Miracle-dz/UniFAR-FTUs huggingface dataset:
Bundling of actin filaments by alpha-actinin depends on its molecular length

Cross-linking of actin filaments (F-actin) into bundles and networks was investigated with three different isoforms of the dumbbell-shaped alpha-actinin homodimer under identical reaction conditions. These were isolated from chicken gizzard smooth muscle, Acanthamoeba, and Dictyostelium, respectively. Examination in the electron microscope revealed that each isoform was able to cross-link F-actin into networks. In addition, F-actin bundles were obtained with chicken gizzard and Acanthamoeba alpha-actinin, but not Dictyostelium alpha- actinin under conditions where actin by itself polymerized into disperse filaments. This F-actin bundle formation critically depended on the proper molar ratio of alpha-actinin to actin, and hence F-actin bundles immediately disappeared when free alpha-actinin was withdrawn from the surrounding medium. The apparent dissociation constants (Kds) at half-saturation of the actin binding sites were 0.4 microM at 22 degrees C and 1.2 microM at 37 degrees C for chicken gizzard, and 2.7 microM at 22 degrees C for both Acanthamoeba and Dictyostelium alpha- actinin. Chicken gizzard and Dictyostelium alpha-actinin predominantly cross-linked actin filaments in an antiparallel fashion, whereas Acanthamoeba alpha-actinin cross-linked actin filaments preferentially in a parallel fashion. The average molecular length of free alpha- actinin was 37 nm for glycerol-sprayed/rotary metal-shadowed and 35 nm for negatively stained chicken gizzard; 46 and 44 nm, respectively, for Acanthamoeba; and 34 and 31 nm, respectively, for Dictyostelium alpha- actinin. In negatively stained preparations we also evaluated the average molecular length of alpha-actinin when bound to actin filaments: 36 nm for chicken gizzard and 35 nm for Acanthamoeba alpha- actinin, a molecular length roughly coinciding with the crossover repeat of the two-stranded F-actin helix (i.e., 36 nm), but only 28 nm for Dictyostelium alpha-actinin. Furthermore, the minimal spacing between cross-linking alpha-actinin molecules along actin filaments was close to 36 nm for both smooth muscle and Acanthamoeba alpha-actinin, but only 31 nm for Dictyostelium alpha-actinin. This observation suggests that the molecular length of the alpha-actinin homodimer may determine its spacing along the actin filament, and hence F-actin bundle formation may require "tight" (i.e., one molecule after the other) and "untwisted" (i.e., the long axis of the molecule being parallel to the actin filament axis) packing of alpha-actinin molecules along the actin filaments.
Promoter-proximal tethering elements regulate enhancer-promoter specificity in the Drosophila Antennapedia complex

Insulator DNAs and promoter competition regulate enhancer–promoter interactions within complex genetic loci. Here we provide evidence for a third mechanism: promoter-proximal tethering elements. The Scr-ftz region of the Antennapedia gene complex includes two known enhancers, AE1 and T1. AE1 selectively interacts with the ftz promoter to maintain pair-rule stripes of ftz expression during gastrulation and germ-band elongation. The T1 enhancer, located 3′ of the ftz gene and ≈25 kb 5′ of the Scr promoter, selectively activates Scr expression in the prothorax and posterior head segments. A variety of P element minigenes were examined in transgenic embryos to determine the basis for specific AE1-ftz and T1-Scr interactions. A 450-bp DNA fragment located ≈100 bp 5′ of the Scr transcription start site is essential for T1-Scr interactions and can mediate long-range activation of a ftz/lacZ reporter gene when placed 5′ of the ftz promoter. We suggest that the Scr450 fragment contains tethering elements that selectively recruit T1 to the Scr promoter. Tethering elements might regulate enhancer–promoter interactions at other complex genetic loci.
Sensorless Sensing in Wireless Networks: Implementation and Measurements

