gebhart/patrepeval huggingface dataset:
Collisional energy dependence of peptide ion fragmentation (2008)

The energy dependence of fragmentation in a collision cell was measured for 2400 protonated peptide ions derived from the digestion of 24 proteins. The collision voltage at which the sum of the fragment ion abundances was equal to the remaining parent ion (V(1/2)) was the principal measure of fragmentation effectiveness. Each class of peptides was characterized by a linear relation between V(1/2) and m/z whose slope depended on the peptide class and, with little adjustment, intersected the origin. Peptide ions where the number of protons is no greater than the number of arginine residues show the greatest slope, V(1/2)/(m/z) = 0.0472 (all slopes in units of V Da(-1) e). For peptides where the number of protons is greater than the number of arginines, but not greater than the total number of basic residues, the slope decreases to 0.0414 for singly charged ions, 0.0382 for doubly charged, 0.0346 for triply charged, and 0.0308 for more highly charged ions. With one mobile proton, the slope is about 0.029 for singly and doubly charged ions and slightly lower for more highly charged ions. With two or more mobile protons the slope is 0.0207. By removing m/z dependence, the deviation of V(1/2) from a line provides a relative measure of the ease of fragmentation of an ion in each class. This information can guide the selection of optimal conditions for tandem mass spectrometry studies in collision cells for selected peptide ions as well as aid in comparing the reactivity of ions differing in m/z and charge state.
Sequencing and characterization of oligosaccharides using infrared multiphoton dissociation and boronic acid derivatization in a quadrupole ion trap (2007)

A simplified method for determining the sequence and branching of oligosaccharides using infrared multiphoton dissociation (IRMPD) in a quadrupole ion trap (QIT) is described. An IR-active boronic acid (IRABA) reagent is used to derivatize the oligosaccharides before IRMPD analysis. The IRABA ligand is designed to both enhance the efficiency of the derivatization reaction and to facilitate the photon absorption process. The resulting IRMPD spectra display oligosaccharide fragments that are formed from primarily one type of diagnostic cleavage, thus making sequencing straightforward. The presence of sequential fragment ions, a phenomenon of IRMPD, permit the comprehensive sequencing of the oligosaccharides studied in a single stage of activation. We demonstrate this approach for two series of oligosaccharides, the lacto-N-fucopentaoses (LNFPs) and the lacto-N-difucohexaoses (LNDFHs).
TFAM’s Contributions to mtDNA Replication and OXPHOS Biogenesis Are Genetically Separable (2022)

The ability of animal orthologs of human mitochondrial transcription factor A (hTFAM) to support the replication of human mitochondrial DNA (hmtDNA) does not follow a simple pattern of phylogenetic closeness or sequence similarity. In particular, TFAM from chickens (<i>Gallus gallus</i>, chTFAM), unlike TFAM from the "living fossil" fish coelacanth (<i>Latimeria chalumnae</i>), cannot support hmtDNA replication. Here, we implemented the recently developed GeneSwap approach for reverse genetic analysis of chTFAM to obtain insights into this apparent contradiction. By implementing limited "humanization" of chTFAM focused either on amino acid residues that make DNA contacts, or the ones with significant variances in side chains, we isolated two variants, Ch13 and Ch22. The former has a low mtDNA copy number (mtCN) but robust respiration. The converse is true of Ch22. Ch13 and Ch22 complement each other's deficiencies. Opposite directionalities of changes in mtCN and respiration were also observed in cells expressing frog TFAM. This led us to conclude that TFAM's contributions to mtDNA replication and respiratory chain biogenesis are genetically separable. We also present evidence that TFAM residues that make DNA contacts play the leading role in mtDNA replication. Finally, we present evidence for a novel mode of regulation of the respiratory chain biogenesis by regulating the supply of rRNA subunits.
Transparent conductive layers for organic solar cells: simulation and experiment (2009)

