Miracle-dz/UniFAR-FTUs huggingface dataset:
The Intraflagellar Transport Machinery of Chlamydomonas reinhardtii

First discovered in the green alga, Chlamydomonas, intraflagellar transport (IFT) is the bidirectional movement of protein particles along the length of eukaryotic cilia and flagella. Composed of ∼16 different proteins, IFT particles are moved out to the distal tip of the organelle by kinesin‐II and are brought back to the cell body by cytoplasmic dynein 1b. Mutant analysis of the IFT motor and particle proteins using diverse organisms has revealed a conserved and essential role for IFT in the assembly and maintenance of cilia and flagella. IFT is thought to mediate this assembly through the delivery of axonemal precursors out to the distal tip of the growing organelle. Consistent with this model, the IFT particle proteins are rich in protein–protein binding motifs, suggesting that the particles may act as scaffolds for the binding of multiple cargoes. With most of the IFT proteins now identified at the level of the gene, this review will briefly examine both the structure and function of the IFT machinery of Chlamydomonas reinhardtii.
Microtribology of Magnetic Media

Scanning tunnelling microscopy (STM), atomic force microscopy (AFM) and the modifications of AFM [such as friction force microscopy (FFM)] are becoming increasingly important in the understanding of fundamental mechanisms of friction, wear and lubrication and in studying the interfacial phenomena in micro- and nanostructures used in magnetic storage devices and microelectromechanical systems (MEMS). This paper describes modified AFM and FFM techniques and presents data on microtribological studies of magnetic media-magnetic tapes and disks. Local variation in microscale friction is found to correspond to the local slope, suggesting that a ratchet mechanism is responsible for this variation. Wear rates for magnetic tapes are approximately constant for various loads and test duration. However, for magnetic disks, the wear of the diamond-like carbon overcoat is catastrophic. Evolution of the wear has also been studied using AFM. AFM has been modified for nanoindentation hardness measurements. It has been shown that hardness of ultra-thin films can be measured using AFM. AFM has also been shown to be useful for nanofabrication.
A S URVEY ON E NERGY E FFICIENT A SYNCHRONOUS W ISE MAC P ROTOCOL FOR W IRELESS S ENSOR N ETWORKS

This paper presents a review on energy efficient WiseMAC Protocol for wireless sensor networks. Among various MAC layer protocol WiseMAC is a known as one of the most energy efficient protocol. Non-persistent carrier sense multiple access (np-CSMA) and the preamble sampling technique are the main techniques used in basic WiseMAC protocol, they are used to reduce the consumption of power when energy is wasted in listening to idle medium. Here we investigate the WiseMAC protocol with the different important schemes that used in implementation of WiseMAC in sensor networks, these schemes are basically emphasizing on energy saving methods in WiseMAC, various modifications are done in original WiseMAC to make them more energy efficient; with the same motive of more energy efficiency, we propose adaptive WiseMAC protocol with dynamic duty cycle and the adaptive Contention Window.
S2k Leitlinie Autoimmune Lebererkrankungen

Zusammenfassung Diese Leitlinie wurde unter Federführung der DGVS und mit Beteiligung benachbarter Fachgebiete erstellt und soll als praktische Hilfe für die Diagnostik und Therapie der Autoimmunen Lebererkrankungen dienen. Sie soll den aktuellen Stand der Wissenschaft darstellen, das Erkennen der Erkrankung fördern und die Behandlung der Patienten verbessern.
Model selection for DCE‐T1 studies in glioblastoma

