gebhart/patrepeval huggingface dataset:
A carboxyl-terminal interaction of lamin B1 is dependent on the CAAX endoprotease Rce1 and carboxymethylation (2003)

The mammalian nuclear lamina protein lamin B1 is posttranslationally modified by farnesylation, endoproteolysis, and carboxymethylation at a carboxyl-terminal CAAX motif. In this work, we demonstrate that the CAAX endoprotease Rce1 is required for lamin B1 endoproteolysis, demonstrate an independent pool of proteolyzed but nonmethylated lamin B1, as well as fully processed lamin B1, in interphase nuclei, and show a role for methylation in the organization of lamin B1 into domains of the nuclear lamina. Deficiency in the endoproteolysis or methylation of lamin B1 results in loss of integrity and deformity of the nuclear lamina. These data show that the organization of the nuclear envelope and lamina is dependent on a mechanism involving the methylation of lamin B1, and they identify a potential mechanism of laminopathy involving a B-type lamin.
Silicon nitride direct bonding (1990)

Direct bonding has been accomplished between silicon nitride coated wafers and both nitride coated and uncoated silicon wafers. Successful bonding occurred when the initial nitride was hydrophilic as deposited or the nitride surface is rendered hydrophilic by a wet oxidation process prior to bonding.
An efficient approach to finding Siraitia grosvenorii triterpene biosynthetic genes by RNA-seq and digital gene expression analysis (2011)

A combination of RNA-seq and DGE analysis based on the next generation sequencing technology was shown to be a powerful method for identifying candidate genes encoding enzymes responsible for the biosynthesis of novel secondary metabolites in a non-model plant. Seven CYP450s and five UDPGs were selected as potential candidates involved in mogrosides biosynthesis. The transcriptome data from this study provides an important resource for understanding the formation of major bioactive constituents in the fruit extract from S. grosvenorii.
<title>Metering: a prepay technique</title> (1997)

The SPYRUS Metering System allows intellectual property suppliers to control access to electronic information with content-based meters. Information is distributed to users in encrypted form, and each user has a hardware token that contains the cryptographic keys necessary to decrypt the information as well as the meters that control the use of each key. The hardware token will not grant access to the information by decrypting it unless the supplier provided meter constraints are met. Since the hardware token includes a built-in real time clock, time-based meters can be enforced without relying on the easily modified computer system clock.
LDGM Codes for Channel Coding and Joint Source-Channel Coding of Correlated Sources (2005)

We propose a coding scheme based on the use of systematic linear codes with low-density generator matrix (LDGM codes) for channel coding and joint source-channel coding of multiterminal correlated binary sources. In both cases, the structures of the LDGM encoder and decoder are shown, and a concatenated scheme aimed at reducing the error floor is proposed. Several decoding possibilities are investigated, compared, and evaluated. For different types of noisy channels and correlation models, the resulting performance is very close to the theoretical limits.
Ligand-independent Activation of the Androgen Receptor by Interleukin-6 and the Role of Steroid Receptor Coactivator-1 in Prostate Cancer Cells (2002)

The androgen receptor (AR) can be activated in the absence of androgens by interleukin-6 (IL-6) in human prostate cancer cells. The events involved in ligand-independent activation of the AR are unknown, but have been suggested to involve phosphorylation of the AR itself or a receptor-associated protein. Steroid receptor coactivator-1 (SRC-1) has been shown to interact with the human AR and to modulate ligand-dependent AR transactivation and is regulated by phosphorylation by MAPK. To date, no one has examined the role of SRC-1 in ligand-independent activation of the AR by IL-6 or other signaling pathways known to activate the full-length receptor. This study addressed this and has revealed the following. 1) SRC-1 similarly enhanced ligand-independent activation of the AR by IL-6 to the same magnitude as that obtained via ligand-dependent activation. 2) Androgen and IL-6 stimulated the MAPK pathway. 3) MAPK was required for both ligand-dependent and ligand-independent activation of the AR. 4) Phosphorylation of SRC-1 by MAPK was required for optimal ligand-independent activation of the AR by IL-6. 5) Protein-protein interaction between endogenous AR and SRC-1 was dependent upon treatment of LNCaP cells with IL-6 or R1881. 6) Protein-protein interaction between the AR N-terminal domain and SRC-1 was independent of MAPK. 7) Ligand-independent activation of the AR did not occur by a mechanism of overexpression of either solely wild-type SRC-1 or mutant SRC-1 that mimics its phosphorylated form.
Role of conjugation and red blood cells for inactivation of circulating catecholamines (1984)

