gebhart/patrepeval huggingface dataset:
The Family of Caenorhabditis elegans Tyrosine Kinase Receptors: Similarities and Differences with Mammalian Receptors (1999)

Transmembrane receptors with tyrosine kinase activity (RTK) constitute a superfamily of proteins present in all metazoans that is associated with the control and regulation of cellular processes. They have been the focus of numerous studies and are a good subject for comparative analyses of multigene families in different species aimed at understanding metazoan evolution. The sequence of the genome of the nematode worm Caenorhabditis elegans is available. This offers a good opportunity to study the superfamily of nematode RTKs in its entirety and to compare it with its mammalian counterpart. We show that the C. elegans RTKs constitute various groups with different phylogenetic relationships with mammalian RTKs. A group of four RTKs show structural similarity with the three mammalian receptors for the vascular endothelial growth factors. Another group comprises RTKs with a short extracellular region, a feature not known in mammals; the genes encoding these RTKs are clustered on chromosome II with other gene families, including genes encoding chitinase-like proteins. Most of the C. elegans RTKs have no direct orthologous relationship with any mammalian RTK, providing an illustration of the importance of the separate evolution of the different phyla.
Performance Evaluation of Multi-Radio Transmission Diversity for TCP Flows (2009)

The effect of the TCP congestion control mechanism over rapidly fluctuating wireless links is a deterioration of the TCP performance. The utilization of multi-radio accesses in future networks by means of packet scheduling and dynamic access selection enriches the arsenal of solutions that mitigate radio channel variations. Packet scheduling over multiple radio accesses at link level provides a novel diversity scheme referred to as Multi-Radio Transmission Diversity (MRTD). This work evaluates, through simulations, the effects of different MRTD schemes for TCP flows over heterogeneous radio links. Results indicate that MRTD schemes provide substantial gains in terms of goodput and show a significant reduction in file download times. These gains are due to the diversity obtained and the suppression of the unwanted duplicate acknowledgements that frequently cause degradation in TCP performance over a radio channel.
Call for Emergency Action to Limit Global Temperature Increases, Restore Biodiversity, and Protect Health (2021)

clinical researchers, medical/health professionals, students, nursing professionals and related professional and academic bodies and institutions.
Bypassing the requirement for aminoacyl-tRNA by a cyclodipeptide synthase enzyme (2021)

Cyclodipeptide synthases (CDPSs) produce a variety of cyclic dipeptide products by utilising two aminoacylated tRNA substrates. We sought to investigate the minimal requirements for substrate usage in this class of enzymes as the relationship between CDPSs and their substrates remains elusive. Here, we investigated the <i>Bacillus thermoamylovorans</i> enzyme, BtCDPS, which synthesises cyclo(l-Leu-l-Leu). We systematically tested where specificity arises and, in the process, uncovered small molecules (activated amino esters) that will suffice as substrates, although catalytically poor. We solved the structure of BtCDPS to 1.7 Å and combining crystallography, enzymatic assays and substrate docking experiments propose a model for how the minimal substrates interact with the enzyme. This work is the first report of a CDPS enzyme utilizing a molecule other than aa-tRNA as a substrate; providing insights into substrate requirements and setting the stage for the design of improved simpler substrates.
The Respiratory Syncytial Virus G Protein Enhances the Immune Responses to the RSV F Protein in an Enveloped Virus-like Particle Vaccine Candidate (2022)