Multipath fading and shadowing are usually regarded as negative phenomena hindering proper radio communication. Adopting a completely different stance, this paper illustrates that such phenomena enable information harvesting from received signal strength leading to a number of original applications requiring no conventional sensing hardware. The radio itself, provided that it can measure the strength of the incoming signal, is the only sensor we use; with this sensor-less sensing approach, any wireless network becomes a sensor network. We show that motion of the nodes in the network or motion of bodies external to the network leaves a characteristic footprint on signal strength patterns, which may be exploited for motion detection. We illustrate a technique to extract an estimate of velocity from signal strength, and we leverage on the spatial memory properties of wireless links to present a method for spatial configuration recognition.
Detection of Some Pathogenic Water Bacterial Contamination Using PCRtechnique

Water contamination is any change in biological properties of water that have a harmful effect on living things. From the beginning of April 2010 till the end of December 2011, One thousand five hundred sixty seven of tap water samples from different parts of Baghdad city were collected, and examined bacteriologic ally by traditional method for detection of pathogenic bacteria. For further detection the molecular study carried out to detected the virulence genes of pathogenic isolates , five isolates of Salmonella spp.gave positive results for the invA gene and prgKgene , three isolates of non-O1 V.cholera were positive for omp Wgene and yielded negative results for the ctxAB gene and the zotgenes but, one of them gave positive result for the tcp gene. Thirteen isolates of Aeromonashydrophila gave positive results for Fla and laf flagellin genes
Glucosamine for Osteoarthritis: Biological Effects, Clinical Efficacy, and Safety on Glucose Metabolism

Osteoarthritis is a chronic degenerative disorder that currently represents one of the main causes of disability within the elderly population and an important presenting complaint overall. The pathophysiologic basis of osteoarthritis entails a complex group of interactions among biochemical and mechanical factors that have been better characterized in light of a recent spike in research on the subject. This has led to an ongoing search for ideal therapeutic management schemes for these patients, where glucosamine is one of the most frequently used alternatives worldwide due to their chondroprotective properties and their long-term effects. Its use in the treatment of osteoarthritis is well established; yet despite being considered effective by many research groups, controversy surrounds their true effectiveness. This situation stems from several methodological aspects which hinder appropriate data analysis and comparison in this context, particularly regarding objectives and target variables. Similar difficulties surround the assessment of the potential ability of glucosamine formulations to alter glucose metabolism. Nevertheless, evidence supporting diabetogenesis by glucosamine remains scarce in humans, and to date, this association should be considered only a theoretical possibility.
Dietary carotenoid pigments and immune function in a songbird with extensive carotenoid-based plumage coloration

Carotenoid pigments can directly enhance the immune responses of vertebrates, and they are used by many animals to create ornamental color displays. It has been hypothesized that these two functions of carotenoid pigments are linked: animals must trade off use of carotenoid pigments for immune function versus ornamental display. We tested two key predictions of this hypothesis with captive American goldfinches, Carduelis tristis, a species with extensive carotenoid-based plumage coloration. First, we tested whether the immune systems of male goldfinches are carotenoid limited during molt by supplying treatment groups with low, approximately normal, or high dietary access to lutein and zeaxanthin. Dietary treatment had a significant effect on plumage and bill color but not on immunocompetence. We compared the cell-mediated and humoral immune responses and the course of disease after infection for males in the different treatments. We observed no significant effect of the carotenoid content of diet on immune response or disease resistance. Second, we tested whether there was a positive relationship between immune function and expression of ornamental coloration by comparing both the pre- and posttreatment plumage coloration of males to their immune responses. We failed to find the predicted trade-off between ornament display and immune function. These findings do not support the hypothesis that songbirds with extensive carotenoid-based plumage displays trade off the use of carotenoids for ornamentation versus immune function. Copyright 2003.
The next-generation 64b SPARC core in a T4 SoC processor