Thin metal films are a desirable alternative to indium tin oxide for utilization in organic solar cells (OSC).We describe background and processing parameters for thin metal films and show examples of top-illuminated OSC employing metal electrodes. Simulations are introduced as tool for OSC fabrication; several pitfalls are presented which must be considered for successful numerical treatment of thin-film layers at coalescence thicknesses and for coherent treatment.
Extracting Building Boundaries from High Resolution Optical Images and LiDAR Data by Integrating the Convolutional Neural Network and the Active Contour Model (2018)

Identifying and extracting building boundaries from remote sensing data has been one of the hot topics in photogrammetry for decades. The active contour model (ACM) is a robust segmentation method that has been widely used in building boundary extraction, but which often results in biased building boundary extraction due to tree and background mixtures. Although the classification methods can improve this efficiently by separating buildings from other objects, there are often ineluctable salt and pepper artifacts. In this paper, we combine the robust classification convolutional neural networks (CNN) and ACM to overcome the current limitations in algorithms for building boundary extraction. We conduct two types of experiments: the first integrates ACM into the CNN construction progress, whereas the second starts building footprint detection with a CNN and then uses ACM for post processing. Three level assessments conducted demonstrate that the proposed methods could efficiently extract building boundaries in five test scenes from two datasets. The achieved mean accuracies in terms of the F1 score for the first type (and the second type) of the experiment are 96.43 ± 3.34% (95.68 ± 3.22%), 88.60 ± 3.99% (89.06 ± 3.96%), and 91.62 ±1.61% (91.47 ± 2.58%) at the scene, object, and pixel levels, respectively. The combined CNN and ACM solutions were shown to be effective at extracting building boundaries from high-resolution optical images and LiDAR data.
Direct Analysis from Phase-Separated Liquid Samples using ADE-OPI-MS: Applicability to High-Throughput Screening for Inhibitors of Diacylglycerol Acyltransferase 2 (2021)

The primary goal of high-throughput screening (HTS) is to rapidly survey a broad collection of compounds, numbering from tens of thousands to millions of members, and identify those that modulate the activity of a therapeutic target of interest. For nearly two decades, mass spectrometry has been used as a label-free, direct-detection method for HTS and is widely acknowledged as being less susceptible to interferences than traditional optical techniques. Despite these advantages, the throughput of conventional MS-based platforms like RapidFire or parallel LC-MS, which typically acquire data at speeds of 6-30 s/sample, can still be limiting for large HTS campaigns. To overcome this bottleneck, the field has recently turned to chromatography-free approaches including MALDI-TOF-MS and acoustic droplet ejection-MS, both of which are capable of throughputs of 1 sample/second or faster. In keeping with these advances, we report here on our own characterization of an acoustic droplet ejection, open port interface (ADE-OPI)-MS system as a platform for HTS using the membrane-associated, lipid metabolizing enzyme diacylglycerol acyltransferase 2 (DGAT2) as a model system. We demonstrate for the first time that the platform is capable of ejecting droplets from phase-separated samples, allowing direct coupling of liquid-liquid extraction with OPI-MS analysis. By applying the platform to screen a 6400-member library, we further demonstrate that the ADE-OPI-MS assay is suitable for HTS and also performs comparably to LC-MS, but with an efficiency gain of >20-fold.
Structural Characterization of the Cyclic Cystine Ladder Motif of θ-Defensins (2012)

The θ-defensins are, to date, the only known ribosomally synthesized cyclic peptides in mammals, and they have promising antimicrobial bioactivities. The characteristic structural motif of the θ-defensins is the cyclic cystine ladder, comprising a cyclic peptide backbone and three parallel disulfide bonds. In contrast to the cyclic cystine knot, which characterizes the plant cyclotides, the cyclic cystine ladder has not been as well described as a structural motif. Here we report the solution structures and nuclear magnetic resonance relaxation properties in aqueous solution of three representative θ-defensins from different species. Our data suggest that the θ-defensins are more rigid and structurally defined than previously thought. In addition, all three θ-defensins were found to self-associate in aqueous solution in a concentration-dependent and reversible manner, a property that might have a role in their mechanism of action. The structural definition of the θ-defensins and the cyclic cystine ladder will help to guide exploitation of these molecules as structural frameworks for the design of peptide drugs.
Active structural acoustic control of cylinder radiation with piezoelectric actuators and PVDF sensors (1992)

