gebhart/patrepeval huggingface dataset:
Another Swedish Family with Complete Properdin Deficiency: Association with Fulminant Meningococcal Disease in one Male Family Member (1989)

Inherited deficiency of the complement component properdin is described in a Swedish family without any previous history of meningococcal infections. The properdin-deficient index patient died from a fulminant infection caused by Neisseria meningitidis serogroup Y. Family investigation revealed properdin deficiency in the patient's half-brother and in the maternal grandfather. The half-brother had a history of pneumococcal pneumonia and meningitis probably caused by Borrelia burgdorferi. Opsonic and bactericidal functions of serum were examined in the half-brother after immunization with tetravalent meningococcal vaccine. Vaccination promoted opsonization of N. meningitidis serogroups C and Y but not of serogroups A and W-135. The serum bactericidal activity increased against serogroup C and to some extent against serogroup W-135. This report emphasizes the importance of investigating the complement system even in families with single cases of fulminant meningococcal disease. Individuals with properdin deficiency might be protected from infection by immunization.
New concept photomask repeater with stitching exposure technique (2001)

We have developed a new mask patterning system, which can fabricate 130nm generation masks by means of a stitching exposure technique. We call this system the Photomask Repeater (PR)1,23,4. The PR is a 5x i-line stepper modified for mask manufacturing with a field size of 22x22mm in a single exposure. However, the device size on a 4x mask is larger than 22x22mm. Furthermore, excellent mask CD uniformity is required. For this purpose the exposure field size was extended with the use of “seamless stitching technology”. This is clearly the key to obtaining a practical, accurate mask patterning system. Results have been achieved on masks with this system showing CD variation of less than +/- 7nm at a stitching area by means of a “gradation filter”. Moreover, overall CD uniformity is 10.36nm (3?), while image placement accuracy is 17.8nm (3?) and 2nd alignment accuracy is 24.1nm (3?). PR is an attractive system for System on Chip mask manufacturing, and is also effective in reducing Turn Around Time.
Data from TTPAL Promotes Colorectal Tumorigenesis by Stabilizing TRIP6 to Activate Wnt/β-Catenin Signaling (2023)

&lt;div&gt;Abstract&lt;p&gt;Copy number alterations are crucial for the development of colorectal cancer. Our whole-genome analysis identified tocopherol alpha transfer protein-like (TTPAL) as preferentially amplified in colorectal cancer. Here we demonstrate that frequent copy number gain of TTPAL leads to gene overexpression in colorectal cancer from a Chinese cohort (&lt;i&gt;n&lt;/i&gt; = 102), which was further validated by a The Cancer Genome Atlas (TCGA) cohort (&lt;i&gt;n&lt;/i&gt; = 376). High expression of TTPAL was significantly associated with shortened survival in patients with colorectal cancer. TTPAL promoted cell viability and clonogenicity, accelerated cell-cycle progression, inhibited cell apoptosis, increased cell migration/invasion ability &lt;i&gt;in vitro&lt;/i&gt;, and promoted tumorigenicity and cancer metastasis &lt;i&gt;in vivo&lt;/i&gt;. TTPAL significantly activated Wnt signaling and increased β-catenin activation and protein expression of cyclin D1 and c-Myc. Coimmunoprecipitation followed by mass spectrometry identified thyroid receptor–interacting protein 6 (TRIP6) as a direct downstream effector of TTPAL. Depletion of TRIP6 significantly abolished the effects of TTPAL on cell proliferation and Wnt activation. Direct binding of TTPAL with TRIP6 in the cytoplasm inhibited ubiquitin-mediated degradation of TRIP6 and, subsequently, increased levels of TRIP6 displaced β-catenin from the tumor suppressor MAGI1 via competitive binding. This sequence of events allows β-catenin to enter the nucleus and promotes oncogenic Wnt/β-catenin signaling. In conclusion, TTPAL is commonly overexpressed in colorectal cancer due to copy number gain, which promotes colorectal tumorigenesis by activating Wnt/β-catenin signaling via stabilization of TRIP6. TTPAL overexpression may serve as an independent new biomarker for the prognosis of patients with colorectal cancer.&lt;/p&gt;Significance:&lt;p&gt;TTPAL, a gene preferentially amplified in colorectal cancer, promotes colon tumorigenesis via activation of the Wnt/β-catenin pathway.&lt;/p&gt;&lt;/div&gt;
5G-6 Forward Looking Intracardiac Imaging Catheters for Electrophysiology (2006)