We investigated the extent of catecholamine (CA) conjugation in plasma and accumulation inside red blood cells (RBCs) after forced immobilization of the rat. A control blood sample was obtained from undisturbed rats resting in home cages via an indwelling aortic catheter. Then rats were immobilized for 2 h, and blood samples were taken during stress at 15 min and 2 h and at 30 min poststress. Both sulfate and glucuronide conjugates were deconjugated by enzymatic hydrolysis and measured by radioenzymatic thin-layer chromatographic methods. In plasma of resting rats, the major conjugate of norepinephrine (NE) is sulfate and that of epinephrine (E) and dopamine (DA) is glucuronide; total conjugates in plasma are 53, 57, and 97% of total NE, E, and DA, respectively. During stress, sulfate conjugates of NE, E, and DA increased significantly along with free NE, E, and DA. DA glucuronide unexpectedly declined at 2 h of stress and 30 min poststress. Concentrations of free CAs rose in RBCs during stress, as did NE sulfate, the only conjugate present in RBC lysate. We conclude that both CA conjugation and RBC accumulation are enhanced when large amounts of free CA enter the circulation as a result of immobilization stress and that the relative importance of these inactivation pathways is different for the three CAs.
An Investigation of Lithium Ion Insertion into Spinel Structure Li‐Mn‐O Compounds (1996)

Two kinds of spinel structure lithium manganese oxides obtained by a melt‐impregnation method were examined in a lithium nonaqueous cell. The first type shows a voltage profile of a typical spinel electrode with the characteristic two‐step process, which delivers a larger capacity, but fading capacity on cycling (type I). The other type delivers a slightly lower capacity and has ideal rechargeability with a quasi‐one‐step process (type II). The mechanism of the lithium ion insertion into the spinel compound was studied by several physical and chemical methods (differential chronopotentiometric curves, cyclic voltammetry, and open‐circuit voltage measurement). X‐ray diffraction was also used to investigate the structural changes for both types of compounds at different oxidation depths at first charge. The results show that a two‐phase reaction (cubic a0 = 8.154 Å and a0 = 8.072 Å) occurred in the range of 0.1 < x <0.45, and a one‐phase reaction [cubic a0 = 8.163 to 8.247 Å] occurred in the range of 0.45 < x < 1.0 for the first charge for the type I spinel. A one‐phase reaction (cubic a0 = 8.105 to 8.223 Å) was observed over the entire intercalated range of 0.25 < x < 1.04 for the type II spinel compound. The capacity fading on cycling for the type I spinel occurs only in the range of 0.1 < x < 0.45, where the shape of the charge and discharge curves in this range was gradually changed to an S‐shape from and L‐shape during cycling. This is attributed to the fact that the two‐phase structure is transformed to more stable one‐phase structure.
Microfluidic Devices for Bioapplications (2010)

Harnessing the ability to precisely and reproducibly actuate fluids and manipulate bioparticles such as DNA, cells, and molecules at the microscale, microfluidics is a powerful tool that is currently revolutionizing chemical and biological analysis by replicating laboratory bench-top technology on a miniature chip-scale device, thus allowing assays to be carried out at a fraction of the time and cost while affording portability and field-use capability. Emerging from a decade of research and development in microfluidic technology are a wide range of promising laboratory and consumer biotechnological applications from microscale genetic and proteomic analysis kits, cell culture and manipulation platforms, biosensors, and pathogen detection systems to point-of-care diagnostic devices, high-throughput combinatorial drug screening platforms, schemes for targeted drug delivery and advanced therapeutics, and novel biomaterials synthesis for tissue engineering. The developments associated with these technological advances along with their respective applications to date are reviewed from a broad perspective and possible future directions that could arise from the current state of the art are discussed.
Suicide gene therapy of graft-versus-host disease induced by central memory human T lymphocytes (2005)