Abstract Respiratory syncytial virus (RSV) is a serious human respiratory pathogen, but no RSV vaccine has been licensed. Many of the vaccine candidates are focused on the viral F protein. However, it is the G protein that binds the likely receptor, CX3CR1, in human alveolar lung cells raising the question of the importance of the G protein in vaccine candidates. Using virus-like particle (VLP) vaccine candidates, we have directly compared VLPs containing only the pre-fusion F protein, only the G protein, or both glycoproteins. We report that VLPs containing both glycoproteins bind to anti-F protein specific monoclonal antibodies differently than VLPs containing only the pre-fusion F protein. Using RSV naïve cotton rats as an animal model, we have found that VLPs assembled only with the pre-F protein stimulated extremely weak neutralizing antibody (NAb) titers as did VLPs assembled with G protein. However, VLPs assembled with both glycoproteins stimulated quite robust neutralizing antibody titers, titers that were significantly higher than the combined titers induced by pre-F only or G only VLPs. VLPs assembled with both glycoproteins induced improved protection of the animals from RSV challenge compared to pre-F VLPs and induced significantly higher levels of antibodies specific for F protein antigenic sites 0, site III, and AM14 binding site compared with VLPs containing only the pre-F protein. These combined results indicate that assembly of pre-F protein with G protein in VLPs further stabilized the pre-fusion conformation or otherwise altered the conformation of the F protein increasing the induction of protective antibodies. Importance RSV causes significant disease in infants, young children, and the elderly. Thus, development of an effective vaccine for these populations is a priority. Most ongoing efforts in RSV vaccine development have focused on the viral fusion (F) protein, however, the importance of inclusion of G in vaccine candidates is unclear. Here, using VLPs assembled with only the F protein or only the G protein or both glycoproteins, we show that VLPs assembled with both glycoproteins are a far superior vaccine, in a cotton rat model, than VLPs containing only F protein or only G protein. The results show that the presence of G protein in the VLPs influences the conformation of the F protein and the immune responses to F protein resulting in significantly higher neutralizing antibody titers and better protection from RSV challenge. These results suggest that inclusion of G protein in a vaccine candidate may improve its effectiveness.
Capability of model EBEYE M for EUV mask production (2012)

According to the ITRS Roadmap [1], within a few years the EUV mask requirement for defect will be detection of defect size of less than 25 nm. Electron Beam (EB) inspection is one of the candidates to meet such a severe defect requirement. EB inspection system, Model EBEYE M※1, has been developed for EUV mask inspection. Model EBEYE M employs Projection Electron Microscope (PEM) technique and image acquisition technique to acquire image with Time Delay Integration (TDI) sensor while the stage moves continuously [2]. Therefore, Model EBEYE M has high performance in terms of sensitivity, throughput and cost. In a previous study, we showed the performance of Model EBEYE M for 2X nm in a development phase whose sensitivity in pattern inspection was around 20 nm and in particle inspection was 20 nm with throughput of 2 hours in 100 mm square [3], [4]. With regard to pattern inspection, Model EBEYE M for High Volume Manufacturing (HVM) is currently under development in the production phase. With regard to particle inspection, Model EBEYE M for 2X nm is currently progressing from the development phase to the production phase. In this paper, the particle inspection performance of Model EBEYE M for 2X nm in the production phase was evaluated. Capture rate and repeatability were used for evaluating productivity. The target set was 100% capture rate of 20 nm. 100% repeatability of 20 nm with 3 inspection runs was also set as a target. Moreover, throughput of 1 hour in 100 mm square, which was higher than for Model EBEYE M for 2X nm in the development phase, was set as a target. To meet these targets, electron optical conditions were optimized by evaluating the Signal-to-Noise Ratio (SNR). As a result, SNR of 30 nm PSL was improved 2.5 times. And the capture rate of 20 nm was improved from 21% with throughput of 2 hours to 100% with throughput of 1 hour. Moreover, the repeatability of 20 nm with 3 inspection runs was 100% with throughput of 1 hour. From these results, we confirmed that Model EBEYE M particle inspection mode could be available for EUV mask production.
Artificial Neural Networks for Diagnosis of Kidney Stones Disease (2012)

