gebhart/patrepeval huggingface dataset:
Transfection of myeloid cell lines using polybrene/DMSO (1988)

Journal Article Transfection of myeloid cell lines using polybrene/DMSO Get access Orin Chisholm, Orin Chisholm Children's Medical Research Foundation, Children's Hospital and University of SydneyCamperdown, NSW 2050, Australia Search for other works by this author on: Oxford Academic PubMed Google Scholar Geoff Symonds Geoff Symonds Children's Medical Research Foundation, Children's Hospital and University of SydneyCamperdown, NSW 2050, Australia Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 16, Issue 5, 11 March 1988, Page 2352, https://doi.org/10.1093/nar/16.5.2352 Published: 11 March 1988 Article history Received: 23 December 1987 Published: 11 March 1988
Metal film removal and patterning using a XeCl laser (1983)

Single-shot removal of thin metal films on various substrates has been studied using a XeCl laser and thresholds compared with theoretical modeling of the interaction. Low thresholds and potential for micron resolution with large area projection patterning techniques are demonstrated.
Expression of the Gene for Mouse Lactate Dehydrogenase C (Ldhc) Is Required for Male Fertility1 (2008)

The lactate dehydrogenase (LDH) protein family members characteristically are distributed in tissue- and cell type-specific patterns and serve as the terminal enzyme of glycolysis, catalyzing reversible oxidation reduction between pyruvate and lactate. They are present as tetramers, and one family member, LDHC, is abundant in spermatocytes, spermatids, and sperm, but also is found in modest amounts in oocytes. We disrupted the Ldhc gene to determine whether LDHC is required for spermatogenesis, oogenesis, and/or sperm and egg function. The targeted disruption of Ldhc severely impaired fertility in male Ldhc(-/-) mice but not in female Ldhc(-/-) mice. Testis and sperm morphology and sperm production appeared to be normal. However, total LDH enzymatic activity was considerably lower in Ldhc(-/-) sperm than in wild type sperm, indicating that the LDHC homotetramer (LDH-C(4)) is responsible for most of the LDH activity in sperm. Although initially motile when isolated, there was a more rapid reduction in the level of ATP and in motility in Ldhc(-)(/-) sperm than in wild-type sperm. Moreover, Ldhc(-/-) sperm did not acquire hyperactivated motility, were unable to penetrate the zona pellucida in vitro, and failed to undergo the phosphorylation events characteristic of capacitation. These studies showed that LDHC plays an essential role in maintenance of the processes of glycolysis and ATP production in the flagellum that are required for male fertility and sperm function.
Resource management with virtual paths in ATM networks (1996)

A virtual path connection (VPC) is a labelled path which can be used to transport a bundle of virtual channel connections (VCCs) and to manage the resources used by these connections. The virtual network is organized as a collection of VPCs which form a VPC, or logical, overlay network. If the VPCs are permanent or semi-permanent and have reserved capacity, establishing new VCCs requires simple connection admission decisions at the VPC terminators of existing VPCs. This would enable faster connection establishment since transit nodes are not involved in the connection setup. The virtual path concept also allows the possibility of segregating traffic types according to quality of service requirements. However, the extent to which VPC provisioning is able to improve network efficiency is dependent on the resource management decisions that determine the VPC topology and capacity allocations. The article surveys resource management using virtual paths in an ATM network. Of interest are techniques which modify the VPC topology and capacity assignments in order to adapt to changing traffic conditions and possible network failures. The resource management activities employed to facilitate such adaptation can be categorized by the timescale on which they operate. On the shortest timescale are strategies for dynamically making minor changes to the VPC topology or capacity assignments. On a somewhat longer timescale are strategies for making more widespread modifications to the VPC overlay network. This would be appropriate for traffic changes based on time of day and for recovering from network failures. Finally, on an even longer timescale, strategies may be employed to design a general VPC overlay network, to be used at startup or after major network upgrades. Solutions to VPC resource management for each of these timescales are discussed.
Antioxidant Treatment of Patients With Friedreich Ataxia (2005)