Minimally invasive electrophysiology interventions to treat cardiac arrhythmias are increasing worldwide due to advances in technologies that enable more effective clinical procedures. A forward imaging ultrasound catheter design has been developed and tested to advance the methods of integration of intracardiac imaging and electrophysiology sensing. The first catheters built have been constructed with a 9F (3 mm) shaft and a large (15F) tip to support experimental wire ports adjacent to a 24 element phased array operating at 14 MHz. The final tip design construction size will be 9F and possess an integrated metal electrode at the catheter distal end. Two forward looking array designs have been developed in parallel to produce two contrasting fine pitch (65 microns) 24 element phased array construction approaches. The first array has been assembled with a standard 2-2 composite PZT technology with the flex circuit mounted on the front facing side, and the second design is a cMUT version with a flip-chip bonded silicon die bonded to a backside flex circuit. The cMUT design requires a special interface to assure a safe element biasing scheme while enhancing the array's linearity and sensitivity. The first PZT array prototypes, built without explicit matching layers, have been characterized and agree with FEA and KLM analyses in operation at 14 MHz. Matching layer variations have been used on the front layer flex circuit to optimize the sensitivity and bandwidth of the PZT arrays while minimizing the thermal boundary layer. Specially designed assembly approaches addressed the challenging forward looking array configurations that utilize interconnection flex circuits with bend radii at 250 microns. Animal studies have been performed utilizing beam forming adaptations for the forward looking imaging catheter operation on a Vingmed Vivid-7 system. The first piezoceramic array devices were used successfully to image the myocardium of the right atrium of a pig while simultaneous tissue ablation was performed
Sensitivity and Generalization in Neural Networks: an Empirical Study (2018)

In practice it is often found that large over-parameterized neural networks generalize better than their smaller counterparts, an observation that appears to conflict with classical notions of function complexity, which typically favor smaller models. In this work, we investigate this tension between complexity and generalization through an extensive empirical exploration of two natural metrics of complexity related to sensitivity to input perturbations. Our experiments survey thousands of models with various fully-connected architectures, optimizers, and other hyper-parameters, as well as four different image classification datasets. 
We find that trained neural networks are more robust to input perturbations in the vicinity of the training data manifold, as measured by the norm of the input-output Jacobian of the network, and that it correlates well with generalization. We further establish that factors associated with poor generalization $-$ such as full-batch training or using random labels $-$ correspond to lower robustness, while factors associated with good generalization $-$ such as data augmentation and ReLU non-linearities $-$ give rise to more robust functions. Finally, we demonstrate how the input-output Jacobian norm can be predictive of generalization at the level of individual test points.
Variation in the AU(AT)-Rich Element within the 3′-Untranslated Region ofPPP1R3Is Associated with Variation in Plasma Glucose in Aboriginal Canadians1 (1998)

We are investigating associations between variations in candidate genes on chromosome 7q and diabetes-related phenotypes in Canadian Oji-Cree. One of these genes encodes the skeletal muscle regulatory G subunit of the glycogen-associated form of protein phosphatase 1 (PPPIR3), which may play a key role in muscle glycogen metabolism. There is a common 5-bp insertion-deletion polymorphism in a messenger ribonucleic acid-stabilizing AU(AT)-rich element within the 3'-untranslated region (UTR) of PPPIR3. The D allele had a frequency of 0.30 in the Oji-Cree. We found that this 3'-UTR variation of PPPIR3 was significantly associated with variation in 2-h postprandial glucose in adult Oji-Cree with type 2 diabetes or impaired glucose tolerance (IGT). Specifically, Oji-Cree with diabetes or IGT who were D/D homozygotes had significantly lower 2-h postprandial plasma glucose than subjects with the other genotypes. There was no association of the PPPIR3 genotype either with the presence of type 2 diabetes or IGT or with other quantitative traits in this sample. These findings suggest that common PPPIR3 3'-UTR variation that potentially affects messenger ribonucleic acid stability is associated with variation in glycemia in Oji-Cree subjects with type 2 diabetes.
Anomaly Detection in Dynamic Networks (2014)