An aluminum cylinder, measuring 1.22 m long with a wall thickness of 2.77 mm and a diameter of 0.254 m, was configured with two rigid end caps and instrumented with piezoceramic actuators and polyvinylidene fluoride (PVDF) sensors for narrow-band active structural acoustic control. All tests were performed in an anechoic environment. In the first test case, the cylinder was driven with a shaker on one end cap, exciting the ‘‘accordion mode’’ of the structure. Significant levels of sound radiation (90 dB) from the end caps were observed in this mode of vibration and the piezoceramic actuators were more than sufficient for controlling the structural acoustic response, yielding 35 dB of global attenuation. In the second test case, the cylinder was driven radially to excite the (0,1) mode of the cylinder as well as higher-order modes to demonstrate the capability of the piezoceramic actuators for controlling the structural acoustic response of the ‘‘breathing mode’’ as well as higher-order cylinder modes. Results from this preliminary study suggest that piezoceramic actuators and PVDF sensors are viable transducers for creating an adaptive/sensory structure for active structural acoustic control on cylinders. [Work supported by ONR.]
DEF STAN 00-970 Requirements for the Design and Airworthiness of Composite Aircraft Structure (2003)

One of the impediments to the introduction of composite structure into Australian Defence Force (ADF) aircraft is the difficulty in identifying those airworthiness requirements specific to these materials. The ADF uses a comparative approach where tenderers propose their own certification basis. This is assessed against the ADF comparative certification basis to ensure that all relevant issues are covered in adequate depth. The ADF comparative certification basis is DEF STAN 00-970 2 supplemented with AAP 7001.054 1. This basis was reviewed. Those requirements relevant to the airworthiness of composite structure were identified and are presented in this report. The requirements for any specific composite part will likely be a sub-set of these and must be developed on a case-by-case basis.
Segregation of type 1 cytokine production in human peripheral blood lymphocytes: phenotypic differences between IFN-γ and IL-2-producing cells in the CD8+ T cell subset (1998)

T cell clones are classified as type 0, 1 or 2 depending on the lymphokines they produce. However, it has remained unclear whether single cells of a given type produce one or several cytokine species. Flow cytometric analysis of peripheral blood lymphocytes (PBL) obtained from 20 healthy donors for the production of the type 1 cytokines IFN-gamma and IL-2 revealed very few cells that co-expressed both cytokines independently of the mitogenic stimulus used for PBL activation. Similarly, kinetic studies of cytokine synthesis indicated a low percentage of IFN-gamma/IL-2 double-positive T cells at all time points. Reverse transcription-PCR analysis of sorted IL-2- and IFN-gamma-positive T cells showed the presence of IL-2- or IFN-gamma-specific mRNA only in those cells expressing the corresponding cytokine. This segregation of the two type 1 cytokines was lost in long-term cultured T cells and in T cell clones. A high percentage of cells expressing only IL-2 or IFN-gamma was observed even when the production of these cytokines was evaluated on CD4- and CD8+ subsets. Moreover, in some healthy individuals, IFN-gamma and IL-2 production by CD8+ T cells was related to CD8+ expression levels and cell size, i. e. IL-2-expressing cells were generally smaller with more intense CD8+ staining as compared with IFN-gamma-producing T cells. These data indicate that activated T lymphocytes are strongly committed in vivo to produce IFN-gamma or IL-2 and emphasizes the independent regulation of the two cytokine genes.
An accelerated signal tracking module using a heterogeneous multi-GPU platform for real-time GNSS software receiver (2015)

This paper presents the design of an accelerated signal tracking module using a heterogeneous multi-graphics processing unit (GPU) platform for real-time global navigation satellite system (GNSS) software receiver. We also propose a load balancing method for the efficient use of the multi-GPU. The proposed method allocates the number of channels to each GPU, and the GPU generates replica signals and performs correlation with the allocated channels. Through experiments, we showed that the proposed load balancing method achieves near optimal performance for GNSS signal tracking and reduces the operation time by 60% compared to that obtained using a single GPU.
Abundance of Repetitive Sequence Elements in the Mouse Testis‐Specific Lactate Dehydrogenase‐C Gene1 (2003)