Dynamic contrast enhanced T1‐weighted MRI using the contrast agent gadopentetate dimeglumine (Gd‐DTPA) was performed on 10 patients with glioblastoma. Nested models with as many as three parameters were used to estimate plasma volume or plasma volume and forward vascular transfer constant (Ktrans) and the reverse vascular transfer constant (kep). These constituted models 1, 2, and 3, respectively. Model 1 predominated in normal nonleaky brain tissue, showing little or no leakage of contrast agent. Model 3 predominated in regions associated with aggressive portions of the tumor, and model 2 bordered model 3 regions, showing leakage at reduced rates. In the patient sample, vp was about four times that of white matter in the enhancing part of the tumor. Ktrans varied by a factor of 10 between the model 2 (1.9 ↔ 10−3 min−1) and model 3 regions (1.9 ↔ 10−2 min−1). The mean calculated interstitial space (model 3) was 5.5%. In model 3 regions, excellent curve fits were obtained to summarize concentration‐time data (mean R2 = 0.99). We conclude that the three parameters of the standard model are sufficient to fit dynamic contrast enhanced T1 data in glioblastoma under the conditions of the experiment. Magn Reson Med, 2012. © 2011 Wiley Periodicals, Inc.
Choosing the right outcomes

Outcome measures are used to monitor the effects of interventions in clinical practice or in formal clinical trials. They may also be used to assess changes within populations either spontaneously or as a result of public‐health measures. They are used to monitor the course of illness as part of a management plan or, for larger groups, to identify changes brought about, for instance, by migration or immunization. The choice of outcome measure depends on the age of the child, the complexity of the outcome (for instance, whether its application is to individuals or populations), and the time scale over which it is necessary to detect changes in outcome. The most commonly used outcome measures are clinical symptoms, which are often compiled into scoring systems. Surprisingly, these are often the least wellvalidated measures of outcome. Physiologic measures, although well validated, are difficult to apply to infants and pre‐school children. The role of inflammatory markers is currently limited to research rather than clinical practice. Other outcome measures such as quality of life, impact‐of‐asthma instruments, and measures to determine the health‐economic aspects of asthma are poorly developed in childhood. The right outcome depends on the question being asked, the age of the subjects, and the time scale and complexity over which measurement is required.
Using development history sticky notes to understand software architecture

Maintenance of evolving software systems has become the most frequently performed activity by software developers. A good understanding of the software system is needed to reduce the cost and length of this activity. Various approaches and tools have been proposed to assist in this process such as code browsers, slicing techniques, etc. These techniques neglect to use a central and vital piece of data available - the historical modification records stored in source control systems. These records offer a rich and detailed account of the evolution of the software system to its current state. In this paper, we present an approach which recovers valuable information from source control systems and attaches this information to the static dependency graph of a software system. We call this recovered information - source sticky notes. We show how to use these notes along with the software reflexion framework to assist in understanding the architecture of large software systems. To demonstrate the viability of our approach, we apply it to understand the architecture of NetBSD - a large open source operating system.
Capturing the relative distribution of features for action recognition

This paper presents an approach to the categorisation of spatio-temporal activity in video, which is based solely on the relative distribution of feature points. Introducing a Relative Motion Descriptor for actions in video, we show that the spatio-temporal distribution of features alone (without explicit appearance information) effectively describes actions, and demonstrate performance consistent with state-of-the-art. Furthermore, we propose that for actions where noisy examples exist, it is not optimal to group all action examples as a single class. Therefore, rather than engineering features that attempt to generalise over noisy examples, our method follows a different approach: We make use of Random Sampling Consensus (RANSAC) to automatically discover and reject outlier examples within classes. We evaluate the Relative Motion Descriptor and outlier rejection approaches on four action datasets, and show that outlier rejection using RANSAC provides a consistent and notable increase in performance, and demonstrate superior performance to more complex multiple-feature based approaches.
Toll-Like Receptors 2-Deficient Mice Are Protected Against Postischemic Coronary Endothelial Dysfunction

