents: Introduction to Body-Centric Wireless Communications. Electromagnetic Properties and Modeling of the Human Body. On-Body Communication Channels at Microwave Frequency Bands.Transmission Mechanism of the Wearable Devices Using the Human Body as a Transmission Channel. Body Centric UWB Communications. Wearable Antennas for Cellular and WLAN Communications. Body-Sensor Networks for Space and Military Applications. Antennas and Propagation for Telemedicine and Telecare: On-Body Systems. Antennas and Propagation for Telemedicine: Implant Systems. Summary.
Activators of protein kinase C decrease Ca2+ spark frequency in smooth muscle cells from cerebral arteries.

Local Ca2+ transients ("Ca2+ sparks") caused by the opening of one or the coordinated opening of a number of tightly clustered ryanodine-sensitive Ca(2+)-release (RyR) channels in the sarcoplasmic reticulum (SR) activate nearby Ca(2+)-dependent K+ (KCa) channels to cause an outward current [referred to as a "spontaneous transient outward current" (STOC)]. These KCa currents cause membrane potential hyperpolarization of arterial myocytes, which would lead to vasodilation through decreasing Ca2+ entry through voltage-dependent Ca2+ channels. Therefore, modulation of Ca2+ spark frequency should be a means to regulation of KCa channel currents and hence membrane potential. We examined the frequency modulation of Ca2+ sparks and STOCs by activation of protein kinase C (PKC). The PKC activators, phorbol 12-myristate 13-acetate (PMA; 10 nM) and 1,2-dioctanoyl-sn-glycerol (1 microM), decreased Ca2+ spark frequency by 72% and 60%, respectively, and PMA reduced STOC frequency by 83%. PMA also decreased STOC amplitude by 22%, which could be explained by an observed reduction (29%) in KCa channel open probability in the absence of Ca2+ sparks. The reduction in STOC frequency occurred in the presence of an inorganic blocker (Cd2+) of voltage-dependent Ca2+ channels. The reduction in Ca2+ spark frequency did not result from SR Ca2+ depletion, since caffeine-induced Ca2+ transients did not decrease in the presence of PMA. These results suggest that activators of PKC can modulate the frequency of Ca2+ sparks, through an effect on the RyR channel, which would decrease STOC frequency (i.e., KCa channel activity).
Divergence Between Respirometry and Physicochemical Methods in the Fractionation of the Chemical Oxygen Demand in Municipal Wastewater

For activated sludge modeling purposes, the methods used to evaluate the readily biodegradable chemical oxygen demand (RBCOD) in the influents are by biological or via physicochemical assays. However, there has not been sufficient wide comparison between these methods. The main goal of this study was to investigate the performance of the main chemical oxygen demand (COD) fractionation protocols, considering a representative wastewater in the context of tropical and developing countries. Different physicochemical characterization procedures, respirometric tests, and chemical analyses were performed. The fate of the soluble COD in the aeration tanks was studied. The results of the study showed that a marked difference may exist, in municipal wastewaters, between the estimates of the RBCOD fractions measured by respirometry and by any of the physicochemical methods. The evaluated influent showed a rather large fraction of COD that was passing the filters without being rapidly biodegradable, but which was removed quickly by enmeshment in the bioflocs. The consequences of such divergences and behavior are discussed.
Over‐imaging in uncomplicated low back pain: a 12‐month audit of a general medical unit

Low back pain is frequently encountered in hospitals and is a leading cause of disability, often involving costly imaging that exposes a patient to radiation. A retrospective 12‐month audit at a South Australian tertiary hospital aimed to evaluate the frequency, modality and appropriateness of imaging in patients with low back pain. Results showed that the general medical unit was unnecessarily ordering imaging in 40% of patients who exhibited no indications warranting such a procedure. A standardised protocol is required to preventing clinicians from requesting imaging solely for the purposes of self‐reassurance, patient reassurance or fear of litigation.
Analysis of an M/M/1 Queue Using Fixed Order of Search for Arrivals and Service

We analyze an M/M/1 queue with a service discipline in which customers, upon arriving when the server is busy, search a sequence of stations for a vacant station at which to wait, and in which the server, upon becoming free when one or more customers are waiting, searches the stations in the same order for a station occupied by a customer to serve. We show how to find complete asymptotic expansions for all the moments of the waiting time in the heavy traffic limit. We show in particular that the variance of the waiting time for this discipline is more similar to that of last-come-first-served (which has a pole of order three as the arrival rate approaches the service rate) than that of first-come-first-served (which has pole of order two).
Cones Respond to Light in the Absence of Transducin β Subunit

Mammalian cones respond to light by closing a cGMP-gated channel via a cascade that includes a heterotrimeric G-protein, cone transducin, comprising Gαt2, Gβ3 and Gγt2 subunits. The function of Gβγ in this cascade has not been examined. Here, we investigate the role of Gβ3 by assessing cone structure and function in Gβ3-null mouse (Gnb3−/−). We found that Gβ3 is required for the normal expression of its partners, because in the Gnb3−/− cone outer segments, the levels of Gαt2 and Gγt2 are reduced by fourfold to sixfold, whereas other components of the cascade remain unaltered. Surprisingly, Gnb3−/− cones produce stable responses with normal kinetics and saturating response amplitudes similar to that of the wild-type, suggesting that cone phototransduction can function efficiently without a Gβ subunit. However, light sensitivity was reduced by approximately fourfold in the knock-out cones. Because the reduction in sensitivity was similar in magnitude to the reduction in Gαt2 level in the cone outer segment, we conclude that activation of Gαt2 in Gnb3−/− cones proceeds at a rate approximately proportional to its outer segment concentration, and that activation of phosphodiesterase and downstream cascade components is normal. These results suggest that the main role of Gβ3 in cones is to establish optimal levels of transducin heteromer in the outer segment, thereby indirectly contributing to robust response properties.
Combining Ontology Queries with Text Search in Service Discovery

We present a querying mechanism for service discovery which combines ontology queries with text search. The underlying service discovery architecture used is GloServ. GloServ uses the Web Ontology Language (OWL) to classify services in an ontology and map knowledge obtained by the ontology onto a hierarchical peer-to-peer network. Initially, an ontology-based first order predicate logic query is issued in order to route the query to the appropriate server and to obtain exact and related service data. Text search further enhances querying by allowing services to be described not only with ontology attributes, but with plain text so that users can query for them using key words. Currently, querying is limited to either simple attribute-value pair searches, ontology queries or text search. Combining ontology queries with text search enhances current service discovery mechanisms.
Analysis of Competing Data Structures: Does Ontological Clarity Produce Better End User Query Performance

End users respond to stakeholders' information requests by using query tools to retrieve information from their organizations' data stores. The structure of these data stores impacts end users' performance, e. g. , the accuracy of their responses. Ontologically clearer conceptual models have been shown to facilitate better problem solving within real-world application domains. If, however, ontologically clearer conceptual models are directly transformed into implementation ( logical) data models, the differences in the number of entities and relationships may cause cognitive issues for end users that are likely to affect their query performance. This paper reports the results of an experiment that investigated the effect on query performance of more traditional logical models compared to ontologically clearer logical models. Results indicate that end users of the ontologically clearer implementation made fewer semantic errors overall. Thus, the benefits of ontological clarity at the conceptual level may translate into similar benefits when querying ontologically clearer logical models. Unfortunately, an examination of the specific types of errors that were made indicated that the benefits are not clear cut. While the removal of optional attributes and relationships led to an overall reduction in the number of errors, closer analyses show that some types of errors ( involving projection and restriction) decreased as expected, while other types of errors ( involving joins) increased.