We have cloned and sequenced the entire mouse ldhc gene and mapped it physically in relation to the somatic ldha gene. The 2 genes were found to be oriented in head-to-tail fashion with about a 6-kilobase (kb) distance between the 3' end of ldha and the 5' end of ldhc. The ldhc gene is composed of 43% repetitive elements compared to only 16% in the ldha gene. Despite the close physical distance of mouse ldha and ldhc, the 2 genes have a very different content of repetitive elements, and this most likely reflects different levels of selective pressure.
Deep-learning framework based on a large ultrasound image database to realize computer-aided diagnosis for liver and breast tumors (2021)

The quality and quantity of training data is vital for computer-aided diagnosis (CADx) based on deep learning. However, the biomedical industry lacks large database of ultrasound images. Therefore, The Japan Society of Ultrasonics in Medicine (JSUM) is currently constructing an ultrasound image database for liver tumors, breast tumors, and heart diseases. As of August 2021, the project has collected more than 140,000 ultrasound images and videos. This database contains ultrasound images, their corresponding labels, and annotation information. That is, the ultrasound image data contains information related to the size and location of the tumor. In this study, we developed a CADx to classify liver tumors and breast tumors by utilizing approximately 71,000 liver tumor and 14,000 breast tumor ultrasound images from the abovementioned database. We classified liver tumors into four classes: cysts, hemangiomas, hepatocellular carcinomas, and metastatic liver cancers. Similarly, we classified breast tumors into four classes: breast cancer, fibroadenoma, cysts, and others. We used a convolutional neural network based on VGG19 for these classifications, and evaluated the accuracy of each case unit by k-fold cross-validation, thereby achieving an accuracy of 91.1% and 85.2% for four-class classification of liver tumor and breast tumor, respectively. In addition, the accuracy, sensitivity, and specificity of the benign/malignant classification based on this result was, respectively, 94.3%, 82.8%, and 96.7% for liver tumors and 89.9%, 92.6%, and 86.6% for breast tumors. Furthermore, when compared with the results obtained in a previous study that utilized a small database, using a large database provided a higher accuracy for both liver and breast tumors.
An infrastructure for extending applications' user experiences across multiple personal devices (2008)

Users increasingly interact with a heterogeneous collection of computing devices. The applications that users employ on those devices, however, still largely provide user experiences that assume the use of a single computer. This failure is due in part to the difficulty of creating user experiences that span multiple devices, particularly the need to manage identifying, connecting to, and communicating with other devices. In this paper we present an infrastructure based on instant messaging that simplifies adding that additional functionality to applications. Our infrastructure elevates device ownership to a first class property, allowing developers to provide functionality that spans personal devices without writing code to manage users' devices or establish connections among them. It also provides simple mechanisms for applications to send information, events, or commands between a user's devices. We demonstrate the effectiveness of our infrastructure by presenting a set of sample applications built with it and a user study demonstrating that developers new to the infrastructure can implement all of the cross-device functionality for three applications in, on average, less than two and a half hours.
A multi-camera system for real-time pose estimation (2007)

This paper presents a multi-camera system that performs face detection and pose estimation in real-time and may be used for intelligent computing within a visual sensor network for surveillance or humancomputer interaction. The system consists of a Scene View Camera (SVC), which operates at a fixed zoom level, and an Object View Camera (OVC), which continuously adjusts its zoom level to match objects of interest. The SVC is set to survey the whole filed of view. Once a region has been identified by the SVC as a potential object of interest, e.g. a face, the OVC zooms in to locate specific features. In this system, face candidate regions are selected based on skin color and face detection is accomplished using a Support Vector Machine classifier. The locations of the eyes and mouth are detected inside the face region using neural network feature detectors. Pose estimation is performed based on a geometrical model, where the head is modeled as a spherical object that rotates upon the vertical axis. The triangle formed by the mouth and eyes defines a vertical plane that intersects the head sphere. By projecting the eyes-mouth triangle onto a two dimensional viewing plane, equations were obtained that describe the change in its angles as the yaw pose angle increases. These equations are then combined and used for efficient pose estimation. The system achieves real-time performance for live video input. Testing results assessing system performance are presented for both still images and video.
Evaluation of Colorectal Cancer Risk and Prevalence by Stool DNA Integrity Detection (2020)