Artificial Neural networks are often used as a powerful discriminating classifier for tasks in medical diagnosis for early detection of diseases. They have several advantages over parametric classifiers such as discriminate analysis. The objective of this paper is to diagnose kidney stone disease by using three different neural network algorithms which have different architecture and characteristics. The aim of this work is to compare the performance of all three neural networks on the basis of its accuracy, time taken to build model, and training data set size. We will use Learning vector quantization (LVQ), two layers feed forward perceptron trained with back propagation training algorithm and Radial basis function (RBF) networks for diagnosis of kidney stone disease. In this work we used Waikato Environment for Knowledge Analysis (WEKA) version 3.7.5 as simulation tool which is an open source tool. The data set we used for diagnosis is real world data with 1000 instances and 8 attributes. In the end part we check the performance comparison of different algorithms to propose the best algorithm for kidney stone diagnosis. So this will helps in early identification of kidney stone in patients and reduces the diagnosis time.
Supplementary Figure 6 from Augmentation of Immune Checkpoint Cancer Immunotherapy with IL18 (2023)

&lt;p&gt;Cytokine production by PECs from pre-implanted mice receiving immune checkpoint blockade plus IL-18 and/or αGM1&lt;/p&gt;
Unity Human Eye Model for Gaze Tracking with a Query-Driven Dynamic Vision Sensor (2022)

Objective measurement of gaze pattern and eye movement during untethered activity has important applications for neuroscience research and neurological disease detection. Current commercial eye-tracking tools rely on desk-top devices with infrared emitters and conventional frame-based cameras. Although wearable options do exist, the large power-consumption from their conventional cameras limit true long-term mobile usage. The query-driven Dynamic Vision Sensor (qDVS) is a neuromorphic camera which dramatically reduces power consumption by outputting only intensity-change threshold events, as opposed to full frames of intensity data. However, such hardware has not yet been implemented for on-body eye-tracking, but the feasibility can be demonstrated using a mathematical simulator to evaluate the eye-tracking ca-pabilities of the qDVS under controlled conditions. Specifically, a framework utilizing a realistic human eye model in the 3D graphics engine, Unity, is presented to enable the controlled and direct comparison of image-based gaze tracking methods. Eye-tracking based on qDVS frames was compared against two different conventional frame eye-tracking methods - the traditional ellipse pupil-fitting algorithm and a deep learning neural network inference model. Gaze accuracy from qDVS frames achieved an average of 93.2% for movement along the primary horizontal axis (pitch angle) and 93.1 % for movement along the primary vertical axis (yaw angle) under 4 different illumination conditions, demonstrating the feasibility for using qDVS hardware cameras for such applications. The quantitative framework for the direct comparison of eye tracking algorithms presented here is made open-source and can be extended to include other eye parameters, such as pupil dilation, reflection, motion artifact, and more.
Removal of time-varying errors in network analyser measurements: system design (2002)

A new approach to network-analyser measurements has been developed, which uses a dynamic-error suppression technique to remove time-varying component-drift errors (such as amplifier- and filter-response changes) and physical-device errors (such as response changes due to cable flexure). This dynamic-error suppression technique is combined with a conventional static-error suppression technique, such as ‘short/open/load/thru’ (SOLT) or ‘thru/reflection/line’ (TRL), to remove all types of errors. This procedure is referred to as the accurate real-time total-error-suppression technique (ARTTEST). Frequency-offsetting mixers are used to produce the normalisation signals that are required for the dynamic-error suppression. The ARTTEST method allows for the simultaneous measurement of data and normalisation signals that reside at unique, but closely spaced frequencies. These simultaneous normalisation signals are used to greatly improve the measurement accuracy of the system. The ARTTEST method is applicable to a wide variety of measurement problems where high-accuracy results are required. The application of this method to a network-analyser application is demonstrated.
Directly Georeferenced Ground Feature Points with UAV Borne Photogrammetric Platform without Ground Control (2013)