Objectives—Toll-like receptors (TLR) 2 are expressed in cardiac and inflammatory cells, and regulate leukocyte function. Because leukocyte adhesion is a critical event in endothelial injury induced by ischemia/reperfusion (I/R), we assessed whether TLR2 were involved in I/R - induced coronary endothelial injury. Methods and Results—Ischemia - reperfusion markedly decreased NO-mediated coronary relaxations to acetylcholine assessed ex vivo. In contrast, in TLR2 deficient mice, I/R paradoxically improved the NO-mediated responses to acetylcholine. To precise the cellular compartment expressing TLR2 which is involved in endothelial injury, we developed bone-marrow chimeric mice by transplanting TLR2−/− bone marrow to WT mice or WT bone marrow to TLR2−/− mice and submitted them to I/R 5 weeks after transplant. Both chimeric mice displayed similar protection as TLR2−/− mice against I/R-induced endothelial dysfunction, suggesting a role of TLR2 expressed on both non-bone marrow cells (in our case presumably endothelial cells and/or cardiomyocytes) and cells of bone marrow origin (presumably neutrophils). TLR2 deficiency was also associated with a smaller infarct size, and reduced reperfusion-induced production of reactive oxygen species and leukocyte infiltration. Conclusions—TLR2 contribute to coronary endothelial dysfunction after I/R, possibly through stimulation of neutrophil- (and free radical-) mediated endothelial injury.
Histone deacetylase 5 interacts with Krüppel-like factor 2 and inhibits its transcriptional activity in endothelium.

AIMS Vascular endothelial dysfunction and inflammation are hallmarks of atherosclerosis. Krüppel-like factor 2 (KLF2) is a key mediator of anti-inflammatory and anti-atherosclerotic properties of the endothelium. However, little is known of the molecular mechanisms for regulating KLF2 transcriptional activation. METHODS AND RESULTS Here, we found that histone deacetylase 5 (HDAC5) associates with KLF2 and represses KLF2 transcriptional activation. HDAC5 resided with KLF2 in the nuclei of human umbilical cord vein endothelial cells (HUVECs). Steady laminar flow attenuated the association of HDAC5 with KLF2 via stimulating HDAC5 phosphorylation-dependent nuclear export in HUVEC. We also mapped the KLF2-HDAC5-interacting domains and found that the N-terminal region of HDAC5 interacts with the C-terminal domain of KLF2. Chromatin immunoprecipitation and luciferase reporter assays showed that HDAC5 through a direct association with KLF2 suppressed KLF2 transcriptional activation. HDAC5 overexpression inhibited KLF2-dependent endothelial nitric oxide synthesis (eNOS) promoter activity in COS7 cell and gene expression in both HUVECs and bovine aortic endothelial cells (BAECs). Conversely, HDAC5 silencing enhanced KLF2 transcription and hence eNOS expression in HUVEC. Moreover, we observed that the level of eNOS protein in the thoracic aorta isolated from HDAC5 knockout mice was higher, whereas expression of pro-inflammatory vascular cell adhesion molecule 1 was lower, compared with those of HDAC5 wild-type mice. CONCLUSIONS We reveal a novel role of HDAC5 in modulating the KLF2 transcriptional activation and eNOS expression. These findings suggest that HDAC5, a binding partner and modulator of KLF2, could be a new therapeutic target to prevent vascular endothelial dysfunction associated with cardiovascular diseases.
Optical Thin Film Technology for Ultrafast Fiber Lasers

This thesis investigates novel dispersion compensation methods for mode-locked fiber lasers and the dynamical properties of ytterbium and thulium-holmium gain materials. The emphasis is on dielectric thin film structures and their integration into fiber cavities to control laser performance. A Gires–Tournois interferometer (GTI) made with electron beam evaporation was used for the first time to compensate for the dispersion of a fiber cavity and thus achieve ultrashort mode-locked pulses. Another thin film dispersion compensator, a Fabry-Pérot etalon, demonstrated in a mode-locked fiber laser, allowed for continuously tunable short pulse operation of an ytterbium fiber laser over a broad wavelength range. In addition to dispersive thin film structures, the thesis also presents a new type of dichroic coating deposited directly onto an optical fiber end. The dichroic coating acts as an output coupler and pump combiner, simultaneously. This enables laser cavities which are substantially shorter than would be possible with conventional fiber components. The compact all-fiber ytterbium fiber laser presented had a record high fundamental repetition rate of 571 MHz with ultrashort, 572 fs, pulses. The energy level scheme of ytterbium and thulium-holmium gain materials was studied for the first time in this thesis by analyzing the laser relaxation oscillations. Both materials exhibited a change in transition mechanism from three-level to four-level laser operation in the long-wavelength tail of the gain bandwidth.
A 2.4-GHz CMOS power amplifier design for low power wireless sensors network