This therapy resulted in sustained improvement in mitochondrial energy synthesis that was associated with a slowing of the progression of certain clinical features and a significant improvement in cardiac function.
Building a Casimir metrology platform with a commercial MEMS sensor (2019)

The Casimir Effect is a physical manifestation of quantum fluctuations of the electromagnetic vacuum. When two metal plates are placed close together, typically much less than a micron, the long wavelength modes between them are frozen out, giving rise to a net attractive force between the plates, scaling as <i>d</i> <sup>-4</sup> (or <i>d</i> <sup>-3</sup> for a spherical-planar geometry) even when they are not electrically charged. In this paper, we observe the Casimir Effect in ambient conditions using a modified capacitive micro-electromechanical system (MEMS) sensor. Using a feedback-assisted pick-and-place assembly process, we are able to attach various microstructures onto the post-release MEMS, converting it from an inertial force sensor to a direct force measurement platform with pN (piconewton) resolution. With this system we are able to directly measure the Casimir force between a silver-coated microsphere and gold-coated silicon plate. This device is a step towards leveraging the Casimir Effect for cheap, sensitive, room temperature quantum metrology.
Patterns of Expression of Human “Ia-Like” Antigens during the Terminal Stages of B Cell Development (1978)

Abstract The “Ia-like” antigens characteristically present on the membrane of B lymphocytes were shown to be absent in most terminally differentiated Ig-producing plasma cells. This was most evident in analyses of myeloma plasma cells that uniformly lacked the Ia-antigens. Also, in B lymphoid cell lines, the lymphoblasts were uniformly Ia-positive but the plasma cells were negative. In contrast, however, the majority of plasma cells produced after pokeweed mitogen stimulation remained positive. Plasma cells in tonsil and in the tissue of peripheral blood of patients with Waldenström's macroglobulinemia were also sometimes Ia-positive although the majority were negative. Studies of membrane IgM and IgD indicated a similar loss in some instances. However, the SIg and Ia antigens were not invariably associated. These results lead to the conclusion that Ia-antigens are differentiation antigens for B cells and are usually lost by the end stage cells in this series.
Spinal Muscular Atrophy (2001)

The spinal muscular atrophies are a group of mostly inherited disorders selectively affecting the lower motor neuron. There is a wide degree of clinical and genetic heterogeneity that must be taken into account when giving prognostic information. Autosomal recessive childhood proximal SMA is the commonest form and is due to mutations in a gene encoding a novel protein, SMN, that appears to play a critical role in RNA metabolism but has also been shown to interact with actin-binding proteins and mediators of programmed cell death. The identification of the genetic basis of SMA has resulted in advances for prenatal diagnosis and in new insights into motor neuron biology. The chromosomal location of two of the rarer dominant forms of SMA has been found. Identification of the molecular pathophysiology of lower motor neuron syndromes can be expected to aid in the development of therapy for these disabling disorders.
USE OF MONOTELOTRISOMICS FOR LINKAGE MAPPING IN BARLEY (1972)

Analysis of bulk F 2 progenies from monotelotrisomic hybrids for two known genes f c and br showed that the gene-centromere distance and frequency of homozygous recessive F 2 segregates were inversely related. Based on this relationship the new genes sb, ea, gs3, f5 were assigned to positions on chromosome 1 relative to the previously mapped genes. The centromere position on chromosome 1 was located between the markers rs and n. Two previously undescribed recessive mutants, revoluted leaf (rvl) and Parkland spot (sp,,b), were associated with the long arm of chromosome 5 through the use of monotelotrisomic 14 + 5L.
Person Re-identification in the Wild (2016)