In order to facilitate applications such as environment detection or disaster monitoring, developing a quickly and low cost system to collect near real time spatial information is very important. Such a rapid spatial information collection capability has become an emerging trend in the technology of remote sensing and mapping application. In this study, a fixed-wing UAV based spatial information acquisition platform is developed and evaluated. The proposed UAV based platform has a direct georeferencing module including an low cost INS/GPS integrated system, low cost digital camera as well as other general UAV modules including immediately video monitoring communication system. This direct georeferencing module is able to provide differential GPS processing with single frequency carrier phase measurements to obtain sufficient positioning accuracy. All those necessary calibration procedures including interior orientation parameters, the lever arm and boresight angle are implemented. In addition, a flight test is performed to verify the positioning accuracy in direct georeferencing mode without using any ground control point that is required for most of current UAV based photogrammetric platforms. In other word, this is one of the pilot studies concerning direct georeferenced based UAV photogrammetric platform. The preliminary results in term of positioning accuracy in direct georeferenced mode without using any GCP illustrate horizontal positioning accuracies in x and y axes are both less than 20 meters, respectively. On the contrary, the positioning accuracy of z axis is less than 50 meters with 600 meters flight height above ground. Such accuracy is good for near real time disaster relief. Therefore, it is a relatively safe and cheap platform to collect critical spatial information for urgent response such as disaster relief and assessment applications where ground control points are not available.
Linear kitchen layout design via machine learning (2022)

Abstract The main objective of this paper is to develop a novel approach for linear kitchen layout design which utilizes information from existing layouts via machine learning algorithms. With the growing popularity of large-scale virtual 3D environments for architectural visualization and the game industry, the manual interior design of virtual scenes becomes prohibitively expensive in terms of time and resources. In our approach, the machine learning model automatically generates layout suggestions. The proposed procedural kitchen generation (PKG) model is a pipeline of six Machine Learning (ML) classifiers that are trained and tested on a kitchen layout dataset created by interior designers. The performances of the model are evaluated for the following classifiers: Random forest, Decision tree, AdaBoost, Naive Bayes, MLP, SVM, and L2 Logistic regression. Random forest, as the best performing classifier is used in the final PKG model, and integrated into Unity Engine for automatic 3D kitchen generation and presentation. The PKG model is evaluated in the quantitative and perceptual study, showing better performance than the prior rule-based method. The perceptual study results demonstrate that our tool can be used to speed up designer's work, improve communication with clients, and educate interior design students.
Broca's region revisited: Cytoarchitecture and intersubject variability (1999)

The sizes of Brodmann's areas 44 and 45 (Broca's speech region) and their extent in relation to macroscopic landmarks and surrounding areas differ considerably among the available cytoarchitectonic maps. Such variability may be due to intersubject differences in anatomy, observer-dependent discrepancies in cytoarchitectonic mapping, or both. Because a reliable definition of cytoarchitectonic borders is important for interpreting functional imaging data, we mapped areas 44 and 45 by means of an observer-independent technique. In 10 human brains, the laminar distributions of cell densities were measured vertical to the cortical surface in serial coronal sections stained for perikarya. Thousands of density profiles were obtained. Cytoarchitectonic borders were defined as statistically significant changes in laminar patterns. The analysis of the three-dimensional reconstructed brains and the two areas showed that cytoarchitectonic borders did not consistently coincide with sulcal contours. Therefore, macroscopic features are not reliable landmarks of cytoarchitectonic borders. Intersubject variability in the cytoarchitecture of areas 44 and 45 was significantly greater than cytoarchitectonic differences between these areas in individual brains. Although the volumes of area 44 differed across subjects by up to a factor of 10, area 44 but not area 45 was left-over-right asymmetrical in all brains. All five male but only three of five female brains had significantly higher cell densities on the left than on the right side. Such hemispheric and gender differences were not detected in area 45. These morphologic asymmetries of area 44 provide a putative correlate of the functional lateralization of speech production.
Abstract 12875: Multi-Omics Analysis Strategy is a Promising Approach for Global Identification of New Biomarkers Evaluating Disease Severity of Patients With Dilated Cardiomyopathy (2014)

