gebhart/patrepeval huggingface dataset:
A Review of Point Cloud Registration Algorithms for Mobile Robotics (2015)

The topic of this review is geometric registration in robotics. Registration algorithms associate sets of data into a common coordinate system. They have been used extensively in object reconstruction, inspection, medical application, and localization of mobile robotics. We focus on mobile robotics applications in which point clouds are to be registered. While the underlying principle of those algorithms is simple, many variations have been proposed for many different applications. In this review, we give a historical perspective of the registration problem and show that the plethora of solutions can be organized and differentiated according to a few elements. Accordingly, we present a formalization of geometric registration and cast algorithms proposed in the literature into this framework. Finally, we review a few applications of this framework in mobile robotics that cover different kinds of platforms, environments, and tasks. These examples allow us to study the specific requirements of each use case and the necessary configuration choices leading to the registration implementation. Ultimately, the objective of this review is to provide guidelines for the choice of geometric registration configuration.
Prediction of peptides binding to the PKA RIIα subunit using a hierarchical strategy (2011)

We propose a hierarchical and efficient approach, which combines molecular dynamics (MD) simulations, free energy calculations, virtual mutagenesis (VM) and bioinformatics analyses, to predict peptides binding to the PKA RIIα regulatory subunit in the human proteome systematically. Our approach successfully retrieved 15 out of 18 documented RIIα-binding peptides. Literature curation supported that many newly predicted peptides might be true AKAPs. Here, we present the first systematic search for AKAP peptides in the human proteome, which is useful to further experimental identification of AKAPs and functional analysis of their biological roles.
Detection of High Molecular Weight Forms of Platelet-Derived Growth Factor by Sequence-Specific Antisera (1984)

Antisera to synthetic peptides representing sequences of both chains of platelet-derived growth factor (PDGF) were used to structurally analyze PDGF isolated from outdated human platelets and PDGF-like proteins in normal and transformed cells. Most PDGF isolated from platelets did not contain the carboxyl portion of PDGF-2 in contrast to p20sis, the major form of p28sis detected in simian sarcoma virus-transformed cells. In addition, higher molecular weight forms of molecules containing PDGF-1 and PDGF-2 sequences were detected in all cell lines tested. These lines were heterogeneous with respect to species, cell type, and transforming agent.
Defining the mammalian CArGome (2005)

Serum response factor (SRF) binds a 1216-fold degenerate cis element known as the CArG box. CArG boxes are found primarily in muscle- and growth-factor-associated genes although the full spectrum of functional CArG elements in the genome (the CArGome) has yet to be defined. Here we describe a genome-wide screen to further define the functional mammalian CArGome. A computational approach involving comparative genomic analyses of human and mouse orthologous genes uncovered >100 hypothetical SRF-dependent genes, including 10 previously identified SRF targets, harboring a conserved CArG element within 4000 bp of the annotated transcription start site (TSS). We PCR-cloned 89 hypothetical SRF targets and subjected each of them to at least two of several validations including luciferase reporter, gel shift, chromatin immunoprecipitation, and mRNA expression following RNAi knockdown of SRF; 60/89 (67%) of the targets were validated. Interestingly, 26 of the validated SRF target genes encode for cytoskeletal/contractile or adhesion proteins. RNAi knockdown of SRF diminishes expression of several SRF-dependent cytoskeletal genes and elicits an attending perturbation in the cytoarchitecture of both human and rodent cells. These data illustrate the power of integrating existing algorithms to interrogate the genome in a relatively unbiased fashion for cis-regulatory element discovery. In this manner, we have further expanded the mammalian CArGome with the discovery of an array of cyto-contractile genes that coordinate normal cytoskeletal homeostasis. We suggest one function of SRF is that of an ancient master regulator of the actin cytoskeleton.
Role of multiple efflux pumps inEscherichia coliin indole expulsion (1999)

