gebhart/patrepeval huggingface dataset:
Cloning and expression of murine immune interferon cDNA. (1983)

The murine immune interferon (IFN-gamma) gene was cloned and expressed under control of the simian virus 40 early promoter in the monkey COS-1 cell line. A protein is secreted from these cells having the biological, antigenic, and biochemical characteristics of natural murine IFN-gamma. Cloned murine IFN-gamma cDNAs were obtained by using RNA from both mitogen-induced murine spleens and the transfected COS cells, and both code for identical proteins. The mature murine IFN-gamma encoded is 136 amino acids long, 10 amino acids shorter than human IFN-gamma. The nucleotide homology between the murine and human IFN-gamma genes is 60-65%, whereas the encoded proteins are only 40% homologous. Murine IFN-gamma cDNA was expressed in Escherichia coli under trp promoter control.
Expression of Central and Peripheral Cannabinoid Receptors in Human Immune Tissues and Leukocyte Subpopulations (1995)

Two proteins with seven transmembrane-spanning domains typical of guanosine-nucleotide-binding-protein-coupled receptors have been identified as cannabinoid receptors; the central cannabinoid receptor, CB1, and the peripheral cannabinoid receptor, CB2, initially described in rat brain and spleen, respectively. Here, we report the distribution patterns for both CB1 and CB2 transcripts in human immune cells and in several human tissues, as analysed using a highly sensitive and quantitative PCR-based method. CB1 was mainly expressed in the central nervous system and, to a lower extent, in several peripheral tissues such as adrenal gland, heart, lung, prostate, uterus, ovary, testis, bone marrow, thymus and tonsils. In contrast, the CB2 gene, which is not expressed in the brain, was particularly abundant in immune tissues, with an expression level 10-100-fold higher than that of CB1. Although CB2 mRNA was also detected in some other peripheral tissues, its level remained very low. In spleen and tonsils, the CB2 mRNA content was equivalent to that of CB1 mRNA in the central nervous system. Among the main human blood cell subpopulations, the distribution pattern of the CB2 mRNA displayed important variations. The rank order of CB2 mRNA levels in these cells was B-cells > natural killer cells >> monocytes > polymorphonuclear neutrophil cells > T8 cells > T4 cells. The same rank order was also established in human cell lines belonging to the myeloid, monocytic and lymphoid lineages. The prevailing expression of the CB2 gene in immune tissues was confirmed by Northern-blot analysis. In addition, the expression of the CB2 protein was demonstrated by an immunohistological analysis performed on tonsil sections using specific anti-(human CB2) IgG; this experiment showed that CB2 expression was restricted to B-lymphocyte-enriched areas of the mantle of secondary lymphoid follicles. These results suggest that (a) CB1 and CB2 can be considered as tissue-selective antigens of the central nervous system and immune system, respectively, and (b) cannabinoids may exert specific receptor-mediated actions on the immune system through the CB2 receptor.
An acoustic automotive engine oil quality sensor (2002)

A prototype model of an on-board automotive engine oil quality sensor is presented. The sensor utilizes changes in oil viscosity as an indicator of the oil quality. The sensor is capable of differentiating between engine oils of different grades and monitoring the degradation processes of oils due to their use in automotive engines and due to artificial contamination by dilution with water, ethylene glycol, and gasoline.
Representation of Concurrency with Ordering Matrices (1973)

A formal technique for the representation of tasks such that the potential concurrency of the task is detectable, and hence exploitable, during the execution of the task is described. Instructions are represented as a pair of binary vectors d and ê which completely describe the sources and sinks specified by the instruction. Tasks are represented as square matrices M called ordering matrices. The values of the elements of these matrices are used to dynamically indicate the necessary ordering of the execution of instructions. It is shown how several different types of ordering matrices, each type having the capability of exhibiting different amounts of potential concurrency, can be calculated from the d and ê vectors of the instructions of a task using ``linear algebraic-like'' operations. For example, intercycle independencies can be detected with a ternary ordering matrix. This matrix can be extended to dynamically detect opportunities for reassigning the resources specified by certain instructions to increase the amount of potential concurrency. Experimental results are presented showing the relative capability of each of these matrix types for exhibiting potential concurrency. These techniques are shown to produce somewhat greater amounts of potential concurrency than other known dynamic techniques. However, the amounts of potential concurrency found are less than those reported for preprocessing detection techniques.
Human retroviruses and AIDS, 1991. [CONTAINS GLOSSARY] (1991)