Nowadays, stool DNA can be isolated and analyzed by several methods. The long fragments of DNA in stool can be detected by a qPCR assay, which provides a reliable probability of the presence of pre-neoplastic or neoplastic colorectal lesions. This method, called fluorescence long DNA (FL-DNA), is a fast, non-invasive procedure that is an improvement upon the primary prevention system. This method is based on evaluation of fecal DNA integrity by quantitative amplification of specific targets of genomic DNA. In particular, the evaluation of DNA fragments longer than 200 bp allows for detection of patients with colorectal lesions with very high specificity. However, this system and all currently available stool DNA tests present some general issues that need to be addressed (e.g., the frequency at which tests should be carried out and optimal number of stool samples collected at each timepoint for each individual). However, the main advantage of FL-DNA is the possibility to use it in association with a test currently used in the CRC screening program, known as the immunochemical-based fecal occult blood test (iFOBT). Indeed, both tests can be performed on the same sample, reducing costs and achieving a better prediction of the eventual presence of colorectal lesions.
Unexpected Reactivity of Trifluoromethyl Diazomethane (CF3CHN2): Electrophilicity of the Terminal N-Atom (2016)

After more than 70 years since its discovery, CF3CHN2 was found to possess a novel reactivity mode: N-terminal electrophile. With C-nucleophiles it gives hydrazones that are easily transformed into valuable CF3-heterocycles.
Can we agree on an ecological classification of subterranean animals? (2008)

That the ties between any obligate subterranean species and the hypogean environment depend on the interplay of a species' own physiological characteristics and all of the ecological characteristics of the adjacent epigean habitat(s), including biotic factors, has been emphasized. The reasons why troglomorphy cannot be included within criteria for classifying cave dwellers have been demonstrated. After a review of historic classifications, standardized definitions of the most widely used terms are proposed. The most easily recognized are four categories which are terminological approximations of the classic Schiner‐Racovitza terminology: (1) troglobiont is a species or population, strictly bound to a hypogean habitat; (2) eutroglophile is an essentially epigean species, but able to maintain a permanent subterranean population; (3) subtroglophile is inclined perpetually or temporarily to inhabit a subterranean habitat but is bound to the surface for some biological functions (e.g. feeding); (4) trogloxene is a species only occurring sporadically underground.
Actions of Terodiline, its Isomers and Main Metabolite on Isolated Detrusor Muscle from Rabbit and Man (1988)

The effects of racemic terodiline on isolated detrusor preparations from rabbit and man were compared with those of its (+)- and (-)-isomers, and with those of its main metabolite, parahydroxy-terodiline. Concentration-response (c-r) relations for carbachol and frequency-response relations for electrical stimulation were determined before and after addition of drugs. In preparations from both rabbit and man, all the drugs tested concentration-dependently shifted the c-r curve for carbachol to the right. (+)-Terodiline was more potent than (+/-)-terodiline, whereas (-)-terodiline and parahydroxy-terodiline were less potent. All drugs in concentrations greater than 10(-6) M had a non-competitive effect, depressing the maximum of the carbachol contraction. All drugs had a depressant effect on electrically evoked contractions. (+)-Terodiline was as effective (rabbit) or more effective (man) than (+/-)-terodiline, whereas (-)-terodiline and parahydroxy-terodiline were less effective. It is concluded that (+)-terodiline contributes to a main part of the detrusor effects of the racemate, and that part of this action is anticholinergic. Parahydroxy-terodiline had a profile of action similar to that of (+/-) terodiline, but its potency was low. Since it is present in plasma in low concentrations, its contribution to the clinical effects of terodiline is probably small. (+)-Terodiline may have a therapeutic potential.