gebhart/patrepeval huggingface dataset:
Cavotricuspid isthmus ablation for atrial flutter: Anatomic challenges and troubleshooting (2020)

In patients with cavotricuspid isthmus (CTI)-dependent atrial flutter, ablation along the CTI is often a routine and straightforward procedure. However, certain aspects of the regional anatomy can pose technical challenges such that bidirectional block across the CTI can be difficult to achieve.1 Using a case example, we review common challenges with CTI ablation, discuss the important anatomic considerations that are relevant to procedural difficulty, and present approaches to troubleshooting.
MODC: A Pareto-Optimal Optimization Approach for Network Traffic Classification Based on the Divide and Conquer Strategy (2018)

Network traffic classification aims to identify categories of traffic or applications of network packets or flows. It is an area that continues to gain attention by researchers due to the necessity of understanding the composition of network traffics, which changes over time, to ensure the network Quality of Service (QoS). Among the different methods of network traffic classification, the payload-based one (DPI) is the most accurate, but presents some drawbacks, such as the inability of classifying encrypted data, the concerns regarding the users’ privacy, the high computational costs, and ambiguity when multiple signatures might match. For that reason, machine learning methods have been proposed to overcome these issues. This work proposes a Multi-Objective Divide and Conquer (MODC) model for network traffic classification, by combining, into a hybrid model, supervised and unsupervised machine learning algorithms, based on the divide and conquer strategy. Additionally, it is a flexible model since it allows network administrators to choose between a set of parameters (pareto-optimal solutions), led by a multi-objective optimization process, by prioritizing flow or byte accuracies. Our method achieved 94.14% of average flow accuracy for the analyzed dataset, outperforming the six DPI-based tools investigated, including two commercial ones, and other machine learning-based methods.
Identification of different target glycoproteins for bovine herpes virus type 1-specific cytotoxic T lymphocytes depending on the method of in vitro stimulation. (1993)

Vaccinia virus recombinants expressing the three major bovine herpes virus-1 (BHV-1) glycoproteins gI, gIII and gIV were used to identify the major target antigens for BHV-1-specific CTL isolated from immune cattle. Peripheral blood mononuclear cells (PBMC) expanded in vitro in the presence of interleukin-2 (IL-2) and lysed both gIII- and gIV-infected target cells. Secondary in vitro stimulation of PBMC was also performed in the presence of either fixed BHV-1-infected autologous fibroblasts or ultraviolet (UV)-inactivated virus. Both methods of antigen presentation allowed the proliferation of BHV-1-specific CTL but the target glycoprotein for these CTL differed depending on the method of stimulation. Vaccinia-gIV-infected targets were lysed predominantly when PBMC were stimulated by fixed infected fibroblasts, whilst PBMC stimulated by UV-inactivated virus lysed mostly vaccinia-gIII-infected targets. This observation could be explained by a different processing pathway of BHV-1 antigens in each cell type involved.
Genome-scale reconstructions of the mammalian secretory pathway predict metabolic costs and limitations of protein secretion (2018)

Abstract In mammalian cells, &gt;25% of synthesized proteins are exported through the secretory pathway. The pathway complexity, however, obfuscates its impact on the secretion of different proteins. Unraveling its impact on diverse proteins is particularly important for biopharmaceutical production. Here we delineate the core secretory pathway functions and integrate them with genome-scale metabolic reconstructions of human, mouse, and Chinese hamster cells. The resulting reconstructions enable the computation of energetic costs and machinery demands of each secreted protein. By integrating additional omics data, we find that highly secretory cells have adapted to reduce expression and secretion of other expensive host cell proteins. Furthermore, we predict metabolic costs and maximum productivities of biotherapeutic proteins and identify protein features that most significantly impact protein secretion. Finally, the model successfully predicts the increase in secretion of a monoclonal antibody after silencing a highly expressed selection marker. This work represents a knowledgebase of the mammalian secretory pathway that serves as a novel tool for systems biotechnology.
A 100-Gb-Ethernet subsystem for next-generation metro-area network (2005)

