Miracle-dz/UniFAR-FTUs huggingface dataset:
The isolated colonic mucosa: a new substrate for tissue reconstruction. Isolation, decellularization and characterization by immunohistochemistry and electron microscopy

This study proposes the use of isolated colonic mucosa as a "scaffold" for cell cultures and potentially for tissue reconstruction. The main goal of this study was to obtain complete decellularization of the specimens while preserving the superficial basement membrane (BM) as a place for cell at-tachment and growth. This decellularization technique uses a chelating agent in combination with mechanical vibration, followed by detergents and DNase. The grade of decellularization achieved is assessed by counting the number of cell nuclei stained with propidium iodide (PI). BM marker proteins such as collagen IV, laminin and perlecan were detected by immunohistochemistry (ICC). Transmission (TEM) and scanning electron microscopy (SEM) were used to examine the BM ultrastructure and surface topography.The results show that the protocol used is suitable for rat colonic mucosa. During the process,material of the lamina lucida (LL) was partly removed from the BM, whereas the lamina densa (LD) seems to have remained unchanged. The BM had become thinner than the control specimens. The nanotopography of the BM surface is charac-terized by globules of 34-60 nm in diameter. Human fetal fibroblasts were successfully cultured on this substrate confirming that cells can adhere to and grow on this substrate, at least for the particular cell line used. It can be said that the colonic mucosa is an interesting substrate for in vitro stud-ies with cells and presumably also for tissue reconstruction.
Statistical Properties of Task Running Times in a Global-Scale Grid Environment

Grid computing technology connects globally distributed processors to develop an immense source of computing power, which enables us to run applications in parallel that would take orders of magnitude more time on a single processor. Key characteristics of a global-scale grid are the strong burstiness in the amount of load on the resources and on the network capacities, and the fact that processors may be appended to or removed from the grid at any time. To cope with these characteristics, it is essential to develop techniques that make applications robust against the dynamics of the grid environment. For these techniques to be effective, it is important to have an understanding of the statistical properties of the dynamics of a grid environment. Today, however, the statistical properties of the dynamic behavior of real global-scale grid environments are not well understood. Our main focus is on highly CPU-intensive grid applications that require huge amounts of processor power for running tasks. Motivated by this, we have performed extensive measurements in a real, global-scale grid environment to study the statistical properties of the running times of tasks on processors. We observe (1) a strong burstiness of the running times over different time scales, (2) a strong heterogeneity of the running-time characteristics among the different hosts, (3) a strong heterogeneity of the running-time characteristics for the same host over different time intervals, and (4) the occurrence of sudden level-switches in the running times, amongst others. These observations are used to develop effective techniques for the prediction of running times. They can be used to develop effective control schemes for robust grid applications.
Dissecting allosteric effects of activator–coactivator complexes using a covalent small molecule ligand

Significance The master coactivator CREB binding protein (CBP)/p300 utilizes several conformationally dynamic protein–protein interaction motifs to regulate the transcriptional status of essential genes. The kinase-inducible domain interacting (KIX) domain within CBP/p300 forms complexes with multiple transcriptional activators, using two allosterically connected binding surfaces. Here transient kinetic experiments of KIX–ligand complexes were used to dissect the underlying mechanism of the allosteric alterations in ternary complex formation. For positive cooperativity, the stabilization of protein–ligand complex as indicated by a decrease in koff is the primary determinant. In contrast, negative cooperativity was derived by a decrease in kon and an increase in koff. As KIX–activator complexes are important models for intrinsically disordered protein complexes, these data provide a broader mechanistic framework for positive and negative cooperativity. Allosteric binding events play a critical role in the formation and stability of transcriptional activator–coactivator complexes, perhaps in part due to the often intrinsically disordered nature of one or more of the constituent partners. The kinase-inducible domain interacting (KIX) domain of the master coactivator CREB binding protein/p300 is a conformationally dynamic domain that complexes with transcriptional activators at two discrete binding sites in allosteric communication. The complexation of KIX with the transcriptional activation domain of mixed-lineage leukemia protein leads to an enhancement of binding by the activation domain of CREB (phosphorylated kinase-inducible domain of CREB) to the second site. A transient kinetic analysis of the ternary complex formation aided by small molecule ligands that induce positive or negative cooperative binding reveals that positive cooperativity is largely governed by stabilization of the bound complex as indicated by a decrease in koff. Thus, this suggests the increased binding affinity for the second ligand is not due to an allosteric creation of a more favorable binding interface by the first ligand. This is consistent with data from us and from others indicating that the on rates of conformationally dynamic proteins approach the limits of diffusion. In contrast, negative cooperativity is manifested by alterations in both kon and koff, suggesting stabilization of the binary complex.
Laboratory on legs: an architecture for adjustable morphology with legged robots