We present a novel large-scale dataset and comprehensive baselines for end-to-end pedestrian detection and person recognition in raw video frames. Our baselines address three issues: the performance of various combinations of detectors and recognizers, mechanisms for pedestrian detection to help improve overall re-identification accuracy and assessing the effectiveness of different detectors for re-identification. We make three distinct contributions. First, a new dataset, PRW, is introduced to evaluate Person Re-identification in the Wild, using videos acquired through six synchronized cameras. It contains 932 identities and 11,816 frames in which pedestrians are annotated with their bounding box positions and identities. Extensive benchmarking results are presented on this dataset. Second, we show that pedestrian detection aids re-identification through two simple yet effective improvements: a discriminatively trained ID-discriminative Embedding (IDE) in the person subspace using convolutional neural network (CNN) features and a Confidence Weighted Similarity (CWS) metric that incorporates detection scores into similarity measurement. Third, we derive insights in evaluating detector performance for the particular scenario of accurate person re-identification.
Expression of basic fibroblast growth factor and its receptor in the retina of Royal College of Surgeons rats. A comparative study. (1993)

Although the mutant gene in RCS rats is expressed in the RPE cells, these results suggest that there is no significant defect in bFGF or bFGF-R expression in the RPE cells of RCS rats, which would be an initiating factor in the development of photoreceptor degeneration in these animals. The lowered bFGF levels in the neural retina at early stages (postnatal day 21) may explain the prolongation of photoreceptor survival when exogenous bFGF is injected.
Josephson parametric converter saturation and higher order effects (2017)

Microwave parametric amplifiers based on Josephson junctions have become indispensable components of many quantum information experiments. One key limitation which has not been well predicted by theory is the gain saturation behavior which limits the amplifier's ability to process large amplitude signals. The typical explanation for this behavior in phase-preserving amplifiers based on three-wave mixing, such as the Josephson Parametric Converter, is pump depletion, in which the consumption of pump photons to produce amplification results in a reduction in gain. However, in this work, we present experimental data and theoretical calculations showing that the fourth-order Kerr nonlinearities inherent in Josephson junctions are the dominant factor. The Kerr-based theory has the unusual property of causing saturation to both lower and higher gains, depending on bias conditions. This work presents an efficient methodology for optimizing device performance in the presence of Kerr nonlinearities while retaining device tunability and points to the necessity of controlling higher-order Hamiltonian terms to make further improvements in parametric devices.
Optimization of Multiple Transverse Hydraulic Fractures in Horizontal Wellbores (2010)

Abstract Hydraulic fracturing and horizontal drilling are the two key technologies that have made the development of unconventional shale formations economical. Hydraulic fracturing has been the major and relatively inexpensive stimulation method used for enhanced oil and gas recovery in the petroleum industry since 1949. The multi-stage and multicluster per stage fracture treatments in horizontal wellbores create a large stimulated reservoir volume (SRV) that increases both production and estimated ultimate recovery (EUR). This paper presents a new analytical solution methodology for predicting the behavior of multiple patterned transverse vertical hydraulic fractures intercepting horizontal wellbores. The numerical solution is applicable for finite-conductivity vertical fractures in rectangular shaped reservoirs. The mathematical formulation is based on the method of images with no flow boundaries for symmetrical patterns. An economics procedure is also presented for optimizing transverse fracture spacing and number of fracture stages/clusters to maximize the Net Present Value (NPV) and Discounted Return on Investment (DROI). The advantages of this approximate analytical production solution for multiple finite-conductivity vertical transverse fractures in horizontal wells and corresponding optimization procedure include: 1) the solution is based on fundamental engineering principles, 2) the production and interference of multiple transverse fractures are predicted to a first-order, and 3) it provides the basis for optimizing fracture and cluster spacing based on NPV and DROI, not just initial production rate. The methodology provides a simple way to predict the production behavior (including interaction) and associated economics of multi-stage/multi-cluster transverse fracture spacing scenarios in horizontal wellbores. The high initial production (IP) rates from multiple transverse fractures and the late time production decline as a result of fracture interference is discussed. Numerous examples are presented illustrating the method for optimizing (maximizing NPV and DROI) multiple transverse vertical hydraulic fractures in horizontal wellbores. Application of this technique will help provide the design engineer with a better tool for designing and optimizing multi-stage/multi-cluster transverse hydraulic fractures in horizontal wellbores. The governing production equations and fundamental procedure for NPV and DROI optimization of transverse fractures in a horizontal wellbore are discussed.
Challenge for future semiconductor development (2003)