This compendium and the accompanying floppy diskettes are the result of an effort to compile and rapidly publish all relevant molecular data concerning the human immunodeficiency viruses (HIV) and related retroviruses.The scope of the compendium and database is best summarized by the five parts that it comprises: (1) HIV and SIV Nucleotide Sequences; (2) Amino Acid Sequences; (3) Analyses; (4) Related Sequences; and (5) Database Communications. Information within all the parts is updated at least twice in each year, which accounts for the modes of binding and pagination in the compendium.
The Distribution of Mycobacterium avium ssp. paratuberculosis in the Environment Surrounding Minnesota Dairy Farms (2004)

The objective of this study was to characterize the distribution of Mycobacterium paratuberculosis (Map) in the environment of infected and uninfected Minnesota dairy farms. Eighty herds known to be infected from Minnesota's Johne's Disease Control Program (JDCP) and 28 herds known to be uninfected from Minnesota Voluntary Johne's Disease Herd Status Program (VJDHSP) were sampled. Fecal samples from up to 100 cows in each herd were cultured in pools of 5 cows. Two environmental samples were obtained from each farm from various locations. All samples were tested using bacterial culture for Map. Eighty percent of the JDCP herds had at least one positive pool. Environmental samples were cultured positive in 78% of the JDCP herds. Two (7%) of the VJDHSP herds had one positive pool, and one herd had one positive environmental sample. Environmental samples were cultured positive in cow alleyways (77% of the herds), manure storage (68%), calving area (21%), sick cow pen (18%), water runoff (6%), and postweaned calves areas (3%). There was an association between maximum level of colonies per tube from cow alleyways and manure storage and fecal pool prevalence. Herds with both areas cultured negative were estimated to have 0.3 to 4% fecal pool prevalence. Herds with both areas having a heavy load of bacteria were estimated to have 53 to 73% fecal pool prevalence. The study results indicate that targeted sampling of cow alleyways and manure storage areas appears to be an alternative strategy for herd screening and Johne's infection status assessment and for estimating herd fecal prevalence.
Messengers, motors and mysteries: sorting of eukaryotic mRNAs by cytoskeletal transport (2011)

It has become increasingly apparent in recent years that the subcellular localization of specific mRNAs is a prevalent method for spatially controlling gene expression. In most cases, targeting of mRNAs is mediated by transport along cytoskeletal filaments by molecular motors. However, the means by which specific messages are recognized and linked to the motors are poorly understood. Here, I will provide an overview of recent progress in elucidating the molecular mechanisms and principles of mRNA transport, including several studies highlighting the co-operation of different motors during the localization process. Important outstanding questions will also be highlighted.
Cryptography, a primer (1981)

From the Publisher:
The first systematic development of the principles and technology underlying the disguising of text and computer data. Formulates the principles underlying encipherment, analyzes a number of basic systems including the ``Enigma machine,'' and treats applications to data processing: public key systems, electronic signatures, communication and file security.
Amplification of PCR products in excess of 600 base pairs using DNA extracted from decalcified, paraffin wax embedded bone marrow trephine biopsies (2000)

This method enables PCR analyses of PBMT biopsies that were not previously possible, offering the prospect of improved accuracy of diagnosis and the monitoring of patients with bone marrow disease.
hRAD30 Mutations in the Variant Form of Xeroderma Pigmentosum (1999)

Xeroderma pigmentosum (XP) is an autosomal recessive disease characterized by a high incidence of skin cancers. Yeast RAD30 encodes a DNA polymerase involved in the error-free bypass of ultraviolet (UV) damage. Here it is shown that XP variant (XP-V) cell lines harbor nonsense or frameshift mutations in hRAD30, the human counterpart of yeast RAD30. Of the eight mutations identified, seven would result in a severely truncated hRad30 protein. These results indicate that defects in hRAD30 cause XP-V, and they suggest that error-free replication of UV lesions by hRad30 plays an important role in minimizing the incidence of sunlight-induced skin cancers.
Hydrogenation of Carbon Dioxide Catalyzed by Ruthenium Trimethylphosphine Complexes:  The Accelerating Effect of Certain Alcohols and Amines (2002)