For mobile robots, the essential units of actuation, computation, and sensing must be designed to fit within the body of the robot. Additional capabilities will largely depend upon a given activity, and should be easily reconfigurable to maximize the diversity of applications and experiments. To address this issue, we introduce a modular architecture originally developed and tested in the design and implementation of the X-RHex hexapod that allows the robot to operate as a mobile laboratory on legs. In the present paper we will introduce the specification, design and very earliest operational data of Canid, an actively driven compliant-spined quadruped whose completely different morphology and intended dynamical operating point are nevertheless built around exactly the same "Lab on Legs" actuation, computation, and sensing infrastructure. We will review as well, more briefly a second RHex variation, the XRL platform, built using the same components.
Cervical artery dissection expands the cardiovascular phenotype in FBN1‐related Weill–Marchesani syndrome

Weill–Marchesani syndrome (WMS) is a rare form of acromelic dysplasia that is characterized by distinctive skeletal, ocular, and cardiovascular abnormalities. Previously described cardiac manifestations of WMS include aortic and pulmonary valve stenosis, mitral valve prolapse, mitral stenosis, and QTc prolongation. Autosomal dominant forms of WMS result from heterozygous pathogenic variants in FBN1, a gene with a well characterized role in the pathogenesis of thoracic aortic aneurysm (TAA) in the context of Marfan syndrome. In contrast, only one patient has been reported with aortic disease in WMS. Although the risk of aortic dissection from preceding TAA remains the leading cause of morbidity for individuals with Marfan syndrome, rare reports of arterial dissection in the peripheral vasculature have been described. Peripheral artery dissection has not been previously reported in other FBN1‐related diseases. We describe a three generation family with FBN1‐related WMS whose cardiovascular manifestations include TAA and cervical artery dissection, thus expanding the cardiovascular phenotype of WMS. Further research is required to quantify these risks and establish appropriate recommendations for cardiovascular imaging, medical management, and prophylactic surgical intervention in individuals with FBN1‐related acromelic dysplasia.
A high dynamic range imaging method for the characterization of periodic errors in diffraction gratings

We report on recent progress in the development of our focal plane imaging system for the detection and characterization of small fabrication errors in diffraction gratings. The instrument uses a purpose-designed high dynamic range imaging method in conjunction with a low-cost digital camera to acquire images with a dynamic range that can now exceed eight orders of magnitude. The sensitivity and utility of the instrument is demonstrated with measurements of three different diffraction gratings. Avenues for further possible improvements of the instrument are discussed.
Garlic Cast: Lightweight and Decentralized Anonymous Content Sharing

Anonymous content sharing over the Internet protects user privacy and content confidentiality. Most overlay anonymous communication protocols employ some relay nodes as the proxies to forward content and require relays to perform cryptography or coding operations on messages. They have two major limitations. First, extra computation overhead may discourage overlay nodes from serving as relays. Second, long forwarding latency at relays makes an anonymous path easier to fail under network churn. In this paper, we present a lightweight and decentralized anonymous content sharing system named Garlic Cast, which requires near-zero computation cost on relays and does not rely on any centralized service. Garlic Cast uses random walks to find proxies in overlay networks and an security-enhanced Information Dispersal Algorithm to search and deliver content files. We have implemented a prototype of Garlic Cast and performed extensive simulation on real overlay topologies. Evaluation results show that the throughput of Garlic Cast is higher than that of RSA-based anonymous routing by over two orders of magnitude. Garlic Cast provides high level of anonymity and is robust to various attacks.
FeasPar - A Feature Structure Parser Learning to Parse Spoken Language

We describe and experimentally evalu-ate a system, FeasPar, that learns parsing spontaneous speech. To train and run FeasPar (Feature Structure Parser), only limited handmodeled knowledge is required. The FeasPar architecture consists of neural networks and a search. The networks spilt the incoming sentence into chunks, which are labeled with feature values and chunk relations. Then, the search (cid:12)nds the most probable and consistent feature structure. FeasPar is trained, tested and evaluated with the Spontaneous Scheduling Task, and compared with a handmodeled LR-parser. The handmodeling e(cid:11)ort for FeasPar is 2 weeks. The handmodeling ef-fort for the LR-parser was 4 months. FeasPar performed better than the LR-parser in all six comparisons that are made.
Change of direction ability test differentiates higher level and lower level soccer referees