Progress in LSI technology has led to the concept of system-on-chip (SOC) that is still evolving to meet various applications for information processing and networking. SOC is composed of different IP cores such as MPU, RAM, RF, Analog, ASIC, DSP, Flash memory and even sensors. To realize high-performance and low power consumption in SOC, the design and fabrication of such complex systems need to overcome difficult technology roadblocks. This paper reviews key issues on 65 to 45nm node CMOS technology and related R&D challenges, together with the future prospects of silicon technology.
Bacterial Vaccine Vectors and Bacillus Calmette-Guerin (1995)

Recent advances in biotechnology now allow a more modern approach to the development of vaccines, particularly that of recombinant vaccines. Bacterial vaccine vectors have the advantage over viral vectors in that the former have the ability to express a greater number of antigens in different forms. Although no recombinant bacterial vaccines are currently in use, bacillus Calmette-Guérin (BCG), Salmonella species, and Escherichia coli are being developed as vaccine vectors. We review plasmid systems and mutant strains developed for the expression of foreign antigens, with particular emphasis on those developed for BCG. We describe the development of antigen expression systems as well as the immune response elicited by recombinant BCG vaccine strains to bacterial and human immunodeficiency virus (HIV) antigens. A modified recombinant BCG carrier with selection for the stable maintenance of rDNA is proposed.
Interdomain movements in metabotropic glutamate receptor activation (2011)

Many cell surface receptors are multimeric proteins, composed of several structural domains, some involved in ligand recognition, whereas others are responsible for signal transduction. In most cases, the mechanism of how ligand interaction in the extracellular domains leads to the activation of effector domains remains largely unknown. Here we examined how the extracellular ligand binding to the venus flytrap (VFT) domains of the dimeric metabotropic glutamate receptors activate the seven transmembrane (7TM) domains responsible for G protein activation. These two domains are interconnected by a cysteine-rich domain (CRD). We show that any of the four disulfide bridges of the CRD are required for the allosteric coupling between the VFT and the 7TM domains. More importantly, we show that a specific association of the two CRDs corresponds to the active state of the receptor. Indeed, a specific crosslinking of the CRDs with intersubunit disulfide bridges leads to fully constitutively active receptors, no longer activated by agonists nor by allosteric modulators. These data demonstrate that intersubunit movement at the level of the CRDs represents a key step in metabotropic glutamate receptor activation.
Involvement of heparin affin regulatory peptide in human prostate cancer (1999)

Our results suggest that HARP may act in a paracrine manner from mesenchymal to tumoral epithelial cells, and may play a role in the molecular mechanisms that regulate prostate tumor cell growth.
Carbohydrate markers of pancreatic cancer (2011)