Power amplifier is the key component in wireless transceiver and its realization and integration in standard CMOS technology is essential for the efficient and cost effective wireless SoCs. In this work, we present a fully integrated differential power amplifier operating at 2.45 GHz realized in 0.18 µM RF CMOS process. The designed power amplifier has a built in capability to modulate the base band data using On — Off Keying (OOK) while providing a single ended output power of over +6.4 dBm to 50 Ω load impedance. Measured Power Added Efficiency (PAE) at the P1 dB of this amplifier operating at 1.8 V is around 18% and a gain flatness of less than 1 dB is observed over the frequency band 2400–2480 MHz.
Deterministic Parallel Sorting Algorithm for 2-D Mesh of Connected Computers

Sorting is one of the most important operations in database systems and its efficiency can influences drastically the overall system performance. To accelerate the performance of database systems, parallelism is applied to the execution of the data administration operations. We propose a new deterministic Parallel Sorting Algorithm (DPSA) that improves the performance of Quick sort in sorting an array of size n. where we use p Processor Elements (PE) that work in parallel to sort a matrix r*c where r is the number of rows r = 3 and c is the number of columns c = n/3. The simulation results show that the performance of the proposed algorithm DPSA out performs Quick sort when it works sequentially.
Sp1 and Egr1 Regulate Transcription of the Dmrt1 Gene in Sertoli Cells1

Abstract Dmrt1 is a recently described gene that is specifically expressed in the gonads and is required for postnatal testis differentiation. Here, we describe the transcriptional mechanisms regulating the Dmrt1 proximal promoter in testicular Sertoli cells. A genomic clone containing exon 1 of the rat Dmrt1 gene and more than 9 kilobases of 5′ flanking sequence was isolated and characterized. Several prominent transcriptional start sites were identified, with the major site located 102 bases from the translational start. The Dmrt1 5′ flanking region from −5000 to +74 was transcriptionally active in primary Sertoli cells, and deletion analysis of this fragment identified 2 major regions needed for full Dmrt1 promoter function. These regions were located between −3200 and −2000 base pairs (bp) and downstream of −150 bp relative to the major transcriptional start site. DNase I footprint analysis of the region downstream of −150 bp revealed 3 regions that are bound by proteins from Sertoli cell nuclear extracts. Site-directed mutagenesis of these regions identified 2 elements that activate the Dmrt1 promoter and 2 that repress it. The positive elements bind the transcription factors Sp1, Sp3, and Egr1, suggesting that these transcription factors play a critical role in Dmrt1 regulation in the testis.
Eurographics/ Ieee-vgtc Symposium on Visualization 2010 Pathline: a Tool for Comparative Functional Genomics

Biologists pioneering the new field of comparative functional genomics attempt to infer the mechanisms of gene regulation by looking for similarities and differences of gene activity over time across multiple species. They use three kinds of data: functional data such as gene activity measurements, pathway data that represent a series of reactions within a cellular process, and phylogenetic relationship data that describe the relatedness of species. No existing visualization tool can visually encode the biologically interesting relationships between multiple pathways , multiple genes, and multiple species. We tackle the challenge of visualizing all aspects of this comparative functional genomics dataset with a new interactive tool called Pathline. In addition to the overall characterization of the problem and design of Pathline, our contributions include two new visual encoding techniques. One is a new method for linearizing metabolic pathways that provides appropriate topological information and supports the comparison of quantitative data along the pathway. The second is the curvemap view, a depiction of time series data for comparison of gene activity and metabolite levels across multiple species. Pathline was developed in close collaboration with a team of genomic scientists. We validate our approach with case studies of the biologists' use of Pathline and report on how they use the tool to confirm existing findings and to discover new scientific insights.
Good Jobs versus Bad Jobs

This article develops a model of noncompetitive labor markets in which high‐wage (good) and low‐wage (bad) jobs coexist. Minimum wages and unemployment benefits shift the composition of employment toward high‐wage jobs. Because the composition of jobs in the laissez‐faire equilibrium is inefficiently biased toward low‐wage jobs, these labor market regulations increase average labor productivity and may improve welfare.
Methyl mercury ototoxicity: A model for the surface preparation technique