An ultra high-speed Ethernet subsystem, which realizes 100-Gb/s throughput and transmission up to 40 km, is examined for next-generation metro-area networks. A parallel link of 12 10-Gb/s synchronized parallel optical lanes is proposed. The 10 optical lanes are used to transmit 10-bit parallel data. The one of redundant lanes transmits a forward error correction code ((132b, 140b) Hamming code) to achieve highly-reliable (BER < 10-12) data transmission, and the other lane transmits a parity data used for the fault-lane recovery. Here, a 64B/66B code-sequence-based de-skewing mechanism is proposed, and its effectiveness to realize low-latency compensation of the inter-lane skew (< 80 ns) is shown. We have implemented the 100-Gb-Ethernet interface architectures into FPGA circuits, and confirmed the performance of 100 Gb/s data communication with compact 385-kgates circuit size, which is practically small for implementation in a single LSI circuit.
Immunolocalization and Redistribution of the FAC1 Protein in Alzheimerʼs Disease (1996)

The presence of senile plaques and neurofibrillary tangles are hallmark neuropathologic features of Alzheimer's disease (AD). Many proteins have previously been immunolocalized to amyloid-containing plaques in AD brain. Using a monoclonal antibody to a recently described developmentally regulated gene product, we demonstrate the presence of FAC1 protein in a subset of diffuse and neuritic plaques in AD brain. FAC1 is not observed in neurofibrillary tangles common in the hippocampus or entorhinal cortex, nor is it localized in diffuse plaques of nondemented elderly control subjects. FAC1 protein is also immunolocalized in swollen dendrites of hippocampal pyramidal cells observed in some cases of early stage AD. Therefore, FAC1 is a novel protein localized in early pathologic features of AD and in a subset of plaques.
Thermal laser ablation with tunable lesion size reveals multiple origins of seizure-like convulsions in Caenorhabditis elegans (2021)

Abstract Laser microsurgery has long been an important means of assessing the functions of specific cells and tissues. Most laser ablation systems use short, highly focused laser pulses to create plasma-mediated lesions with dimensions on the order of the wavelength of light. While the small size of the lesion enables ablation with high spatial resolution, it also makes it difficult to ablate larger structures. We developed an infrared laser ablation system capable of thermally lesioning tissues with spot sizes tunable by the duration and amplitude of laser pulses. We used our laser system in the roundworm C. elegans to kill single neurons and to sever the dorsal and ventral nerve cords, structures that are difficult to lesion using a plasma-based ablation system. We used these ablations to investigate the source of convulsions in a gain-of-function mutant for the acetylcholine receptor ACR-2. Severing the ventral nerve cord caused convulsions to occur independently anterior and posterior to the lesion, suggesting that convulsions can arise independently from distinct subsets of the motor circuit.
Evaluation of a Functional Position for Lateral Radiograph Acquisition in Adolescent Idiopathic Scoliosis (2004)

The fists on clavicles position for lateral radiograph acquisition has less negative shift in SVA, and in patients with spinal instrumentation, less compensatory posterior rotation of the pelvis. This position is more representative of a patient's functional balance while still allowing adequate lateral radiographic visualization of the spine.
T cell immunity does not age in a long-lived rodent species (2018)

Numerous studies have demonstrated that the percentage of naïve T cells and diversity of T cell receptor (TCR) repertoire decrease with age, with some findings likewise suggesting that increased repertoire diversity may be associated with longer lifespan and healthy aging. In this work, we have analyzed peripheral TCR diversity from humans, mice, and blind mole-rats ( Spalax spp .)—long-lived, hypoxia- and cancer-tolerant rodents. We employed a quantitative approach to TCR repertoire profiling based on 5’RACE with unique molecular identifiers (UMI) to achieve accurate comparison of repertoire diversity, which also required development of specific wet lab protocol and TCR gene reference for Spalax . Our direct comparison reveals a striking phenomenon. Whereas TCR diversity of mice and humans decreases with age, resulting primarily from the shrinkage of the naive T cell pool, Spalax TCR diversity remains stable even for the animals that reach extreme old age (15-17 years). This indicates that T cell immunity does not meaningfully age in long-lived rodents, at least in terms of the classical understanding of immunosenescence, which is associated with the accumulation of large numbers of memory clones. We suggest that the extraordinary longevity of Spalax may be attributable at least in part to the distinctive organization of their T cell immunity. Our findings should therefore encourage a close re-examination of the contribution of immunosenescence to life span in mammals.
Chemical Degradation Pathways in Siloxane Polymers Following Phenyl Excitations (2018)