Escherichia coli chromosome encodes several multidrug transporters. Despite their protective function against antibacterial agents, the specific physiological actions of these transporters are not fully understood. E. coli produces indole, a metabolite of tryptophan, under physiological conditions. Defined inactivation of the acrEF gene, the product of which is known as an energy-dependent multiple drug efflux pump, decreased indole excretion while reintroduction of the acrEF gene restored it. A DeltaacrEF mutant accumulated more intracellular indole than the parent. This mutant was more susceptible to the growth-inhibitory effect of indole than the parent. These results indicate that the AcrEF system plays a significant role in indole efflux.
Micromotion of mammalian cells measured electrically. (1991)

Motility is a fundamental property of mammalian cells that normally is observed in tissue culture by time lapse microscopy where resolution is limited by the wavelength of light. This paper examines a powerful electrical technique by which cell motion is quantitatively measured at the nanometer level. In this method, the cells are cultured on small evaporated gold electrodes carrying weak ac currents. A large change in the measured electrical impedance of the electrodes is observed when cells attach and spread on these electrodes. When the impedance is tracked as a function of time, fluctuations are observed that are a direct measure of cell motion. Surprisingly, these fluctuations continue even when the cell layer becomes confluent. By comparing the measured impedance with a theoretical model, it is clear that under these circumstances the average motions of the cell layer of 1 nm can be inferred from the measurements. We refer to this aspect of cell motility as micromotion.
Device characterization on monocrystalline silicon grown over SiO2by the ELO (epitaxial lateral overgrowth) process (1983)

MOS and lateral bipolar transistors have been fabricated on epitaxial silicon layers which have been laterally overgrown over SiO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> . These device characteristics were than compared to those measured on devices fabricated on homoepitaxial silicon and bulk silicon. The measurements indicate essentially identical MOS device characteristics for all three materials with a typical hole field effect mobility of about 180 cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> /vs. Lifetime measurements using pulsed C-V techniques showed essentially the same values for ELO material and homoepitaxial material with the ELO value being about 20 µS for 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">15</sup> cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> doping level. These lifetime values correlate will with diode and bipolar transistor measurements.
Bone morphogenetic protein-6 is a marker of serous acinar cell differentiation in normal and neoplastic human salivary gland. (1999)

Bone morphogenetic protein (BMP-6, also known as vegetal-pale-gene-related and decaplentaplegic-vegetal-related) is a member of the transforming growth factor-beta superfamily of multifunctional signaling molecules. BMP-6 appears to play various biological roles in developing tissues, including regulation of epithelial differentiation. To study the possible involvement of BMP-6 in normal and neoplastic human salivary glands, we compared its mRNA and protein expression in 4 fetal and 15 adult salivary glands and in 22 benign and 32 malignant salivary gland tumors. In situ hybridization and Northern blot analysis indicated that BMP-6 transcripts are expressed at low levels in acinar cells of adult submandibular glands but not in ductal or stromal cells. BMP-6 was immunolocated specifically in serous acini of parotid and submandibular glands. None was found in primitive fetal acini or any other types of cell in adult salivary glands, including mucous acini and epithelial cells of intercalated, striated, and excretory ducts. All 16 cases of acinic cell carcinoma consistently exhibited cytoplasmic BMP-6 staining in the acinar tumor cells. Other cell types in these tumors, including intercalated duct-like cells, clear, vacuolated cells, and nonspecific glandular cells, exhibited no cytoplasmic BMP-6 staining. Other benign and malignant salivary gland tumors lacked BMP-6 immunoreactivity, except in areas of squamous differentiation. The results indicate that in salivary glands, BMP-6 expression is uniquely associated with acinar cell differentiation and suggest that BMP-6 may play a role in salivary gland function. More importantly, our experience of differential diagnostic problems related to salivary gland tumors suggests that the demonstration of consistent and specific BMP-6 immunoreactivity in acinic cell carcinoma is likely to be of clinical value.
Invasive lobular and invasive ductal carcinoma of the breast show distinct patterns of vascular endothelial growth factor expression and angiogenesis (1998)