Anomaly detection in dynamic communication networks has many important security applications. These networks can be extremely large and so detecting any changes in their structure can be computationally challenging; hence, computationally fast, parallelisable methods for monitoring the network are paramount. For this reason the methods presented here use independent node and edge based models to detect locally anomalous substructures within communication networks. As a first stage, the aim is to detect changes in the data streams arising from node or edge communications. Throughout the thesis simple, conjugate Bayesian models for counting processes are used to model these data streams. A second stage of analysis can then be performed on a much reduced subset of the network comprising nodes and edges which have been identified as potentially anomalous in the first stage. The first method assumes communications in a network arise from an inhomogeneous Poisson process with piecewise constant intensity. Anomaly detection is then treated as a changepoint problem on the intensities. The changepoint model is extended to incorporate seasonal behavior inherent in communication networks. This seasonal behavior is also viewed as a changepoint problem acting on a piecewise constant Poisson process. In a static time frame, inference is made on this extended model via a Gibbs sampling strategy. In a sequential time frame, where the data arrive as a stream, a novel, fast Sequential Monte Carlo (SMC) algorithm is introduced to sample from the sequence of posterior distributions of the change points over time. A second method is considered for monitoring communications in a large scale computer network. The usage patterns in these types of networks are very bursty in nature and don’t fit a Poisson process model. For tractable inference, discrete time models are considered, where the data are aggregated into discrete time periods and probability models are fitted to the communication counts. In a sequential analysis, anomalous behavior is then identified from outlying behavior with respect to the fitted predictive probability models. Seasonality is again incorporated into the model and is treated as a changepoint model on the transition probabilities of a discrete time Markov process. Second stage analytics are then developed which combine anomalous edges to identify anomalous substructures in the network.
Broadcast and Select Reconfigurable Spatial Add Drop Multiplexer for Spatial Channel Ring Network (2020)

We report a novel reconfigurable spatial add/drop multiplexer with a broadcast-and-select configuration for future spatial channel ring networks. A prototype is demonstrated using a 1×2 multicore-fiber splitter and a 1×2 core selective switch.
Evaluation of Methods to Assess in vivo Activity of Engineered Genome-Editing Nucleases in Protoplasts (2019)

Genome-editing is being implemented in increasing number of plant species using engineered sequence specific nucleases (SSNs) such as Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated systems (CRISPR/Cas9), Transcription activator like effector nucleases (TALENs), and more recently CRISPR/Cas12a. As the tissue culture and regeneration procedures to generate gene-edited events are time consuming, large-scale screening methodologies that rapidly facilitate validation of genome-editing reagents are critical. Plant protoplast cells provide a rapid platform to validate genome-editing reagents. Protoplast transfection with plasmids expressing genome-editing reagents represents an efficient and cost-effective method to screen for <i>in vivo</i> activity of genome-editing constructs and resulting targeted mutagenesis. In this study, we compared three existing methods for detection of editing activity, the T7 endonuclease I assay (T7EI), PCR/restriction enzyme (PCR/RE) digestion, and amplicon-sequencing, with an alternative method which involves tagging a double-stranded oligodeoxynucleotide (dsODN) into the SSN-induced double stranded break and detection of on-target activity of gene-editing reagents by PCR and agarose gel electrophoresis. To validate these methods, multiple reagents including TALENs, CRISPR/Cas9 and Cas9 variants, eCas9(1.1) (enhanced specificity) and Cas9-HF1 (high-fidelity1) were engineered for targeted mutagenesis of <i>Acetolactate synthase1</i> (<i>ALS1</i>), <i>5-Enolpyruvylshikimate- 3-phosphate synthase1</i> (<i>EPSPS1</i>) and their paralogs in potato. While all methods detected editing activity, the PCR detection of dsODN integration provided the most straightforward and easiest method to assess on-target activity of the SSN as well as a method for initial qualitative evaluation of the functionality of genome-editing constructs. Quantitative data on mutagenesis frequencies obtained by amplicon-sequencing of <i>ALS1</i> revealed that the mutagenesis frequency of CRISPR/Cas9 reagents is better than TALENs. Context-based choice of method for evaluation of gene-editing reagents in protoplast systems, along with advantages and limitations associated with each method, are discussed.
Autonomous navigation for BigDog (2010)

BigDog is a four legged robot with exceptional rough-terrain mobility. In this paper, we equip BigDog with a laser scanner, stereo vision system, and perception and navigation algorithms. Using these sensors and algorithms, BigDog performs autonomous navigation to goal positions in unstructured forest environments. The robot perceives obstacles, such as trees, boulders, and ground features, and steers to avoid them on its way to the goal. We describe the hardware and software implementation of the navigation system and summarize performance. During field tests in unstructured wooded terrain, BigDog reached its goal position 23 of 26 runs and traveled over 130 meters at a time without operator involvement.
Carbonium Ion (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Isoform-selective PI3K inhibitors as novel therapeutics for the treatment of acute myocardial infarction (2007)

In the present paper, we review the preclinical development of TG100-115, a PI3K (phosphoinositide 3-kinase) gamma/delta isoform-specific inhibitor currently in clinical trials for the reduction of acute MI (myocardial infarction). An overview is presented outlining the pathogenesis of acute MI and the rationale for clinical use of PI3K gamma/delta-specific inhibitors in this indication. TG100-115's broad anti-inflammatory activities are described, as well as its ability to discriminate between cellular signalling pathways downstream of receptor tyrosine kinase ligands such as vascular endothelial growth factor. Finally, we review TG100-115's potent cardioprotective activities as revealed in rigorous animal models of acute MI, and, based on these data, this compound's potential for clinical utility.
Using Bayesian networks and rule-based trending to predict patient status in the intensive care unit. (2009)