A trace amount of alcohol cocatalyst and a stoichiometric amount of base are required during the hydrogenation of CO(2) to formic acid catalyzed by ruthenium trimethylphosphine complexes. Variation of the choice of alcohol and base causes wide variation in the rate of reaction. Acidic, nonbulky alcohols and triflic acid increase the rate of hydrogenation an order of magnitude above that which can be obtained with traditionally used methanol or water. Similarly, use of DBU rather than NEt(3) increases the rate of reaction by an order of magnitude. Turnover frequencies up to 95,000 h(-1) have now been obtained, and even higher rates should be possible using the cocatalyst and amine combinations identified herein. Preliminary in situ NMR spectroscopic observations are described, and the possible roles of the alcohol and base are discussed.
<title>Toward sub-0.1-um CD measurements using scatterometry</title> (1996)

Scatterometry, defined as the angle resolved characterization of light scattered from a surface, is an attractive tool for the metrology of semiconductor devices. It is simple, rapid, non destructive, relatively inexpensive and can be used in-situ. This paper illustrates the use of scatterometry to characterize fine pitch gratings having linewidths less than or equal to 0.1 micrometer. These gratings diffract light only in the zeroth order as their pitch-to-wavelength ratio is much smaller than one, hence they are also known as 0-order gratings. Metrology of 0-order gratings brings forth new issues, chiefly (1) lack of diffraction sensitivity to variation in the grating parameters, and (2) non-uniqueness of the 'diffraction signatures.' We use the gratings in conical mounting to enhance the diffraction sensitivity and have circumvented the non-uniqueness issue in two ways: (1) limiting the parameter space of the search algorithm and (2) using different incident field polarizations. We employ constrained optimization techniques to efficiently scan the parameter space. Our results agree well with cross-sectional SEM measurements and demonstrate the feasibility of scatterometry for these structures. We are also using shorter wavelengths for the metrology of 0-order gratings, and preliminary results using (lambda) equals 442 nm demonstrate that the diffraction is more sensitive to the variation in grating linewidth and etch depth.
Relationships Linking Amplification Level to Gene Over-Expression in Gliomas (2010)

Here we show that the tissue-specific pattern of gene expression is maintained upon amplification in gliomas. Our study relies on a single type of tumour and a limited number of cases. However, it strongly suggests that, even when amplified, genes that are normally silent in a given cell type play no role in tumour progression. The loose relationships between mRNA level and protein accumulation and/or activity indicate that translational or post-translational events play a key role in fine-tuning the final outcome of amplification in gliomas.
Peptides with Carboxyl-Terminal Sequence of Alanine—Proline: Detection by a Human Monoclonal Antibody (1995)

A human B lymphoblastoid cell line JWCI-L94 secretes an IgM human monoclonal antibody (HuMAb) that reacts with human melanoma cell lines, M14 and M12. To identify the antigenic epitope of this antibody, we screened lambda gt11 expression libraries constructed from M14 and M12. A total of 12 immunoreactive clones were isolated, and their DNA sequences were determined. The only sequence shared by all these clones was alanine-proline (A-P) at the carboxyl (C) terminal. HuMAb L94 reacted not only with C-terminal A-P-containing fusion proteins, but also with the synthetic dipeptide A-P. None of the peptides containing A-P internally or amino terminally reacted to HuMAb L94. Proline or alanine alone had no ability to bind to HuMAb L94. When alanine was replaced by glycine (G-P) or proline (P-P), the binding activity of these peptides was similar to that of A-P. On the other hand, when alanine was replaced by serine, valine, leucine, glutamine, lysine, methionine, phenylalanine, or hydroxyl proline, the resulting peptide completely lost the antigenic activity of HuMAb L94. These results demonstrate that HuMAb L94 recognizes C-terminal A-P, G-P, or P-P, and that a human antibody can recognize peptides as small as a two-amino acid residue.
Critical respiratory failure in pregnancy complicated with COVID-19: A case report (2021)