The T4 microprocessor introduces the next generation dual-issue, out-of-order SPARC core that delivers up to 5x integer and 7x floating-point single-thread performance improvement for both commercial and industry standard work- loads. Eight SPARC cores, a crossbar and a unified 16-way 4MB L3 cache are implemented in the same system-on-chip platform as the predecessor T3 to utilize established coherency (CLC), DDR3 (MCU), PCIE Gen2 (PEU) and 1G/10G Ethernet interfaces (NIL)). Further, T4's pin, thermal and power compatibility with the previous generation enables faster time to market for new multi-socket systems. The 403mm2 die has 855 million transistors of four different types and 12 metal layers fabricated using TSMC's 40nm process.
Testing Properties of Collections of Distributions

We propose a framework for studying property testing of collections of distributions, where the number of distributions in the collection is a parameter of the problem. Previous work on property testing of distributions considered single distributions or pairs of distributions. We suggest two models that differ in the way the algorithm is given access to samples from the distributions. In one model the algorithm may ask for a sample from any distribution of its choice, and in the other the choice of the distribution is random. Our main focus is on the basic problem of distinguishing between the case that all the distributions in the collection are the same (or very similar), and the case that it is necessary to modify the distributions in the collection in a non-negligible manner so as to obtain this property. We give almost tight upper and lower bounds for this testing problem, as well as study an extension to a clusterability property. One of our lower bounds directly implies a lower bound on testing independence of a joint distribution, a result which was left open by previous work.
Memory Outcome after Left Anterior Temporal Lobectomy in Patients with Expected and Reversed Wada Memory Asymmetry Scores

Summary: Purpose: The ideal candidate for anterior temporal lobectomy surgery shows a Wada memory asymmetry (WMA) score characterized by better memory performance in the hemisphere contralateral to the seizure focus relative to the ipsilateral (surgical) hemisphere. However, some surgical candidates show a reversed WMA or better Wada memory performance in the hemisphere of surgical interest relative to the hemisphere contralateral to the seizure focus. To date, no data are available contrasting memory and seizure outcome for these two Wada groups. The present study compared memory and seizure outcome after left anterior temporal lobectomy (L‐ATL) in patients showing expected and reversed WMA scores, and also examined the relationship of the individual hemisphere Wada memory scores for predicting verbal memory outcome after L‐ATL.
CD4+ T Cell Depletion, Immune Activation and Increased Production of Regulatory T Cells in the Thymus of HIV-Infected Individuals

Mechanisms by which HIV affects the thymus are multiple and only partially known, and the role of thymic dysfunction in HIV/AIDS immunopathogenesis remains poorly understood. To evaluate the effects of HIV infection on intra-thymic precursors of T cells in HIV-infected adults, we conducted a detailed immunophenotypic study of thymic tissue isolated from 7 HIV-infected and 10 HIV-negative adults who were to undergo heart surgery. We found that thymuses of HIV-infected individuals were characterized by a relative depletion of CD4+ single positive T cells and a corresponding enrichment of CD8+ single positive T cells. In addition, thymocytes derived from HIV-infected subjects showed increased levels of activated and proliferating cells. Our analysis also revealed a decreased expression of interleukin-7 receptor in early thymocytes from HIV-infected individuals, along with an increase in this same expression in mature double- and single-positive cells. Frequency of regulatory T cells (CD25+FoxP3+) was significantly increased in HIV-infected thymuses, particularly in priorly-committed CD4 single positive cells. Our data suggest that HIV infection is associated with a complex set of changes in the immunophenotype of thymocytes, including a reduction of intrathymic CD4+ T cell precursors, increased expression of activation markers, changes in the expression pattern of IL-7R and enrichment of T regulatory cells generation.
Some applications of wireless sensor networks