Multivariate Bayesian models trained with machine learning, in conjunction with rule-based time-series statistical techniques, are explored for the purpose of improving patient monitoring. Three vital sign data streams and known outcomes for 36 intensive care unit (ICU) patients were captured retrospectively and used to train a set of Bayesian net models and to construct time-series models. Models were validated on a reserved dataset from 16 additional patients. Receiver operating characteristic (ROC) curves were calculated. Area under the curve (AUC) was 91% for predicting improving outcome. The model's AUC for predicting declining outcome increased from 70% to 85% when the model was indexed to personalized baselines for each patient. The rule-based trending and alerting system was accurate 100% of the time in alerting a subsequent decline in condition. These techniques promise to improve the monitoring of ICU patients with high-sensitivity alerts, fewer false alarms, and earlier intervention.
Microfluidics and Surface-Enhanced Raman Spectroscopy: A Perfect Match for New Analytical Tools (2019)

In this perspective article, we emphasize the combination of Surface-Enhanced Raman Spectroscopy (SERS) and Microfluidic devices. SERS approaches have been widely studied and used for multiple applications including trace molecules detection, in situ analysis of biological samples and monitoring or, all of them with good results, however still with limitations of the technique, for example regarding with improved precision and reproducibility. These implications can be overcome by microfluidic approaches. The resulting coupling Microfluidics - SERS (MF-SERS) has recently gained increasing attention by creating thundering opportunities for the analytical field. For this purpose, we introduce some of the strategies developed to implement SERS within microfluidic reactor along with a brief overview of the most recent MF-SERS applications for biology, health and environmental concerns. Eventually, we will discuss future research opportunities of such systems.
Predicting NMR Relaxation Rates in Anisotropically Tumbling Proteins through Networks of Coupled Rotators (2008)

We show that the prediction of (15)N relaxation rates in proteins can be extended to systems with anisotropic global rotational diffusion by using a network of coupled rotators (NCR), starting from a three-dimensional structure. The relaxation rates predicted by this method are confronted in several examples with experiments performed by other groups. The NCR spectral density functions are compared with the results obtained from reduced spectral density mapping. The consequence of the timescales of internal motions on the predicted relaxation rates and the effects of the predicted local anisotropy-present only in the case of anisotropic overall tumbling-on dynamic parameters, are discussed.
Foreword (2019)

Presents the introductory welcome message from the conference proceedings. May include the conference officers' congratulations to all involved with the conference event and publication of the proceedings record.
Understanding UAV Cellular Communications: From Existing Networks to\n Massive MIMO (2018)

The purpose of this article is to bestow the reader with a timely study of\nUAV cellular communications, bridging the gap between the 3GPP standardization\nstatus quo and the more forward-looking research. Special emphasis is placed on\nthe downlink command and control (C&amp;C) channel to aerial users, whose\nreliability is deemed of paramount technological importance for the commercial\nsuccess of UAV cellular communications. Through a realistic side-by-side\ncomparison of two network deployments -- a present-day cellular infrastructure\nversus a next-generation massive MIMO system -- a plurality of key facts are\ncast light upon, with the three main ones summarized as follows: (i) UAV cell\nselection is essentially driven by the secondary lobes of a base station's\nradiation pattern, causing UAVs to associate to far-flung cells; (ii) over a 10\nMHz bandwidth, and for UAV heights of up to 300 m, massive MIMO networks can\nsupport 100 kbps C&amp;C channels in 74% of the cases when the uplink pilots for\nchannel estimation are reused among base station sites, and in 96% of the cases\nwithout pilot reuse across the network; (iii) supporting UAV C&amp;C channels can\nconsiderably affect the performance of ground users on account of severe pilot\ncontamination, unless suitable power control policies are in place.\n
The role of threading dislocations and unintentionally incorporated impurities on the bulk electron conductivity of In-face InN (2009)

The origin of bulk electrons in In-face InN has been studied by considering the effects of both unintentionally incorporated impurities and threading dislocation densities on electron transport properties. The concentration of unintentionally incorporated oxygen and hydrogen scaled with the bulk electron concentration while threading dislocations had no discernable effect on the electron concentration. We conclude that unintentional impurities were the significant source of electrons and threading dislocations acted only as scattering centers limiting the electron mobility in as-grown InN films. Further, we present In-face InN growth techniques controlling the incorporation of oxygen and hydrogen and reducing threading dislocation densities.