A critical review of recent articles in which the surface preparation technique was employed is presented. Many of the reports were deficient in terms of five important criteria which would insure reproducibility of experiments, comparability of results from different investigators, and detection of a low level of cellular pathology. These criteria are: inclusion of concurrent controls; use of adequate number of control and treated animals to insure the detection of meaningful treatment‐control differences; adequate examination of controls; quantitative expression of cellular pathology, and the use of statistical analyses to test for significant differences.
Data fusion for the management of multimedia documents

Multimedia documents are increasingly numerous. Their efficient management requires tools to provide services that measure up to users' expectations, based on the contents of these voluminous document databases. This implies a number of challenges. Although we can extract highly symbolic concepts from texts, a wide semantic gap appears when processing images and sound. Thus, we propose using data fusion to capture the semantic field of the elements extracted from these media. On the other hand, if creating ontology makes it possible to manage the concept of "trade" in texts, additional data can be exploited from document contents. In the first instance, we suggest bringing together concepts and words through data fusion.
EFFICIENT MULTIPLIER- LESS VLSI ARCHITECTURES FOR FOLDED PIPELINED COMPLEX FFT CORE 2013

Fast Fourier transform (FFT) has become ubiquitous in many engineering applications. FFT is one of the most employed blocks in many communication and signal processing systems. Efficient algorithms are being designed to improve the architecture of FFT. Higher radix FFT algorithms have the traditional advantage of using less number of computational elements and are more suitable for calculating FFT of long data sequence. Among the different proposed algorithms, the split-radix FFT has shown considerable improvement in terms of reducing hardware complexity of the architecture compared to radix-2 and radix-4 FFT algorithms. Here radix-4, radix-8, and split-radix algorithms have been used in the design of different proposed complex FFT cores. The growing popularity of adopting virtual instrumentation (modular, customizable, software-defined instrumentation) has only became possible due to the use of LabVIEW with a highly interactive process known as graphical system design. The CompactRIO programmable automation controller is an advanced embedded control and data acquisition system designed for applications that require high performance and reliability. The work explains the real-time implementation of 256-point FFT and finding the power spectrum using LabVIEW and CompactRIO. New distributed arithmetic (NEDA) is one of the most used techniques in implementing multiplier-less architectures of many digital systems. In this thesis, four architectures for different FFT cores have been proposed: • Real-time implementation of FFT using CompactRIO • 32-Point Complex FFT Core Using Split-Radix Algorithm • 64-Point Complex FFT Core Using Radix-4 Algorithm • 64-Point Complex FFT Core Using Radix-8 Algorithm The proposed designs have implemented in both FPGA as well as ASIC design flows. 180nm process technology is being used for ASIC implementation. The results show the improvements of proposed designs compared to the other existing architectures.
Low Complexity Max-log LLR Computation for Nonuniform PAM Constellations

In this letter, we derive a low-complexity method for demodulating nonuniform PAM signals. With uniform Gray-coded M-PAM constellations, the reflective symmetry can be exploited to demodulate the signals with low complexity. However with nonuniform constellations, this symmetry is lost and more complicated computations are required. We derive an analytic expression for the max-log LLR functions and show that they are piecewise linear functions. Based on this, we devise a demodulation algorithm that has complexity O (log2 M) as opposed to O (M) for the exhaustive search. We also present an approximation with reduced complexity and only modest performance degradation.
"What are they Thinking?" - Accessing Collective Intelligence in Twitter

In today’s social networks like Twitter and Facebook, each day millions of status updates provide a huge source of information on current sentiments of their users. However, still it is unclear how to structure problems in a way that they can be answered based on social networking activities. Facilitating an exploratory prototype, we tested the direct retrieval of user opinions during the FIFA World Cup 2010 in Twitter. Our findings based on an initial research framework suggest that using social networks can serve as an access point to collective intelligence. However, the experiment also showed weaknesses of the used approach. Therefore we discuss an updated research model based on our results which provides a foundation for future works.