We use ensembles of quantum-based molecular dynamics simulations to predict the chemical reactions that follow radiation-induced excitations of phenyl groups in a model copolymer of polydimethylsiloxane and polydiphenylsiloxane. Our simulations span a wide range of highly porous and condensed phase densities, and include both wet and dry conditions. We observe that in the absence of water, excited phenyl groups tend to abstract hydrogen from other methyl or phenyl side groups to produce benzene, with the under-hydrogenated group initiating subsequent intrachain cyclization reactions. These systems also yield minor products of diphenyl moieties formed by the complete abstraction of both phenyl groups from a single polydiphenylsiloxane subunit. In contrast, we find that the presence of water promotes the formation of free benzene and silanol side groups, reduces the likelyhood for intrachain cyclization reactions, and completely suppresses the formation of diphenyl species. In addition, we predict that water plays a critical role in chain scission reactions, which indicates a possible synergistic effect between environmental moisture and radiation that could promote alterations of a larger polymer network. These results could have impact in interpreting accelerated aging experiments, where polymer decomposition reactions and network rearrangements are thought to have a significant effect on the ensuing mechanical properties.
Increasing the Rate of Magnesium Intercalation Underneath Epitaxial Graphene on 6H‐SiC(0001) (2021)

Abstract Magnesium intercalated “quasi‐freestanding” bilayer graphene on 6H‐SiC(0001) (Mg‐QFSBLG) has many favorable properties (e.g., highly n‐type doped, relatively stable in ambient conditions). However, intercalation of Mg underneath monolayer graphene is challenging, requiring multiple intercalation steps. Here, these challenges are overcome and the rate of Mg intercalation is significantly increased by laser patterning (ablating) the graphene to form micron‐sized discontinuities. Low energy electron diffraction is then used to verify Mg‐intercalation and conversion to Mg‐QFSBLG, and X‐ray photoelectron spectroscopy to determine the Mg intercalation rate for patterned and non‐patterned samples. By modeling Mg intercalation with the Verhulst equation, it is found that the intercalation rate increase for the patterned sample is 4.5 ± 1.7. Since the edge length of the patterned sample is ≈5.2 times that of the non‐patterned sample, the model implies that the increased intercalation rate is proportional to the increase in edge length. Moreover, Mg intercalation likely begins at graphene discontinuities in pristine samples (not step edges or flat terraces), where the 2D‐like crystal growth of Mg‐silicide proceeds. The laser patterning technique may enable the rapid intercalation of other atomic or molecular species, thereby expanding upon the library of intercalants used to modify the characteristics of graphene, or other 2D materials and heterostructures.
Extracting Named Entities from Pseudo Speech Transcriptions (2005)

Speech transcriptions are very complex to process by taggers for conventional written language due to the lack of capitalization and punctuation marks. We report in this paper our first attempt toward named entity recognition on speech transcriptions. In this work, we experimented on simulated speech transcriptions. Our experimental result s show that our method is robust and achieves high classification accuracies.
Enhanced flexible mask specifications (2003)

A new methodology for a mask quality, flexible mask specifications, is proposed. This methodology consists of two major concepts. One is a <i>flexibly</i> selected pattern to guarantee a mask quality for each device and each level of a device. This pattern, hot spot pattern, is selected using a full chip level lithography simulation. The other is <i>flexibly</i> changeable combination of each tolerance of each error component (e.g. CD mean to target, CD uniformity). A mask quality is judged by not each error component, but a total lithography margin. In this methodology, following two points are important. A hot spot pattern should be correctly selected in terms of having large impact on critical dimension (CD) on wafers. An amount of lithography margin reduction due to mask manufacturing error should be correctly estimated. We have improved this methodology in those two points. Firstly, a hot spot pattern is selected in terms of difference of Dose-MEF factor in addition to a pattern having small lithography margin. A Dose-MEF factor defines as ratio of target exposure shift to mask CD error. A difference of Dose-MEF reduces a common lithography margin with patterns having CD errors. Secondary, we measure all kinds of hot spot patterns directly. A common lithography margin is obtained from Exposure-defocus tree (ED-tree) based on actual measurement data. Applying these improved methodologies to memory device mask with 130nm node, we can obtain a lithography margin precisely in comparison with the previous method.
Bipolar State-Variable Filter for High Frequencies (1990)