The case is presented of a 29-year-old primiparous woman who was COVID-19-positive at 34 weeks of gestation and who developed severe acute respiratory distress syndrome. After a four-day history of fever and mild dyspnea, she was referred to hospital. Ciclesonide, dexamethasone, heparin sodium, and sulbactam/ampicillin were initiated, followed by remdesivir and tocilizumab. On the fourth day after admission (at 34 weeks 5 days of gestation), respiratory failure required ventilator management. An emergency cesarean section was performed and a 2565-g male infant was delivered with an Apgar score of 8/8 and negative COVID-19 status. However, on the following day the patient's respiratory condition deteriorated and mechanical ventilation was initiated. Subsequently, her respiratory condition quickly improved and mechanical ventilation was terminated 4 days after intubation. She was discharged 12 days after cesarean delivery. Our case provides additional evidence that raises concerns regarding the unfavorable maternal consequences of COVID-19 infection during pregnancy.
Systematic Investigation of Preparing Biocompatible, Single, and Small ZnS-Capped CdSe Quantum Dots with Amphiphilic Polymers (2008)

The successful transfer of nanoparticles between solvents is critical for many applications. We evaluated the impact of amphiphilic polymer composition on the size, transfer efficiency, and biocompatibility of tri-n-octylphosphine oxide/hexadecylamine-stabilized semiconductor ZnS-capped CdSe and CdS-capped CdTe(x)Se(1-x) quantum dots (QDs). We also investigated the adsorption of various proteins onto the surface of these QDs and studied the effect of surface chemistry on non-specific protein binding. The results from these studies will have implications in the design of QDs and other nanoparticles for biological and biomedical applications.
Flavivirus-induced antibody cross-reactivity (2011)

Dengue viruses (DENV) cause countless human deaths each year, whilst West Nile virus (WNV) has re-emerged as an important human pathogen. There are currently no WNV or DENV vaccines licensed for human use, yet vaccines exist against other flaviviruses. To investigate flavivirus cross-reactivity, sera from a human cohort with a history of vaccination against tick-borne encephalitis virus (TBEV), Japanese encephalitis virus (JEV) and yellow fever virus (YFV) were tested for antibodies by plaque reduction neutralization test. Neutralization of louping ill virus (LIV) occurred, but no significant neutralization of Murray Valley encephalitis virus was observed. Sera from some individuals vaccinated against TBEV and JEV neutralized WNV, which was enhanced by YFV vaccination in some recipients. Similarly, some individuals neutralized DENV-2, but this was not significantly influenced by YFV vaccination. Antigenic cartography techniques were used to generate a geometric illustration of the neutralization titres of selected sera against WNV, TBEV, JEV, LIV, YFV and DENV-2. This demonstrated the individual variation in antibody responses. Most sera had detectable titres against LIV and some had titres against WNV and DENV-2. Generally, LIV titres were similar to titres against TBEV, confirming the close antigenic relationship between TBEV and LIV. JEV was also antigenically closer to TBEV than WNV, using these sera. The use of sera from individuals vaccinated against multiple pathogens is unique relative to previous applications of antigenic cartography techniques. It is evident from these data that notable differences exist between amino acid sequence identity and mapped antigenic relationships within the family Flaviviridae.
Enhancement of slow wave sleep: implications for insomnia. (2009)

Slow wave sleep (SWS) is defined as the sum of stage 3 and stage 4 sleep and is characterized by high-voltage, synchronized electroencephalographic (EEG) waveforms, often measured as slow wave activity (SWA). SWS has been widely hypothesized to be a time of relatively heightened neurophysiologic restoration or recuperation.1,2 This viewpoint is prompted by a number of observations including: (1) enhanced SWA following sleep deprivation in proportion to the duration of prior wakefulness3; (2) reduced SWA during nocturnal sleep following afternoon/evening naps4; (3) a gradual decline in SWA across a night of sleep5; and (4) increased SWS following nights of fragmented sleep.6 Within the two-process model of sleep regulation, heightened SWS/SWA has been viewed as reflecting Process S, the homeostatic component.7 Other authors have proposed that increased SWS/SWA represents ongoing cortical recovery from activities during prior wakefulness.8

