gebhart/patrepeval huggingface dataset:
Domain identification by clustering sequence alignments. (1998)

A sequence databases are growing rapidly, results from sequence comparison searches using fast search methods such as BLAST and FASTA tend to be long and difficult to digest. In this paper, we present a new method to extract domain information from sequence comparison searches by clustering the resulting alignments according to their similarity to the query sequence. Efficient tree structures and algorithms are used to organize the alignment data such that structurally conserved elements can be easily identified. The hierarchical nature of the data structures used and the flexible X-Window based interface provide an efficient and intuitive means to explore the alignment data at different levels so the main domains as well as distantly related features can be explored.
Parameter Optimization of Kernel-based One-class Classifier on Imbalance Learning (2006)

Compared with conventional two-class learning schemes, one-class classification simply uses a single class in the classifier training phase. Applying one-class classification to learn from unbalanced data set is regarded as the recognition based learning and has shown to have the potential of achieving better performance. Similar to two-class learning, parameter selection is a significant issue, especially when the classifier is sensitive to the parameters. For one-class learning scheme with the kernel function, such as one-class Support Vector Machine and Support Vector Data Description, besides the parameters involved in the kernel, there is another one-class specific parameter: the rejection rate v. In this paper, we proposed a general framework to involve the majority class in solving the parameter selection problem. In this framework, we first use the minority target class for training in the one-class classification stage; then we use both minority and majority class for estimating the generalization performance of the constructed classifier. This generalization performance is set as the optimization criteria. We employed the Grid search and Experiment Design search to attain various parameter settings. Experiments on UCI and Reuters text data show that the parameter optimized one-class classifiers outperform all the standard one-class learning schemes we examined.
Algorand: Scaling Byzantine Agreements for Cryptocurrencies. (2017)

Algorand is a new cryptocurrency that confirms transactions with latency on the order of a minute while scaling to many users. Algorand ensures that users never have divergent views of confirmed transactions, even if some of the users are malicious and the network is temporarily partitioned. In contrast, existing cryptocurrencies allow for temporary forks and therefore require a long time, on the order of an hour, to confirm transactions with high confidence. Algorand uses a new Byzantine Agreement (BA) protocol to reach consensus among users on the next set of transactions. To scale the consensus to many users, Algorand uses a novel mechanism based on Verifiable Random Functions that allows users to privately check whether they are selected to participate in the BA to agree on the next set of transactions, and to include a proof of their selection in their network messages. In Algorand's BA protocol, users do not keep any private state except for their private keys, which allows Algorand to replace participants immediately after they send a message. This mitigates targeted attacks on chosen participants after their identity is revealed. We implement Algorand and evaluate its performance on 1,000 EC2 virtual machines, simulating up to 500,000 users. Experimental results show that Algorand confirms transactions in under a minute, achieves 125x Bitcoin's throughput, and incurs almost no penalty for scaling to more users.
Arachnoid Trabeculae and CSF Roles in Blunt Head Impacts (2003)

The blunt head impacts due to vehicular collisions, contact sports or falls cause relative motion between the brain and skull and an increase in contact and shear stresses in meningeal region. Several models have been developed to better understand brain injuries. In this study the mechanical role of the fibrous trabeculae and the Cerebrospinal Fluid (CSF) in Subarachnoid space (SAS) is investigated. Two-dimensional solid and fluid global models of the head and a local model of the SAS trabeculae were developed. The CSF pressure distribution and the trabeculae deformations were determined. It is concluded that the arachnoid trabeculae reduce the pressure in the CSF and both play a major role in damping the blunt head impact.
Oral Fluid Biomarkers for Diagnosing Gingivitis in Human: A Cross-Sectional Study (2020)