In allogeneic hematopoietic cell transplantation (allo-HCT), the immune recognition of host antigens by donor T lymphocytes leads to a beneficial graft-versus-leukemia (GvL) effect as well as to life-threatening graft-versus-host disease (GvHD). Genetic modification of T lymphocytes with a retroviral vector (RV) expressing the herpes simplex virus-thymidine kinase (TK) suicide gene confers selective sensitivity to the prodrug ganciclovir (GCV). In patients, the infusion of TK+ lymphocytes and the subsequent administration of GCV resulted in a time-wise modulation of antihost reactivity for a GvL effect, while controlling GvHD. Because activation required for genetic modification with RV may reduce antihost reactivity, we investigated the requirements for maximizing the potency of human TK+ lymphocytes. Whereas T-cell receptor triggering alone led to effector memory (EM) TK+ lymphocytes, the addition of CD28 costimulation through cell-sized beads resulted in the generation of central memory (CM) TK+ lymphocytes. In a quantitative model for GvHD using nonobese diabetic/severely combined immunodeficient mice, CM TK+ lymphocytes were more potent than EM TK+ lymphocytes. GCV administration efficiently controlled GvHD induced by CM TK+ lymphocytes. These results warrant the clinical investigation of CM suicide gene-modified human T lymphocytes for safe and effective allo-HCT.
Diagnostic Devices for Isothermal Nucleic Acid Amplification (2012)

Since the development of the polymerase chain reaction (PCR) technique, genomic information has been retrievable from lesser amounts of DNA than previously possible. PCR-based amplifications require high-precision instruments to perform temperature cycling reactions; further, they are cumbersome for routine clinical use. However, the use of isothermal approaches can eliminate many complications associated with thermocycling. The application of diagnostic devices for isothermal DNA amplification has recently been studied extensively. In this paper, we describe the basic concepts of several isothermal amplification approaches and review recent progress in diagnostic device development.
The effects of head-mounted display mechanics on distance judgments in virtual environments (2004)

In virtual environments that use head-mounted displays (HMD), distance judgments to targets on the ground are compressed, at least when indicated through visually-directed walking tasks. The same tasks performed in the real world yield veridical results over distances ranging from 2m to 25m. This paper describes experiments aimed at determining if mechanical aspects of HMDs such as mass and moments of inertia are responsible for the apparent distortion of distance. Our results indicate that the mechanical aspects of HMDs cannot explain the full magnitude of distance underestimation seen in HMD-based virtual environments, though they may account for a portion of the effect.
Full-field characterization of femtosecond pulses after nonlinear propagation (1998)

Summary form only given. The nonlinear Schrodinger equation is often used to model the evolution of ultrashort pulses. However, as peak powers increase and spot sizes decrease, details surrounding the propagation of femtosecond pulses become unknown. In this context, the measured amplitude and phase of the electric field on a femtosecond time scale is valuable information in the study of light-matter interactions. We use second-harmonic frequency-resolved optical gating (SHG-FROG) and spectral interferometry as tools for tracking the nonlinear propagation of intense femtosecond pulses in fused silica.
Plasmid-mediated susceptibility to intestinal microbial antagonisms in Escherichia coli (1985)

Self-transferable plasmid pIP1100 confers to Escherichia coli an unusually high level of resistance (1 to 2 mg/ml) to erythromycin by production of an erythromycin esterase. The effect of pIP1100 on the destiny of E. coli strains in the intestines of gnotobiotic mice was studied. In germfree mice, pIP1100 was efficiently transferred to a plasmid-free E. coli recipient. Intestinal counts of the donor, the recipient, and the transconjugants were greater than 8.5 log CFU/g of feces. When erythromycin was added to the diet of the mice, counts of the plasmid-bearing strains were only slightly lowered and partial inactivation of erythromycin was observed in the feces. Transfer of pIP1100 also occurred in human-flora-associated mice. In this model all the E. coli strains were subject to microbial antagonisms caused by the anaerobic components of the flora. However, strains harboring pIP1100 were strongly inhibited (less than 2.5 log CFU/g of feces), whereas their plasmid-free counterparts persisted at much higher population levels (greater than 5.2 log CFU/g of feces). The ecological disadvantage conferred by pIP1100 to E. coli when a complex human flora was concomitantly present in the intestine of the mice persisted during erythromycin administration. These results provide an explanation for the low incidence of isolation of highly erythromycin-resistant E. coli strains despite the extensive use of the antibiotic.
Performance of multicarrier DS CDMA systems (1996)