A time-continuous programmable State-Variable filter is presented that has been realised using bipolar OTA's. A high input resistance and a good linearity is maintained irrespective of the programming of the transconductance using an OTA with a separated voltage-to-current input stage and a current-attenuation stage. A special common-mode loop is implemented to avoid the charging of the filter capacitors by an output bias current. Filters can be designed with resonance frequencies up to 40 MHz and Q factors ranging from 1 to 10.
Silandiole: eine neue Klasse potenter Protease-Inhibitoren (1998)

Als Übergangszustandsanaloga für die Hydrolyse von Peptiden dienen komplexe Silandiole wie 1, die das Angiotensin Converting Enzyme (ACE) im nanomalaren Bereich inhibieren können. Einfache Silandiole und Silantriole haben sich hingegen bei früheren Versuchen, Enzyme zu inhibieren, als inaktiv erwiesen.
Infinite Nature: Perpetual View Generation of Natural Scenes from a Single Image (2020)

We introduce the problem of perpetual view generation - long-range generation of novel views corresponding to an arbitrarily long camera trajectory given a single image. This is a challenging problem that goes far beyond the capabilities of current view synthesis methods, which quickly degenerate when presented with large camera motions. Methods for video generation also have limited ability to produce long sequences and are often agnostic to scene geometry. We take a hybrid approach that integrates both geometry and image synthesis in an iterative `\emph{render}, \emph{refine} and \emph{repeat}' framework, allowing for long-range generation that cover large distances after hundreds of frames. Our approach can be trained from a set of monocular video sequences. We propose a dataset of aerial footage of coastal scenes, and compare our method with recent view synthesis and conditional video generation baselines, showing that it can generate plausible scenes for much longer time horizons over large camera trajectories compared to existing methods. Project page at https://infinite-nature.github.io/.
Mixed-quantum-state detection with inconclusive results (2003)

We consider the problem of designing an optimal quantum detector with a fixed rate of inconclusive results that maximizes the probability of correct detection, when distinguishing between a collection of mixed quantum states. We show that the design of the optimal detector can be formulated as a semidefinite programming problem, and derive a set of necessary and sufficient conditions for an optimal measurement. We then develop a sufficient condition for the scaled inverse measurement to maximize the probability of correct detection for the case in which the rate of inconclusive results exceeds a certain threshold. Using this condition we derive the optimal measurement for linearly independent pure-state sets, and for mixed-state sets with a broad class of symmetries. Specifically, we consider geometrically uniform (GU) state sets and compound geometrically uniform (CGU) state sets with generators that satisfy a certain constraint. We then show that the optimal measurements corresponding to GU and CGU state sets with arbitrary generators are also GU and CGU, respectively, with generators that can be computed very efficiently in polynomial time within any desired accuracy by solving a reduced size semidefinite programming problem.
Complexity reduced mode selection of H.264/AVC intra coding (2008)

One of the new features in the H.264/AVC encoder is the use of Lagrangian rate-distortion optimization (RDO) method during mode decision at the macroblock level. The RDO technique has been employed in H.264/AVC for intra prediction mode selection to achieve better coding efficiency. But the computation complexity of mode decision algorithm is extremely high. To reduce the complexity of mode decision, we propose an efficient and fast 4 times 4 intra prediction mode selection scheme. The proposed method reduces the candidate of the prediction modes based on the sum of absolute transformed difference (SATD) between the original block and the intra predicted block. Rank of each mode is obtained based on the SATD value. The candidate modes are further reduced by using the combination of rank and most probable mode. Simulation results demonstrate that the proposed mode decision method reduces about 95% of mode decision time of intra coding with ignorable degradation of coding performance.
Vicinal Si(100) surfaces under external strain (1996)