Diagnoses based on oral fluid biomarkers have been introduced to overcome limitations of periodontal probe-based diagnoses. Diagnostic ability of certain biomarkers for periodontitis have been identified and widely studied, however, such studies targeting gingivitis is scarce. The aims of this study were to determine and compare the efficacies and accuracies of eight biomarkers in diagnosing gingivitis with the aid of receiver operating characteristic (ROC) curves. The probing depth (PD), clinical attachment loss (CAL), bleeding on probing (BOP), gingival index (GI), and plaque index (PI) were examined in 100 participants. Gingival crevicular fluid was collected using paper points, and whole-saliva samples were collected using cotton roll. Samples were analyzed using enzyme-linked immunosorbent assay kits for the different biomarkers. The levels of matrix metalloproteinase (MMP)-8, MMP-9, lactoferrin, cystatin C, myeloperoxidase (MPO), platelet-activating factor, cathepsin B, and pyridinoline cross-linked carboxyterminal telopeptide of type I collagen were analyzed. MPO and MMP-8 levels in saliva were strongly correlated with gingivitis, with Pearson's correlation coefficients of 0.399 and 0.217, respectively. The area under the curve (AUC) was largest for MMP-8, at 0.814, followed by values of 0.793 and 0.777 for MPO and MMP-9, respectively. The clinical parameters of GI and PI showed strong correlations and large AUC values, whereas PD and CAL did not. MMP-8 and MPO were found to be effective for diagnosing gingivitis. Further investigations based on the results of this study may identify clinically useful biomarkers for the accurate and early detection of gingivitis.
Characterization of a 3-phase a.c. free burning arc plasma. (2006)

International audience
Deep Learning for MR Angiography: Automated Detection of Cerebral Aneurysms (2018)

Purpose To develop and evaluate a supportive algorithm using deep learning for detecting cerebral aneurysms at time-of-flight MR angiography to provide a second assessment of images already interpreted by radiologists. Materials and Methods MR images reported by radiologists to contain aneurysms were extracted from four institutions for the period from November 2006 through October 2017. The images were divided into three data sets: training data set, internal test data set, and external test data set. The algorithm was constructed by deep learning with the training data set, and its sensitivity to detect aneurysms in the test data sets was evaluated. To find aneurysms that had been overlooked in the initial reports, two radiologists independently performed a blinded interpretation of aneurysm candidates detected by the algorithm. When there was disagreement, the final diagnosis was made in consensus. The number of newly detected aneurysms was also evaluated. Results The training data set, which provided training and validation data, included 748 aneurysms (mean size, 3.1 mm ± 2.0 [standard deviation]) from 683 examinations; 318 of these examinations were on male patients (mean age, 63 years ± 13) and 365 were on female patients (mean age, 64 years ± 13). Test data were provided by the internal test data set (649 aneurysms [mean size, 4.1 mm ± 3.2] in 521 examinations, including 177 male patients and 344 female patients with mean age of 66 years ± 12 and 67 years ± 13, respectively) and the external test data set (80 aneurysms [mean size, 4.1 mm ± 2.1] in 67 examinations, including 19 male patients and 48 female patients with mean age of 63 years ± 12 and 68 years ± 12, respectively). The sensitivity was 91% (592 of 649) and 93% (74 of 80) for the internal and external test data sets, respectively. The algorithm improved aneurysm detection in the internal and external test data sets by 4.8% (31 of 649) and 13% (10 of 80), respectively, compared with the initial reports. Conclusion A deep learning algorithm detected cerebral aneurysms in radiologic reports with high sensitivity and improved aneurysm detection compared with the initial reports. © RSNA, 2018 See also the editorial by Flanders in this issue.
Study of LRRK2 variation in tauopathy: Progressive supranuclear palsy and corticobasal degeneration (2016)

Our study confirms the presence of pathogenic and potentially pathogenic LRRK2 mutations in pathologically confirmed primary tauopathies, albeit with low frequency. In contrast to PD, common LRRK2 variants do not appear to play a major role in determining PSP and corticobasal degeneration risk. © 2016 International Parkinson and Movement Disorder Society.
A Tutorial on IEEE 802.11ax High Efficiency WLANs (2018)