In this paper, we apply a multicarrier signaling technique to a direct-sequence CDMA system, where a data sequence multiplied by a spreading sequence modulates multiple carriers, rather than a single carrier. The receiver provides a correlator for each carrier, and the outputs of the correlators are combined with a maximal-ratio combiner. This type of signaling has the desirable properties of exhibiting a narrowband interference suppression effect, along with robustness to fading, without requiring the use of either an explicit RAKE structure or an interference suppression filter. We use bandlimited spreading waveforms to prevent self-interference, and we evaluate system performance over a frequency selective Rayleigh channel in the presence of partial band interference; we also compare system performance with that of a single-carrier RAKE system.
Quantitative Analysis of Mitoxantrone by Surface-Enhanced Resonance Raman Scattering (2002)

Mitoxantrone is an anticancer agent for which it is important to know the concentration in blood during therapy. Current methods of analysis are cumbersome, requiring a pretreatment stage. A method based on surface-enhanced resonance Raman scattering (SERRS) has been developed using a flow cell and silver colloid as the SERRS substrate. It is simple, sensitive, fast, and reliable. Both blood plasma and serum can be analyzed directly, but fresh serum is preferred here due to reduced fluorescence in the clinical samples available. Fluorescence is reduced further by the dilution of the serum in the flow cell and by quenching by the silver of surface-adsorbed material. The effectiveness of the latter process is dependent on the contact time between the serum and the silver. The linear range encompasses the range of concentrations detected previously in patient samples using HPLC methods. In a comparative study of a series of samples taken from a patient at different times, there is good agreement between the results obtained by HPLC and SERRS with no significant difference between them at the 95% limit. The limit of detection in serum using the final optimized procedure for SERRS was 4.0 x 10(-11) M (0.02 ng/mL) mitoxantrone. The ease with which the SERRS analysis can be carried out makes it the preferred choice of technique for mitoxantrone analysis.
Identification of multiple, differentially expressed messenger RNAs in dermal fibroblasts from patients with systemic sclerosis (1999)

The application of DDRT-PCR to scleroderma research has identified many mRNAs whose altered expression in scleroderma has not yet been described, thus providing new information for further investigation and potential targets for the development of novel therapies.
Calcium/Calmodulin-Dependent Protein Kinase Kinase:  Identification of Regulatory Domains (1997)

We recently cloned a calmodulin-dependent protein kinase kinase (CaM-KK) which phosphorylates and activates CaM-KI and CaM-KIV [Tokumitsu, H., Enslen, H., and Soderling, T. R. (1995) J. Biol. Chem. 270, 19320-19324]. In the present study, we have identified its regulatory CaM-binding and autoinhibitory domains (CBD and AID, respectively) using a series of COOH-terminal truncations and site-directed mutants expressed in COS-7 cells. Truncation mutant CaM-KK1-463 activated CaM-KIV and bound CaM similar to wild-type enzyme (CaM-KK1-505); CaM-KK1-448 did not bind CaM and was largely inactive; and CaM-KK1-434 also did not bind CaM but activated a CaM-independent mutant of CaM-KIV in the absence of Ca2+/CaM. Substitution of triple negative charges (Asp) at positions 455RKR, 448ILV, or 443SWT blocked CaM binding and suppressed by 70-90% CaM-KK activities. Mutants 438VKL and 435KNS to DDD exhibited partial Ca2+/CaM-independent activities. These results identify overlapping AID and CBD between residues 430 and 460 in CaM-KK, similar to other CaM-Ks. Consistent with this assignment, the synthetic peptide corresponding to residues 438-463 bound CaM in a Ca2+-dependent manner with a Kd in the low nanomolar range. Furthermore, phosphorylation by cAMP-kinase of Ser458 at the COOH-terminus of the CBD in CaM-KK, which suppresses subsequent CaM binding [Wayman, G., Tokumitsu, H., and Soderling, T. R. (1997) J. Biol. Chem. 272, 16073-16076], was blocked by prior binding of Ca2+/CaM to CaM-KK.
Generation of primary antigen-specific human cytotoxic T lymphocytes in human/mouse radiation chimera (1996)