This report examines the agility and level of acceleration capacity of Spanish soccer referees and investigates the possible differences between field referees of different categories. The speed test consisted of 3 maximum acceleration stretches of 15 metres. The change of direction ability (CODA) test used in this study was a modification of the Modified Agility Test (MAT). The study included a sample of 41 Spanish soccer field referees from the Navarre Committee of Soccer Referees divided into two groups: i) the higher level group (G1, n = 20): 2ndA, 2ndB and 3rd division referees from the Spanish National Soccer League (28.43 ± 1.39 years); and ii) the lower level group (G2, n = 21): Navarre Provincial League soccer referees (29.54 ± 1.87 years). Significant differences were found with respect to the CODA between G1 (5.72 ± 0.13 s) and G2 (6.06 ± 0.30 s), while no differences were encountered between groups in acceleration ability. No significant correlations were obtained in G1 between agility and the capacity to accelerate. Significant correlations were found between sprint and agility times in the G2 and in the total group. The results of this study showed that agility can be used as a discriminating factor for differentiating between national and regional field referees; however, no observable differences were found over the 5 and 15 m sprint tests.
An assessment of patient-based and practice infrastructure-based measures of the patient-centered medical home: do we need to ask the patient?

OBJECTIVE To examine the importance of patient-based measures and practice infrastructure measures of the patient-centered medical home (PCMH). DATA SOURCES A total of 3,671 patient surveys of 202 physicians completing the American Board of Internal Medicine (ABIM) 2006 Comprehensive Care Practice Improvement Module and 14,457 patient chart reviews from 592 physicians completing ABIM's 2007 Diabetes and Hypertension Practice Improvement Module. METHODOLOGY We estimated the association of patient-centered care and practice infrastructure measures with patient rating of physician quality. We then estimated the association of practice infrastructure and patient rating of care quality with blood pressure (BP) control. RESULTS Patient-centered care measures dominated practice infrastructure as predictors of patient rating of physician quality. Having all patient-centered care measures in place versus none was associated with an absolute 75.2 percent increase in the likelihood of receiving a top rating. Both patient rating of care quality and practice infrastructure predicted BP control. Receiving a rating of excellent on care quality from all patients was associated with an absolute 4.2 percent improvement in BP control. For reaching the maximum practice-infrastructure score, this figure was 4.5 percent. CONCLUSION Assessment of physician practices for PCMH qualification should consider both patient based patient-centered care measures and practice infrastructure measures.
Multi-Analyst , Multi-Matrix Performance of the QuEChERS Approach for Pesticide Residues in Foods and Feeds Using HPLC / MS / MS Analysis with Different Calibration Techniques

Three different calibration approaches were applied in HPLC/MS/MS using electrospray ionization for the determination of 14 diverse pesticide residues at different levels in a variety of food matrixes. This study was conducted as part of a 4 day training course for 17 chemists to learn the “quick, easy, cheap, effective, rugged, and safe” (QuEChERS) approach to pesticide residue analysis in foods. The analysts were divided into four different teams for the analysis of 12 different matrixes (strawberries, plums, carrots, green peppers, milk, molasses, alfalfa oats, corn silage, dry pet food, soybean, almonds, and foliage). The acetate-buffered QuEChERS protocol gave excellent results in the spiked samples for all matrixes tested. The HPLC/MS/MS calibration techniques consisted of external standardization in solvent solutions, matrix-matching, and the echo-peak technique. Peak areas were normalized to an internal standard in all three approaches. Matrix effects were observed with the corn silage, carrot, and foliage extracts, but they were minimal or nonexistent in the other matrixes. Matrix-matching best compensated for matrix effects, but has logistical difficulties in real-world application and required extra sample preparation compared to the other approaches. The echo-peak technique reduced matrix effects but did not eliminate them.
Particle swarm optimization based on island models

Particle Swarm Optimization (PSO) algorithm is a metaheuristic. This method has been used for solving optimization problems. As many other metaheuristics, several modifications in this method have been carried out in order to improve the performance of the search. Island models is a structured population mechanism used in evolutionary algorithms to preserve the population diversity and thus to improve their performances. In this paper, the island model concepts are embedded into the PSO algorithm to improve its diversity as well as its convergence, where the new method is referred to as island-PSO. In this approach, the particles are distrusted into separate sub-swarm named (islands). After specific generations, a number of particles run an exchange through a migration process. This process is performed to keep the diversity into the PSO algorithm and to allow the islands to interact with each other. The experimental results using a set of benchmark functions show that the island model context is crucial to the PSO performance and the comparative study shows the efficiency of using island models.
OATS: The Open Annotation and Tagging System

This paper presents the Open Annotation and Tagging System (OATS) which draws on previous work in social navigation support, web annotations systems, collaborative tagging and educational metadata. The OATS system augments the text highlighting metaphor by providing a “collaborative tagging” and annotation interface which enables social navigation support. These tools aim to help learners in learning managements systems to better organize and navigate content. While there are many examples of web annotation systems, none provide a combination of annotations, tagging, and value-added functionality, which are decoupled from the system in which they are used, through a web service interface. This proof-of-concept system identifies a relatively simple method for developing value-added functionality that can be more easily incorporated in a wide range of systems used in e-learning.
Design of Novel and Selective Inhibitors of Urokinase-type Plasminogen Activator with Improved Pharmacokinetic Properties for Use as Antimetastatic Agents*[boxs]