While celebrating the 21st year since the very first IEEE 802.11 “legacy” 2 Mbit/s wireless local area network standard, the latest Wi-Fi newborn is today reaching the finish line, topping the remarkable speed of 10 Gbit/s. IEEE 802.11ax was launched in May 2014 with the goal of enhancing throughput-per-area in high-density scenarios. The first 802.11ax draft versions, namely, D1.0 and D2.0, were released at the end of 2016 and 2017. Focusing on a more mature version D3.0, in this tutorial paper, we help the reader to smoothly enter into the several major 802.11ax breakthroughs, including a brand new orthogonal frequency-division multiple access-based random access approach as well as novel spatial frequency reuse techniques. In addition, this tutorial will highlight selected significant improvements (including physical layer enhancements, multi-user multiple input multiple output extensions, power saving advances, and so on) which make this standard a very significant step forward with respect to its predecessor 802.11ac.
Inhibition of Soluble Epoxide Hydrolase Limits Niacin-induced Vasodilation in Mice (2012)

Inhibition of sEH markedly reduces niacin-induced flushing in this model without an apparent effect on the response to PGD2. sEH inhibition may be a new therapeutic approach to limit flushing in humans.
St. Cloud State University ACM chapter wins 2nd annual Webbie prize (1997)

No abstract available.
Endothelial Cell Guidance in 3D Patterned Scaffolds (2010)

Primary endothelial cells are guided in an agarose hydrogel scaffold that is chemically patterned with an immobilized concentration gradient of VEGF165 using multiphoton laser patterning. It is particularly compelling that, in this 3D patterned hydrogel, endothelial cells differentiate to tip and stalk cells, having the morphology that is observed in vivo. Detailed facts of importance to specialist readers are published as ”Supporting Information”. Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Position Paper: Mobile Phones may be the Right Devices for Supporting Developing World Accessibility, but is the WWW the Right Service Delivery Model? (2006)

In this paper we detail the synergies we have observed between the features and limitations of mobile phones, and the usability and accessibility requirements of rural developing world users. This includes support for sequential interaction, multimedia input and output, asynchronous messaging and a universally familiar numeric keypad. However, we argue that the WWW as currently conceived may be an inappropriate model for delivering mobile information services in this context. We highlight a number of tensions we have observed between the traditional web model, and the design synergies that we have uncovered. To demonstrate an alternative framework, we describe CAM — a platform for delivering mobile information services in the rural developing world. Supporting scripted execution, media-driven, tangible interaction as well as an offline usage model, CAM is uniquely adapted both to rural accessibility requirements and the inherent capabilities of mobile phones. By learning from the CAM design, we can either improve the design of existing mobile web standards and services, or implement a more appropriate framework altogether.
Coordinated Regulation of Hepatic Energy Stores by Leptin and Hypothalamic Agouti-Related Protein (2013)

Like obesity, prolonged food deprivation induces severe hepatic steatosis; however, the functional significance of this phenomenon is not well understood. In this study, we show that the fall in plasma leptin concentration during fasting is required for the development of hepatic steatosis in mice. Removal of leptin receptors from AGRP neurons diminishes fasting-induced hepatic steatosis. Furthermore, the suppressive effects of leptin on fasting-induced hepatic steatosis are absent in mice lacking the gene encoding agouti-related protein (Agrp), suggesting that this function of leptin is mediated by AGRP. Prolonged fasting leads to suppression of hepatic sympathetic activity, increased expression of acyl CoA:diacylglycerol acyltransferase-2 in the liver, and elevation of hepatic triglyceride content and all of these effects are blunted in the absence of AGRP. AGRP deficiency, despite having no effects on feeding or body adiposity in the free-fed state, impairs triglyceride and ketone body release from the liver during prolonged fasting. Furthermore, reducing CNS Agrp expression in wild-type mice by RNAi protected against the development of hepatic steatosis not only during starvation, but also in response to consumption of a high-fat diet. These findings identify the leptin-AGRP circuit as a critical modulator of hepatic triglyceride stores in starvation and suggest a vital role for this circuit in sustaining the supply of energy from the liver to extrahepatic tissues during periods of prolonged food deprivation.
Characterization of the most frequent ATP7B mutation causing Wilson disease in hepatocytes from patient induced pluripotent stem cells (2018)