Pancreatic cancer is the fourth most common cause of death from cancer in the world and the sixth in Europe. Pancreatic cancer is more frequent in males than females. Worldwide, following diagnosis of pancreatic cancer, <2% of patients survive for 5 years, 8% survive for 2 years and <50% survive for only approx. 3 months. The biggest risk factor in pancreatic cancer is age, with a peak of morbidity at 65 years. Difficulty in the diagnosis of pancreatic cancer causes a delay in its detection. It is one of the most difficult cancers to diagnose and therefore to treat successfully. Additional detection of carbohydrate markers may offer a better diagnosis of pancreatic cancer. Carbohydrate markers of cancer may be produced by the cancer itself or by the body in response to cancer, whose presence in body fluids suggests the presence and growth of the cancer. The most widely used, and best-recognized, carbohydrate marker of pancreatic cancer is CA 19-9 [CA (carbohydrate antigen) 19-9]. However, the relatively non-specific nature of CA 19-9 limits its routine use in the early diagnosis of pancreatic cancer, but it may be useful in monitoring treatment of pancreatic cancer (e.g. the effectiveness of chemotherapy), as a complement to other diagnostic methods. Some other carbohydrate markers of pancreatic cancer may be considered, such as CEA (carcinoembryonic antigen), CA 50 and CA 242, and the mucins MUC1, MUC2 and MUC5AC, but enzymes involved in the processing of glycoconjugates could also be involved. Our preliminary research shows that the activity of lysosomal exoglycosidases, including HEX (N-acetyl-β-D-hexosaminidase), GAL (β-D-galactosidase), FUC (α-L-fucosidase) and MAN (α-D-mannosidase), in serum and urine may be used in the diagnosis of pancreatic cancer.
Induced Codeposition: I. An Experimental Investigation of Ni‐Mo Alloys (1996)

The electrodeposition of nickel‐molybdenum alloys was studied on rotating cylinder electrodes. The current density, electrode rotation rate, electrolyte temperature, and species concentrations were shown to influence alloy composition. The mass‐transport limiting species were identified for different operating conditions and electrolyte compositions in order to study the rate‐limiting steps of induced codeposition. If the concentration of nickel in the electrolyte was much larger than that of molybdate the molybdenum content in the alloy increased with rotation rate. On the other hand, if the concentration of molybdate in the electrolyte was larger than that of nickel the alloy composition was found to be independent of rotation rate. These results were applied to the deposition of compositionally modulated Ni‐Mo alloys exhibiting larger periodic variations in Mo concentration than hitherto reported.
Information Coding in Artificial Olfaction Multisensor Arrays (2003)

High-density sensor arrays were prepared with microbead vapor sensors to explore and compare the information coded in sensor response profiles following odor stimulus. The coded information in the sensor-odor response profiles, which is used for odor discrimination purposes, was extracted from the microsensor arrays via two different approaches. In the first approach, the responses from individual microsensors were separated (decoded array) and independently processed. In the second approach, response profiles from all microsensors within the entire array, i.e., the sensor ensemble, were combined to create one response per odor stimulus (nondecoded array). Although the amount of response data is markedly reduced in the second approach, the system shows comparable odor discrimination rates for the two signal extraction methods. The ensemble approach streamlines system resources without decreasing system performance. These signal compression approaches may simulate or parallel information coding in the mammalian olfactory system.
Next Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows (2012)

Whole-genome and exome sequencing have already proven to be essential and powerful methods to identify genes responsible for simple Mendelian inherited disorders. These methods can be applied to complex disorders as well, and have been adopted as one of the current mainstream approaches in population genetics. These achievements have been made possible by next generation sequencing (NGS) technologies, which require substantial bioinformatics resources to analyze the dense and complex sequence data. The huge analytical burden of data from genome sequencing might be seen as a bottleneck slowing the publication of NGS papers at this time, especially in psychiatric genetics. We review the existing methods for processing NGS data, to place into context the rationale for the design of a computational resource. We describe our method, the Graphical Pipeline for Computational Genomics (GPCG), to perform the computational steps required to analyze NGS data. The GPCG implements flexible workflows for basic sequence alignment, sequence data quality control, single nucleotide polymorphism analysis, copy number variant identification, annotation, and visualization of results. These workflows cover all the analytical steps required for NGS data, from processing the raw reads to variant calling and annotation. The current version of the pipeline is freely available at http://pipeline.loni.ucla.edu. These applications of NGS analysis may gain clinical utility in the near future (e.g., identifying miRNA signatures in diseases) when the bioinformatics approach is made feasible. Taken together, the annotation tools and strategies that have been developed to retrieve information and test hypotheses about the functional role of variants present in the human genome will help to pinpoint the genetic risk factors for psychiatric disorders.