A number of agents have been found to increase the time spent in SWS (Table 1). Interestingly, despite the common observation of enhanced SWS, these drugs have several different mechanisms of action. For example, tiagabine is an inhibitor of GAT-1, one of four transporter proteins that promote the reuptake of γ-aminobutyric acid (GABA) into presynaptic terminals and surrounding glial cells. GAT-1 inhibition results in increased synaptic levels of GABA9 and heightened inhibitory activity. In contrast, gaboxadol is an extrasynaptic GABAA receptor agonist that is selective for δ receptors.10 When activated, α4-δ receptors produce a tonic inhibitory conductance, which is thought to result in a more stable inhibitory pattern compared with phasic synaptic inhibition.11 Other drugs have no direct GABAergic effects yet also increase SWS. Examples include α2-δ calcium channel ligands (e.g., gabapentin and pregabalin), serotonin (5HT)2A receptor antagonists (e.g., eplivanserin and ritanserin), and drugs that are active at multiple receptors (e.g., mirtazapine, trazodone, and olanzapine).



Table 1

Drugs Known to Increase Slow Wave Sleep



The availability of drugs that increase SWS has led to research on the behavioral and phenomenologic correlates of pharmacologic SWS enhancement. This article examines the pharmacologic enhancement of SWS with emphasis on two studies12,13 designed to determine whether increasing SWS (with either tiagabine or gaboxadol) reduces the established neurobehavioral and physiologic deficits associated with sleep restriction. In addition, the potential role of SWS enhancement as a novel approach to the treatment of insomnia is considered.
MicroRNA expression in Sézary syndrome: identification, function, and diagnostic potential (2010)

MicroRNAs are commonly aberrantly expressed in many cancers. Very little is known of their role in T-cell lymphoma, however. We therefore elucidated the complete miRNome of purified T cells from 21 patients diagnosed with Sézary Syndrome (SzS), a rare aggressive primary cutaneous T-cell (CD4(+)) lymphoma. Unsupervised cluster analysis of microarray data revealed that the microRNA expression profile was distinct from CD4(+) T-cell controls and B-cell lymphomas. The majority (104 of 114) of SzS-associated microRNAs (P < .05) were down-regulated and their expression pattern was largely consistent with previously reported genomic copy number abnormalities and were found to be highly enriched (P < .001) for aberrantly expressed target genes. Levels of miR-223 distinguished SzS samples (n = 32) from healthy controls (n = 19) and patients with mycosis fungoides (n = 11) in more than 90% of samples. Furthermore, we demonstrate that the down-regulation of intronically encoded miR-342 plays a role in the pathogenesis of SzS by inhibiting apoptosis, and describe a novel mechanism of regulation for this microRNA via binding of miR-199a* to its host gene. We also provide the first in vivo evidence for down-regulation of the miR-17-92 cluster in malignancy and demonstrate that ectopic miR-17-5p expression increases apoptosis and decreases cell proliferation in SzS cells.
Cross-spectral analysis of physiological tremor and muscle activity. I. Theory and application to unsynchronized EMG (1998)

We investigate the relationship between the extensor electromyogram (EMG) and tremor time series in physiological hand tremor by cross-spectral analysis. Special attention is directed to the phase spectrum and the effects of observational noise. We calculate the theoretical phase spectrum for a second order linear stochastic process and compare the results to measured tremor data recorded from subjects who did not show a synchronized EMG activity in the corresponding extensor muscle. The results show that physiological tremor is well described by the proposed model and that the measured EMG represents a Newtonian force by which the muscle acts on the hand.
The Tale of the TALEs (2012)

Biologists have turned plant pest proteins into tools for studying and reshaping genomes of many species.
Enhanced tolerance to bacterial pathogens caused by the transgenic expression of barley lipid transfer protein LTP2 (1997)

Purified lipid transfer protein LTP2 from barley applied on tobacco leaves eliminated symptoms caused by infiltration of Pseudomonas syringae pv. tabaci 153. Growth of the pathogen in leaves of transgenic tobacco plants was retarded when compared with non-transformed controls. The percentage of inoculation points that showed necrotic lesions was greatly reduced in transgenic tobacco (17-38% versus 78%) and the average size of these lesions was 61-81% that of control. The average total lesion area (necrosis and chlorosis) in the transgenic plants was also reduced (38% of control). Arabidopsis thaliana transgenic plants inoculated with P. syringae pv. tomato DC3000 also had lower percentages of necrotic lesions (22-38% versus 76%), a reduced average area for each lesion (53-67% of control), and a smaller total lesion area per inoculation (43% of control). These results further support the assignment of a defense role for LTPs and highlight their biotechnological potential.