H1069Q substitution represents the most frequent mutation of the copper transporter ATP7B causing Wilson disease in Caucasian population. ATP7B localizes to the Golgi complex in hepatocytes but moves in response to copper overload to the endo-lysosomal compartment to support copper excretion via bile canaliculi. In heterologous or hepatoma-derived cell lines, overexpressed ATP7B-H1069Q is strongly retained in the ER and fails to move to the post-Golgi sites, resulting in toxic copper accumulation. However, this pathogenic mechanism has never been tested in patients' hepatocytes, while animal models recapitulating this form of WD are still lacking. To reach this goal, we have reprogrammed skin fibroblasts of homozygous ATP7B-H1069Q patients into induced pluripotent stem cells and differentiated them into hepatocyte-like cells. Surprisingly, in HLCs we found one third of ATP7B-H1069Q localized in the Golgi complex and able to move to the endo-lysosomal compartment upon copper stimulation. However, despite normal mRNA levels, the expression of the mutant protein was only 20% compared to the control because of endoplasmic reticulum-associated degradation. These results pinpoint rapid degradation as the major cause for loss of ATP7B function in H1069Q patients, and thus as the primary target for designing therapeutic strategies to rescue ATP7B-H1069Q function.
Proactive Drone-Cell Deployment: Overload Relief for a Cellular Network Under Flash Crowd Traffic (2017)

This paper is concerned with providing radio access network (RAN) elements (supply) for flash crowd traffic demands. The concept of multi-tier cells [heterogeneous networks (HetNets)] has been introduced in 5G network proposals to alleviate the erratic supply–demand mismatch. However, since the locations of the RAN elements are determined mainly based on the long-term traffic behavior in 5G networks, even the HetNet architecture will have difficulty in coping up with the cell overload induced by flash crowd traffic. In this paper, we propose a proactive drone-cell deployment framework to alleviate overload conditions caused by flash crowd traffic in 5G networks. First, a hybrid distribution and three kinds of flash crowd traffic are developed in this framework. Second, we propose a prediction scheme and an operation control scheme to solve the deployment problem of drone cells according to the information collected from the sensor network. Third, the software-defined networking technology is employed to seamlessly integrate and disintegrate drone cells by reconfiguring the network. Our experimental results have shown that the proposed framework can effectively address the overload caused by flash crowd traffic.
Billion-level durable ArF excimer laser with highly stable energy (1999)

We have succeeded in the development of the ArF excimer laser with high performance and durability, by researching and developing of the spectral measurement and gas control technologies, laser chamber with radio frequency preionizer, the high repetition rate solid state pulse power module and the optimized highly durable optical module. As regards spectral measurement technologies, the true instrumental function of a monitor etalon have been measured by our developed 193nm coherent light source. Spectrum of ArF laser could be obtained precisely by deconvolution performed using the covolved spectrum of the ArF laser and the measured instrumental function of the monitor etalon. As for gas control technologies, the influence of impurities given to the ArF laser performance was bigger about 5-20 times compared with the KrF one. And we have paid attention that low concentration Xe gas has effect to the triple output energy. The durability test of 2 billion pulses has been done for the first time in the world. The developed ArF laser kept the integrated energy stability less than +/- 0.6 percent and spectral band-width of FWHM less than 0.8 pm. The result showed, developed laser has an enough performance for lithography even after the pulse number exceeds 2 billion pulses.
Managing multi-configurable terminals (2003)

The advent of software defined architecture allowing flexible software configuration of terminals demands an increased capability for the management applications in charge of configuring such equipment. We address in this paper an architecture for the configuration of software defined radio, which allows the configuration of multi-technology terminals.
Insulin-like growth factor I-mediated protection from rapamycin-induced apoptosis is independent of Ras-Erk1-Erk2 and phosphatidylinositol 3'-kinase-Akt signaling pathways. (2003)