Grâce aux progres fait dans le domaine de la miniaturisation des systemes de micro-electromecaniques (MEMS), il est apparu un nouveau type de reseaux mobiles : les reseaux de capteurs (sensor networks). Ces reseaux utilisent de petits objets capables de recueillir des informations sur leur environnement proche. Dans le reseau, il existe une ou plusieurs stations de surveillance chargees de collecter les informations envoyees par les capteurs via une interface de communication sans fil. Ces informations peuvent etre transmises a la station de surveillance directement ou en mode multi-sauts. Ces caracteristiques ouvrent de nouvelles perspectives aussi bien en termes theoriques que pour des applications pratiques d'interet immediat. Ces reseaux peuvent etre deployes dans des environnements aussi divers qu'une maison, un commerce, un entrepot, une ville, ou encore dans des environnements hostiles comme un terrain militaire, un volcan, un site de tremblements de terre, ou meme dans une foret, dans l'air, la mer, les fleuves, etc. Dans cet article, nous presentons un etat de l'art sur les reseaux de capteurs.
Top European Retailers and Customer-Centred Web Structuring Bla enka Kne eviæ *

The past decade was the decade of ‘e-everything’ and many authors praised the efficiency of web usage for different business purposes. But practice showed that the web as a communication and distribution channel is not as powerful as it was claimed to be. After the dotcom explosion, the process of sobering-up followed and a large number of pure e-companies were shut-down. On the other hand, in the same period traditional companies discovered that the web can be used as an additional communication and distribution channel. This paper explains how the largest brick-and-mortar European retail companies structure their web sites making them useful for their customers.
A Computer‐Aided Diagnostic Algorithm Improves the Accuracy of Transesophageal Echocardiography for Left Atrial Thrombi

We investigated whether transesophageal echocardiography (TEE) assisted with a computer‐aided diagnostic (CAD) algorithm was superior to TEE in diagnosing left atrial (LA)/left atrial appendage (LAA) thrombi in patients with atrial fibrillation (AF) in a single prospective study.
Genomics and proteomics: a signal processor's tour

The theory and methods of signal processing are becoming increasingly important in molecular biology. Digital filtering techniques, transform domain methods, and Markov models have played important roles in gene identification, biological sequence analysis, and alignment. This paper contains a brief review of molecular biology, followed by a review of the applications of signal processing theory. This includes the problem of gene finding using digital filtering, and the use of transform domain methods in the study of protein binding spots. The relatively new topic of noncoding genes, and the associated problem of identifying ncRNA buried in DNA sequences are also described. This includes a discussion of hidden Markov models and context free grammars. Several new directions in genomic signal processing are briefly outlined in the end.
Cognitive function, health-related quality of life, and symptoms of depression and anxiety sensitivity are impaired in patients with the postural orthostatic tachycardia syndrome (POTS)

The Postural Orthostatic Tachycardia Syndrome (POTS) is a condition in which heart rate increases abnormally when the individual assumes an upright position. In addition to the marked tachycardia, presyncope, and syncope, patients with POTS often complain of light-headedness, fatigue, and difficulty in concentrating. The present study assessed individuals with POTS for psychiatric comorbidity, anxiety sensitivity and health related quality of life and examined general cognitive ability. Data was obtained from patients with POTS (n = 15, 12 female, aged 30 ± 3 years) and age matched healthy subjects (n = 30, 21 female, aged 32 ± 2 years). Patients with POTS commonly presented with symptoms of depression, elevated anxiety and increased anxiety sensitivity, particularly with regards to cardiac symptoms, and had a poorer health related quality of life in both the physical and mental health domains. While patients with POTS performed worse in tests of current intellectual functioning (verbal and non-verbal IQ) and in measures of focused attention (digits forward) and short term memory (digits back), test results were influenced largely by years of education and the underlying level of depression and anxiety. Acute changes in cognitive performance in response to head up tilt were evident in the POTS patients. From results obtained, it was concluded that participants with POTS have an increased prevalence of depression and higher levels of anxiety. These underlying symptoms impact on cognition in patients with POTS, particularly in the cognitive domains of attention and short-term memory. Our results indicate that psychological interventions may aid in recovery and facilitate uptake and adherence of other treatment modalities in patients with POTS.
Flexible Clusters for High-Performance Computing