Angiogenesis is essential for tumour growth and important in tumour metastasis and prognosis. Vascular endothelial growth factor (VEGF) stimulates endothelial proliferation in vitro and angiogenesis in vivo. VEGF expression has been correlated with high vascularity in tumours, including carcinoma of the breast. This study investigated VEGF expression and vascularity of invasive lobular (n = 10) and invasive ductal carcinoma (n = 28), and pure ductal carcinoma in situ of the breast (n = 33). VEGF protein expression was studied with immunohistochemistry and VEGF mRNA with in situ hybridization. Vascular density was assessed on sections stained for von Willebrand factor. There was more expression of both VEGF protein (P = 0.006) and mRNA (P = 0.002) in invasive ductal than in invasive lobular carcinoma. VEGF protein (rs = 0.32, P = 0.047) and mRNA (rs = 0.56, P = 0.04) correlated with vascular density in invasive ductal carcinoma. In invasive lobular carcinoma, vascular density did not correlate with VEGF mRNA (rs = 0.15, P = 0.35) and was inversely related to VEGF protein (rs = -0.57, P = 0.04). There were no significant differences in vascular density between the two types of invasive carcinoma, suggesting that VEGF is important in angiogenesis in invasive ductal carcinoma, but that other angiogenic factors are important in invasive lobular carcinoma. Although VEGF protein was frequently expressed in ductal carcinoma in situ, no relationship was found between VEGF and the two patterns of angiogenesis previously described.
Sensitive and accurate detection of copy number variants using read depth of coverage (2009)

Methods for the direct detection of copy number variation (CNV) genome-wide have become effective instruments for identifying genetic risk factors for disease. The application of next-generation sequencing platforms to genetic studies promises to improve sensitivity to detect CNVs as well as inversions, indels, and SNPs. New computational approaches are needed to systematically detect these variants from genome sequence data. Existing sequence-based approaches for CNV detection are primarily based on paired-end read mapping (PEM) as reported previously by Tuzun et al. and Korbel et al. Due to limitations of the PEM approach, some classes of CNVs are difficult to ascertain, including large insertions and variants located within complex genomic regions. To overcome these limitations, we developed a method for CNV detection using read depth of coverage. Event-wise testing (EWT) is a method based on significance testing. In contrast to standard segmentation algorithms that typically operate by performing likelihood evaluation for every point in the genome, EWT works on intervals of data points, rapidly searching for specific classes of events. Overall false-positive rate is controlled by testing the significance of each possible event and adjusting for multiple testing. Deletions and duplications detected in an individual genome by EWT are examined across multiple genomes to identify polymorphism between individuals. We estimated error rates using simulations based on real data, and we applied EWT to the analysis of chromosome 1 from paired-end shotgun sequence data (30x) on five individuals. Our results suggest that analysis of read depth is an effective approach for the detection of CNVs, and it captures structural variants that are refractory to established PEM-based methods.
High-Throughput Fluorescence-Activated Nanoscale Subcellular Sorter with Single-Molecule Sensitivity (2012)

Recent single-cell and single-molecule studies have shown that a variety of subpopulations exist within biological systems, such as synaptic vesicles, that have previously been overlooked in common bulk studies. By isolating and enriching these various subpopulations, detailed analysis with a variety of analytical techniques can be done to further understand the role that various subpopulations play in cellular dynamics and how alterations to these subpopulations affect the overall function of the biological system. Previous sorters lack the sensitivity, sorting speed, and efficiency to isolate synaptic vesicles and other nanoscale systems. This paper describes the development of a fluorescence-activated nanoscale subcellular sorter that can sort nearly 10 million objects per hour with single-molecule sensitivity. Utilizing a near-nanoscale channel system, we were able to achieve upward of 91% recovery of desired objects with a 99.7% purity.
The MHC I immunopeptidome conveys to the cell surface an integrative view of cellular regulation (2011)