The mTOR inhibitor rapamycin induces G1 cell cycle accumulation and p53-independent apoptosis of the human rhabdomyosarcoma cell line Rh1. Insulin-like growth factor I (IGF-I) and insulin, but not epidermal growth factor or platelet-derived growth factor, completely prevented apoptosis of this cell line. Because the Ras-Erk1-Erk2 and phosphatidylinositol 3'-kinase (PI3K)-Akt pathways are implicated in the survival of various cancer cells, we determined whether protection from rapamycin-induced apoptosis by IGF-I requires one or both of these pathways. Despite the blocking of Ras-Erk signaling by the addition of PD 98059 (a MEK1 inhibitor) or by the overexpression of dominant-negative RasN17, IGF-I completely prevented rapamycin-induced death. Inhibition of Ras signaling did not prevent Akt activation by IGF-I. To determine the role of the PI3K-Akt pathway in rescuing cells from apoptosis caused by rapamycin, cells expressing dominant-negative Akt were tested. This mutant protein inhibited IGF-I-induced phosphorylation of Akt and blocked phosphorylation of glycogen synthase kinase 3. The prevention of rapamycin-induced apoptosis by IGF-I was not inhibited by expression of dominant-negative Akt either alone or under conditions in which LY 294002 inhibited PI3K signaling. Furthermore, IGF-I prevented rapamycin-induced apoptosis when the Ras-Erk1-Erk2 and PI3K-Akt pathways were blocked simultaneously. Similar experiments in a second rhabdomyosarcoma cell line, Rh30, using pharmacological inhibitors of PI3K or MEK1, alone or in combination, failed to block IGF-I rescue from rapamycin-induced apoptosis. Therefore, we conclude that a novel pathway(s) is responsible for the IGF-I-mediated protection against rapamycin-induced apoptosis in these rhabdomyosarcoma cells.
Supercontinuum generation in dispersion-managed tapered-rib waveguide (2013)

We have designed a tapered-rib waveguide and numerically studied the generation of supercontinuum using such waveguides. The Air-SF57 glass-SiO(2) waveguide is 3 cm long, with a varying etched depth to manage the total dispersion. Numerical simulations are conducted for input pulses at a wavelength of 1.55 μm with a width of 150 fs and peak power of 5 kW. The proposed waveguide geometry greatly broadens the output spectrum, extending from ∼1 to ∼6 μm, caused by the continuous modification of the phase-matching condition for the generated waves.
DNA damage repair and survival outcomes in advanced gastric cancer patients treated with first-line chemotherapy (2017)

The DNA damage response (DDR) network is exploited by cancer cells to withstand chemotherapy. Gastric cancer (GC) carries deregulation of the DDR and harbors genetic defects that fuel its activation. The ATM-Chk2 and ATR-Chk1-Wee1 axes are deputed to initiate DNA repair. Overactivation of these pathways in cancer cells may represent an adaptive response for compensating genetic defects deregulating G<sub>1</sub> -S transition (e.g., TP53) and ATM/ATR-initiated DNA repair (e.g., ARID1A). We hypothesized that DDR-linked biomarkers may predict clinical outcomes in GC patients treated with chemotherapy. Immunohistochemical assessment of DDR kinases (pATM, pChk2, pChk1 and pWee1) and DNA damage markers (γ-H2AX and pRPA32) was performed in biological samples from 110 advanced GC patients treated with first-line chemotherapy, either in phase II trials or in routine clinical practice. In 90 patients, this characterization was integrated with targeted ultra-deep sequencing for evaluating the mutational status of TP53 and ARID1A. We recorded a positive association between the investigated biomarkers. The combination of two biomarkers (γ-H2AX<sup>high</sup> /pATM<sup>high</sup> ) was an adverse factor for both progression-free survival (multivariate Cox: HR 2.23, 95%CI: 1.47-3.40) and overall survival (multivariate Cox: HR: 2.07, 95%CI: 1.20-3.58). The relationship between the γ-H2AX<sup>high</sup> /pATM<sup>high</sup> model and progression-free survival was consistent across the different TP53 backgrounds and was maintained in the ARID1A wild-type setting. Conversely, this association was no longer observed in an ARID1A-mutated subgroup. The γ-H2AX<sup>high</sup> /pATM<sup>high</sup> model negatively impacted survival outcomes in GC patients treated with chemotherapy. The mutational status of ARID1A, but apparently not TP53 mutations, affects its predictive significance.