Severe combined immunodeficient (SCID) mice are increasingly used as hosts for the adoptive transfer of human lymphocytes. Human antibody responses can be obtained in these xenogeneic chimeras, but information about the functionality of the human T cells in SCID mice is limited and controversial. Studies using human peripheral blood lymphocytes (PBL) injected intraperitoneally (IP) into SCID mice (hu-PBL-SCID mice) have shown that human T cells from these chimeras are anergic and have a defective signaling via the T-cell receptor. In addition, their antigenic repertoire is limited to xenoreactive clones. In the present study, we tested the functionality of human T cell in a recently described chimeric model. In this system, BALB/c mice are conditioned by irradiation and then transplanted with SCID bone marrow, followed by IP injection of human PBL. Our experiments demonstrated that human T cells, recovered from these hu-PBL-BALB mice within 1 month posttransplant, proliferated and expressed activation markers upon stimulation with anti-CD3 monoclonal antibody. A vigorous antiallogeneic human cytotoxic T-lymphocyte (CTL) response could be generated in these mice by immunizing them with irradiated allogeneic cells. Moreover, anti-human immunodeficiency virus type 1 (HIV-1) Net-specific human CTLs could be generated in vivo from naive lymphocytes by immunization of mouse-human chimeras with a recombinant vaccinia-nef virus. This model may be used to evaluate potential immunomodulatory drugs or cytokines, and could provide a relevant model for testing HIV vaccines, for production of antiviral T-cell clones for adoptive therapy, and for studying human T-cell responses in vivo.
Pharmacokinetics of human granulocyte-macrophage colony-stimulating factor using a sensitive immunoassay (1988)

A sensitive and reliable sandwich enzyme-linked immunosorbent assay (ELISA) has been developed for recombinant human granulocyte-macrophage colony-stimulating factor (hGM-CSF). The assay is quantitative between 100 pg/mL and 2.5 ng/mL for bacterially synthesized hGM-CSF in human serum and is more sensitive and specific than the semisolid agar bioassay. As part of a phase I study, the pharmacokinetics of intravenous (IV) bolus injection and subcutaneous (SC) administration of hGM-CSF were studied. Following a single IV dose, an initial high blood level of hGM-CSF occurred, followed by a rapid decrease occurring in two apparent phases with a half-life (t1/2)alpha of less than five minutes and a t1/2 beta of 150 minutes. After an SC injection, detectable serum levels occurred within 15 to 30 minutes, and serum levels were sustained for a variable time depending on the dose. At the highest SC dose (10 micrograms/kg), a serum level of greater than 1 ng/mL (65 pmol/L) was maintained for greater than 12 hours after a single injection. This corresponds to the concentration of hGM-CSF supporting near-maximum proliferation in vitro.
The siRNA Non-seed Region and Its Target Sequences Are Auxiliary Determinants of Off-Target Effects (2015)

RNA interference (RNAi) is a powerful tool for post-transcriptional gene silencing. However, the siRNA guide strand may bind unintended off-target transcripts via partial sequence complementarity by a mechanism closely mirroring micro RNA (miRNA) silencing. To better understand these off-target effects, we investigated the correlation between sequence features within various subsections of siRNA guide strands, and its corresponding target sequences, with off-target activities. Our results confirm previous reports that strength of base-pairing in the siRNA seed region is the primary factor determining the efficiency of offtarget silencing. However, the degree of downregulation of off-target transcripts with shared seed sequence is not necessarily similar, suggesting that there are additional auxiliary factors that influence the silencing potential. Here, we demonstrate that both the melting temperature (Tm) in a subsection of siRNA non-seed region, and the GC contents of its corresponding target sequences, are negatively correlated with the efficiency of off-target effect. Analysis of experimentally validated miRNA targets demonstrated a similar trend, indicating a putative conserved mechanistic feature of seed region-dependent targeting mechanism. These observations may prove useful as parameters for off-target prediction algorithms and improve siRNA 'specificity' design rules.
Deformation and Collapse of Microtubules on the Nanometer Scale (2003)

We probe the local mechanical properties of microtubules at the nanometer scale by radial indentation with a scanning force microscope tip. We find a linear elastic regime that can be described by both thin-shell theory and finite element methods, in which microtubules are modeled as hollow tubes. We also find a nonlinear regime and catastrophic collapse of the microtubules under large loads. The main physics of protein shells at the nanometer scale shows simultaneously aspects of continuum elasticity in their linear response, as well as molecular graininess in their nonlinear behavior.