Self/non-self discrimination is a fundamental requirement of life. Endogenous peptides presented by major histocompatibility complex class I (MHC I) molecules represent the essence of self for CD8 T lymphocytes. These MHC I peptides (MIPs) are collectively referred to as the immunopeptidome. From a systems-level perspective, very little is known about the origin, composition and plasticity of the immunopeptidome. Here, we show that the immunopeptidome, and therefore the nature of the immune self, is plastic and moulded by cellular metabolic activity. By using a quantitative high-throughput mass spectrometry-based approach, we found that altering cellular metabolism via the inhibition of the mammalian target of rapamycin results in dynamic changes in the cell surface MIPs landscape. Moreover, we provide systems-level evidence that the immunopeptidome projects at the cell surface a representation of biochemical networks and metabolic events regulated at multiple levels inside the cell. Our findings open up new perspectives in systems immunology and predictive biology. Indeed, predicting variations in the immunopeptidome in response to cell-intrinsic and -extrinsic factors could be relevant to the rational design of immunotherapeutic interventions.
High-Performance Pattern-Matching for Intrusion Detection (2006)

New generations of network intrusion detection systems create the need for advanced pattern-matching engines. This paper presents a novel scheme for pattern-matching, called BFPM, that exploits a hardware-based programmable statemachine technology to achieve deterministic processing rates that are independent of input and pattern characteristics on the order of 10 Gb/s for FPGA and at least 20 Gb/s for ASIC implementations. BFPM supports dynamic updates and is one of the most storage-efficient schemes in the industry, supporting two thousand patterns extracted from Snort with a total of 32 K characters in only 128 KB of memory.
The role of glycosphingolipid metabolism in the developing brain (2008)

Glycosphingolipids (GSLs) are amphipathic lipids ubiquitously expressed in all vertebrate cells and body fluids, but they are especially abundant in the nervous system. The synthesis of GSLs generally is initiated in the endoplasmic reticulum and completed in the Golgi apparatus, followed by transportation to the plasma membrane surface as an integral component. The amount and expression patterns of GSLs change drastically in brains during the embryonic to postnatal stages. Recent studies have revealed that GSLs are highly localized in cell surface microdomains and function as important components that mediate signal transduction and cell adhesion. Also in developing brains, GSLs are suggested to play important roles in nervous system formation. Disturbance of GSL expression and metabolism affects brain function, resulting in a variety of diseases, particularly lysosomal storage diseases. In this review, we describe some aspects of the roles of GSLs, especially of gangliosides, in brain development.
Optical estimation of fractal dimension for image assessment (1992)

We modeled an optical system for estimation of the fractal dimension to provide a measure of surface roughness for an entire image and for image segmentation. Although the simulated optical result was similar to that calculated by digital techniques, both suffered from problems known to occur with estimating fractal dimension. Furthermore, the optical estimation did not have as good a resolution as that obtained with digital estimates due primarily to the limited dynamic range of the detector.
Expansion of mesenchymal stem cells using a microcarrier-based cultivation system: growth and metabolism (2008)

For the continuous and fast expansion of mesenchymal stem cells (MSCs), microcarriers have gained increasing interest. The aim of this study was to evaluate the growth and metabolism profiles of MSCs, expanded in a microcarrier-based cultivation system. We investigated various cultivation conditions to expand goat mesenchymal stem cells on Cytodex 1 microcarriers. These conditions differed in feeding regime, i.e. the addition of fresh proliferation medium, with or without new microcarriers. For all conditions, cell attachment, cell proliferation, energy source consumption, metabolite production, and cell distribution on the microcarriers were studied. Attachment efficiencies of 40% were obtained followed by successful expansion up to 15 cultivation days. Depending on the feeding regime, an exponential growth, stationary growth, and decline growth phase could be distinguished. Addition of 30% fresh medium containing microcarriers every three days showed the longest continuous proliferation of goat MSCs on microcarriers. This feeding regime has the advantage that metabolites, such as ammonia, are diluted and that new energy sources, such as glucose and glutamine, and additional surface area are provided to the cells. In addition, by adding extra microcarriers a more homogenous cell distribution on the microcarriers is obtained as a result of bead-to-bead transfer. A correlation between nutrient consumption, metabolite production and cell growth was observed. The decreasing yield of lactate from glucose over time indicated a possible shift in cellular metabolism.
A taxonomy for networked virtual environments (1997)