High Performance Computational Clusters are, in general, rather rigid objects that present to their user a limited number of degrees of freedom related, usually, only to the specification of the resources requested and to the selection of specific applications and libraries. While in standard production environments this is reasonable and actually desirable, it can become an hindrance when one needs a dynamic and flexible computational environment, for instance for experiments and evaluation, where very different computational approaches, e.g., map-reduce, standard parallel jobs and virtual HPC clusters need to coexist on the same physical facility. In this paper we will present our efforts to address some of these challenges while maintaining a unified cluster management environment.
Ökonomische und naturschutzfachliche Überlegungen zur Ausgestaltung lokaler Agrarumweltprogramme - diskutiert am Beispiel eines Programms zur moorschonenden Entwicklung landwirtschaftlicher Betriebe

Der vorliegende Beitrag stellt ein lokales Agrarumweltprogramm zur moorschonenden und naturschutzgerechten Entwicklung landwirtschaftlicher Betriebe vor. Anhand ausgewahlter Modellbetriebe wird das Programm hinsichtlich betriebswirtschaftlicher Gesichtspunkte analysiert. Aufbauend auf diese Analyse werden die Moglichkeiten und Grenzen lokaler Agrarumweltprogramme diskutiert und es werden Empfehlungen fur die Ausgestaltung solcher Programme formuliert. Es zeigt sich, dass die Vorteile eines lokalen Vorgehens insbesondere in der Einbindung lokaler Stakeholder liegen. Schwierigkeiten bestehen vor allem hinsichtlich der Erfullung von Kontroll- und Wettbewerbsvorgaben der Europaischen Union.
Obtaining Provably Legitimate Internet Topologies

What topologies should be used to evaluate protocols for interdomain routing? Using the most current Internet topology is not practical since its size is prohibitive for detailed, packet-level interdomain simulations. Besides being of moderate size, the topology should be policy-aware, that is, it needs to represent business relationships between adjacent nodes (that represent autonomous systems). In this paper, we address this issue by providing a framework to generate small, realistic, and policy-aware topologies. We propose HBR, a novel sampling method, which exploits the inherent hierarchy of the policy-aware Internet topology. We formally prove that our approach generates connected and legitimate topologies, which are compatible with the policy-based routing conventions and rules. Using simulations, we show that HBR generates topologies that: 1) maintain the graph properties of the real topology; 2) provide reasonably realistic interdomain simulation results while reducing the computational complexity by several orders of magnitude as compared to the initial topology. Our approach provides a permanent solution to the problem of interdomain routing evaluations: Given a more accurate and complete topology, HBR can generate better small topologies in the future.
Stumping along a Summary for Exploration & Exploitation Challenge 2011

The Pascal Exploration & Exploitation challenge 2011 seeks to evaluate algorithms for the online website content selection problem. This article presents the solution we used to achieve second place in this challenge and some side-experiments we performed. The methods we evaluated are all structured in three layers. The first layer provides an online summary of the data stream for continuous and nominal data. Continuous data are handled using an online quantile summary. Nominal data are summarized with a hash-based counting structure. With these techniques, we managed to build an accurate stream summary with a small memory footprint. The second layer uses the summary to build predictors. We exploited several kinds of trees from simple decision stumps to deep multivariate ones. For the last layer, we explored several combination strategies: online bagging, exponential weighting, linear ranker, and simple averaging.
Enabling Helical Needle Trajectories with Minimal Actuation : A Screw-Based Approach to Concentric Tube Needle Deployment

The clinical need for needle-based therapies capable of accessing tissues unreachable by conventional needles has motivated substantial research into steerable needles (see [1] and [2] for a review of these technologies). In particular, it has been observed that curved paths can be useful in percutaneous procedures [3]. Gilbert, et al., showed that helically pre-curved concentric tube nitinol needles can be deployed in a follow-the-leader (FTL) fashion, such that the needle shaft follows the path traced out by the tip [4]. Further information on concentric tube robots and the mechanics-based models that govern their motion can be found in [5] and [6].