Introduction: Dilated cardiomyopathy (DCM) is an intractable disease and no radical treatment other than cardiac transplantation has been available until today. Because the number of donor heart is limited in Japan, implantation of left ventricular assist device (LVAD) is increasing. Patients can be weaned from LVAD, but no explicit criterion for weaning has been established. Aim: Discovery of novel biomarkers for evaluating severity/recovery of the DCM and biochemical status of the cardiomyocytes. Methods: Multi-omics analyses were performed with left ventricular tissues from heart transplant recipients or autopsy cases with idiopathic DCM and dilated phase of HCM (n=19), and compared with non-heart disease controls (n=8). Proteomic analysis was carried out with a Triple TOF5600 mass spectrometer and quantitatively compared using a 2DICAL software. Transcriptomic and epigenomic (DNA methylation) analysis were performed with Agilent DNA Microarray 44K and Infinium Methylation450 BeadChip kits. Results: 16...
Stabilization of an intramolecular hydrogen-bond block in an s-triazine insensitive high-energy material (2019)

A unique intramolecular hydrogen-bond block was stabilized in <italic>s</italic>-triazine insensitive high-energy materials with face-to-face stacking.
Stretching Peptides to Generate Small Molecule β-Strand Mimics (2023)

Advances in the modulation of protein-protein interactions (PPIs) enable both characterization of PPI networks that govern diseases and design of therapeutics and probes. The shallow protein surfaces that dominate PPIs are challenging to target using standard methods, and approaches for accessing extended backbone structures are limited. Here, we incorporate a rigid, linear, diyne brace between side chains at the <i>i</i> to <i>i+</i>2 positions to generate a family of low-molecular-weight, extended-backbone peptide macrocycles. NMR and density functional theory studies show that these stretched peptides adopt stable, rigid conformations in solution and can be tuned to explore extended peptide conformational space. The diyne brace is formed in excellent conversions (>95%) and amenable to high-throughput synthesis. The minimalist structure-inducing tripeptide core (<300 Da) is amenable to further synthetic elaboration. Diyne-braced inhibitors of bacterial type 1 signal peptidase demonstrate the utility of the technique.
Estimation of synthetic accessibility score of drug-like molecules based on molecular complexity and fragment contributions (2009)

A novel method to estimate synthetic accessibility of molecules has been developed. This method uses historical synthetic knowledge obtained by analyzing information from millions of already synthesized chemicals and considers also molecule complexity. The method is sufficiently fast and provides results consistent with estimation of ease of synthesis by experienced medicinal chemists. The calculated SAscore may be used to support various drug discovery processes where a large number of molecules needs to be ranked based on their synthetic accessibility, for example when purchasing samples for screening, selecting hits from high-throughput screening for follow-up, or ranking molecules generated by various de novo design approaches.
Practical design and its evaluations for nested transmit diversity (2010)

This paper provides the practical design of the transmit diversity technique with a nested coding technique and evaluates its performance via computer simulations. Similar to network coding techniques, the nested transmit diversity combines the transmit data with XOR operation. As a characteristic of the proposed transmit diversity, it can obtain diversity gain without some extra resources (e.g., transmit/receive antenna). In the proposed system, the transmitter simultaneously transmits two or more data sequences with a superposition technique, namely, nested coding technique. Suppose the case of two data superposing, the transmitting signal is composed of two data sequences, one is the data sequence to be currently transmitted, the other is the previously transmitted data sequence. In this case, the receiver has two types of decoding method corresponding to the previous decoding result. When successfully decoded at previous time slot, since the receiver knows the data-sequence transmitted at previous time slot which is referred to as superposition factor, it can completely remove the superposition factor with XOR manner. Different from a network coding, even if the receiver does not know the superposition factor (failed to decode the data), it can attempt to decode both data sequences. In this paper, we focus on the pragmatic design of nested transmit diversity. In order to achieve further improvement, we propose a reverse order decoding scheme. We reveal that the proposed nested transmit diversity can achieve diversity gain without extra resources.