We discuss virtual environments in the context of how to distribute network communications, views, data, and processes while emphasizing those aspects critical to scaling environments. Systems that demand strong data consistency, causality, and reliable communications while supporting real-time interaction are not likely to scale very well. Furthermore, geographically dispersed systems require high-speed, multicast communication.
Capturing the Natural Diversity of the Human Antibody Response against Vaccinia Virus (2010)

The eradication of smallpox (variola) and the subsequent cessation of routine vaccination have left modern society vulnerable to bioterrorism employing this devastating contagious disease. The existing, licensed vaccines based on live vaccinia virus (VACV) are contraindicated for a substantial number of people, and prophylactic vaccination of large populations is not reasonable when there is little risk of exposure. Consequently, there is an emerging need to develop efficient and safe therapeutics to be used shortly before or after exposure, either alone or in combination with vaccination. We have characterized the human antibody response to smallpox vaccine (VACV Lister) in immunized volunteers and isolated a large number of VACV-specific antibodies that recognize a variety of different VACV antigens. Using this broad antibody panel, we have generated a fully human, recombinant analogue to plasma-derived vaccinia immunoglobulin (VIG), which mirrors the diversity and specificity of the human antibody immune response and offers the advantage of unlimited supply and reproducible specificity and activity. The recombinant VIG was found to display a high specific binding activity toward VACV antigens, potent in vitro VACV neutralizing activity, and a highly protective efficacy against VACV challenge in the mouse tail lesion model when given either prophylactically or therapeutically. Altogether, the results suggest that this compound has the potential to be used as an effective postexposure prophylaxis or treatment of disease caused by orthopoxviruses.
Structure of the Nucleotide-Diphospho-Sugar Transferase, SpsA from Bacillus subtilis, in Native and Nucleotide-Complexed Forms, (1999)

The enzymatic formation of glycosidic bonds may be catalyzed by the transfer of the glycosyl moiety from an activated nucleotide-diphospho-sugar donor to a specific acceptor. SpsA is a glycosyltransferase implicated in the synthesis of the spore coat of Bacillus subtilis, whose homologues include cellulose synthase and many lipopolysaccharide and bacterial O-antigen synthases. The three-dimensional crystal structure of SpsA has been determined by conventional MIR techniques at a resolution of 1.5 A. It is a two-domain protein with a nucleotide-binding domain together with an acceptor binding domain which features a disordered loop spanning the active site. The structures of SpsA in complex with both Mg-UDP and Mn-UDP have also been determined at 2.0 and 1.7 A, respectively. These complexes, together with the sequence conservation, begin to shed light on the mechanism of this ubiquitous family of inverting glycosyltransferases.
Human genetic diseases of proteolysis (1999)

Although in the past protein stability commonly has been considered an inherent property of a given protein, the truth is far more complex. Elaborate enzymatic systems exist in multiple intracellular compartments to hydrolyze proteins. These systems are capable of providing a sensitive mechanism to regulate protein expression, a mechanism that is complementary to the transcriptional and translational control mechanisms that influence protein synthesis. The power of regulated proteolysis has been well-demonstrated in the abrupt degradation of cyclins that underlies eukaryotic cell cycle progression. Coincidental with the recent rapid gains in understanding proteolysis at a biochemical level, several human diseases have been found to result from disordered proteolysis. This article reviews several examples of human disease resulting from mutations of genes encoding serine proteases, cysteine proteases, and their inhibitors. Examples are also presented of human diseases resulting from disorders in the highly intricate ubiquitin-proteasome pathway of protein degradation. It is certain that many more human diseases will be associated in the future with disorders of proteolysis.
Inhibition of merozoite invasion and transient de-sequestration by sevuparin in humans with Plasmodium falciparum malaria (2017)

ClinicalTrials.gov NCT01442168.