The serine protease urokinase-type plasminogen activator (uPA) interacts with a specific receptor (uPAR) on the surface of various cell types, including tumor cells, and plays a crucial role in pericellular proteolysis. High levels of uPA and uPAR often correlate with poor prognosis of cancer patients. Therefore, the specific inhibition of uPA with small molecule active-site inhibitors is one strategy to decrease the invasive and metastatic activity of tumor cells. We have developed a series of highly potent and selective uPA inhibitors with a C-terminal 4-amidinobenzylamide residue. Optimization was directed toward reducing the fast elimination from circulation that was observed with initial analogues. The x-ray structures of three inhibitor/uPA complexes have been solved and were used to improve the inhibition efficacy. One of the most potent and selective derivatives, benzylsulfonyl-d-Ser-Ser-4-amidinobenzylamide (inhibitor 26), inhibits uPA with a Ki of 20 nm. This inhibitor was used in a fibrosarcoma model in nude mice using lacZ-tagged human HT1080 cells, to prevent experimental lung metastasis formation. Compared with control (100%), an inhibitor dose of 2 × 1.5 mg/kg/day reduced the number of experimental metastases to 4.6 ± 1%. Under these conditions inhibitor 26 also significantly prolonged survival. All mice from the control group died within 43 days after tumor cell inoculation, whereas 50% of mice from the inhibitor-treated group survived more than 117 days. This study demonstrates that the specific inhibition of uPA by these inhibitors may be a useful strategy for the treatment of cancer to prevent metastasis.
Performance Evaluation of FMOSSIM, a Concurrent Switch-Level Fault Simulator

This paper presents measurements obtained while performing fault simulations of MOS circuits modeled at the switch level. In this model the transistor structure of the circuit is represented explicitly as a network of charge storage nodes connected by bidirectional transistor switches. Since the logic model of the simulator closely matches the actual structure of MOS circuits, such faults as stuck-open and closed transistors as well as short and open-circuited wires can be simulated. By using concurrent simulation techniques, we obtain a performance level comparable to fault simulators using logic gate models. Our measurements indicate that fault simulation times grow as the product of the circuit size and number of patterns, assuming the number of faults to be simulated is proportional to the circuit size. However, fault simulation times depend strongly on the rate at which the test patterns detect the faults.
Inverse Bit Plane Decoding Order for Turbo Code Based Distributed Video Coding

For turbo code based Wyner-Ziv codecs, we propose to use an inverse bit plane decoding order. The investigations have shown that the knowledge about MSB's has only a marginal influence on LSB's, which can be regarded as noise, while the influence of LSB's on MSB's tends to be higher. As a results, we obtain a coding gain of up to 0.3 dB, especially for the sequences, which can only be decoded with a coding efficiency lower than H.264/AVC intra. Furthermore, the distribution of the requests for additional parity bits over the back channel is different compared to the conventional decoding order, resulting in a high number of requests for the last bit plane and a low number of requests for the other bit planes. Therefore, the decoder can request several puncturing levels for LSB's in one step, reducing the number of turbo decoding loops. Hence, transmitting the LSB's first, we can obtain a decoding speedup of 30%, thus making DVC more attractive for real-time applications.
Daily and circadian rhythms of synaptic frequency in the first visual neuropile of the housefly’s (Musca domestica L.) optic lobe

Photoreceptors of the fly’s compound eye generally show no very obvious daily or circadian rhythms, a lack which prompted us to examine whether their function might be regulated not in the retina, but at the site of transmission in the first visual neuropile, or lamina. Here, photoreceptor terminals (R1–R6) are reciprocally interconnected with one class of lamina monopolar cell, L2: L2 receives input from R1–R6 at so-called tetrad synapses, and in turn is presynaptic to R1–R6 at feedback synapses. We have calculated the mean frequencies of these synaptic profiles in electron micrographs of single lamina sections. L2 feedback synapses were more numerous at night than during the day, whereas the number of tetrads showed only small modulations between day and night. These changes persisted amongst feedback synapses in flies held in constant darkness, and are thus circadian. In contrast to the slow modulations during a 24 h cycle, the number of L2 feedback synapses after 1 h light pulse in flies held in constant darkness showed no clear change, whereas it increased the number of tetrad profiles. These findings support the occurrence of cyclical daily and circadian changes amongst the two lamina synaptic populations, with tetrads showing rather weak modulations in frequency, but more pronounced responses to the light pulse than feedback synapses.