The phase diagram of vicinal Si(100) surfaces is calculated as a function of misorientation angle, temperature, and applied external strain. It is shown that a change of the applied external strain can lead to a phase transition between the single-layer step surface phase and the double-layer step surface phase. The effect of temperature is shown to be negligible up to 300 K. The order parameter of the surface phase transition is also calculated to make contact with experimental measurements. \textcopyright{} 1996 The American Physical Society.
A Novel Low‐Torque Ball Re‐Positioning Scheme Based on a Sliding‐Mode Ball Observer for an Automatic Balancer System (2008)

A novel low‐torque ball re‐positioning scheme based on a sliding‐mode ball observer is developed in this study with the aim to precisely reside the rolling ball inside an automatic balancer system (ABS) to its desired position – 180 degree opposite to the inherent imbalance of the rotating system which the ABS is attached to. In this way, the ABS is capable of substantially reducing radial vibrations of the rotating system for a decent balancing. For preliminary feasibility, the case of a single ball is considered in this study. The first step is to establish the dynamic model of the system, which is followed by the analysis to ensure stability of the desired ball position. The second step is to forge a sliding‐mode observer for estimating on‐line position and velocity of the ball. With ball estimation capability, a low‐torque speed regulator that essentially generates a series of speed drops to the neighborhood of suspension resonance is proposed to overcome practical ball rolling friction for residing the ball at the desired position. The design characteristic of low‐torque required for the regulator is particularly suited to most of commercial spindle motors which can only output limited torques at high speeds. Finally, simulations and experiments are conducted for a benchmark problem of optical disc drives in order to verify the effectiveness of the proposed scheme of the sliding‐mode observer and the low‐torque speed regulator.
High-Performance Solution-Deposited Ambipolar Organic Transistors Based on Terrylene Diimides (2010)

The thin film transistor characteristics of a soluble molecular semiconductor, terrylene tetracarboxdiimide (TDI), a homologue of perylene tetracarboxdiimide (PDI), have been investigated. In a bottom-gate device structure with benzocyclobutene gate dielectric, n-type behavior with electron mobility of 1.1 × 10−2 cm2 V−1 s−1 has been observed after thermal annealing. When applied in the top-gate structure with a polycyclohexylethylene-based gate dielectric, TDI devices exhibit ambipolar transport with electron and hole mobility of 7.2 × 10−3 cm2 V−1 s−1 and 2.2 × 10−3 cm2 V−1 s−1 respectively. The correlation between morphology and field-effect mobility was investigated by atomic force microscopy (AFM) and X-ray diffraction (XRD) studies. Spin-coated, annealed TDI film crystallize in a terrace structure, and the molecules are packed in an “edge-on” structure, thus forming a favorable packing arrangement for charge transport in the plane of the film.
Neuron-specific protein network mapping of autism risk genes identifies shared biological mechanisms and disease relevant pathologies (2022)

Manuscript summary There are hundreds of risk genes associated with autism spectrum disorder (ASD), but signaling networks at the protein level remain unexplored. We use neuron-specific proximity-labeling proteomics (BioID) to identify protein-protein interaction (PPI) networks for 41 ASD-risk genes. Neuron-specific PPI networks, including synaptic transmission proteins, are disrupted by de novo missense variants. The PPI network map reveals convergent pathways, including mitochondrial/metabolic processes, Wnt signaling, and MAPK signaling. CRISPR knockout reveal an association between mitochondrial activity and ASD-risk genes. The PPI network shows an enrichment of 112 additional ASD-risk genes and differentially expressed genes from post-mortem ASD patients. Clustering of risk genes based on PPI networks identifies gene groups corresponding to clinical behavior score severity. Our data reveal that cell type-specific PPI networks can identify individual and convergent ASD signaling networks, provide a method to assess patient variants, and reveal biological insight into disease mechanisms and sub-cohorts of ASD.