gebhart/patrepeval huggingface dataset:
Novel method of preparing acellular cardiovascular grafts by decellularization with poly(ethylene glycol) (2003)

We have developed a new method of preparing acellular vascular grafts. Cellular components, including cell membranes and proteins in cytosol, were efficiently extracted from the vessels in a concentrated aqueous solution of poly(ethylene glycol), an amphiphilic biocompatible polymer. The residual DNA was digested by deoxyribonuclease I treatment after extraction with poly(ethylene glycol). The two-step extraction process proved quite effective at removing the cellular components while causing little damage to the extracellular matrices. We did not use any detergent that would damage the extracellular matrices. Therefore, vascular endothelial cells grew well on the acellular vessels after recellularization, promising longi-patent cardiovascular grafts.
Generation of Genome-Wide CD8 T Cell Responses in HLA-A*0201 Transgenic Mice by an HIV-1 Ubiquitin Expression Library Immunization Vaccine (2002)

HIV-1 is a fundamentally difficult target for vaccines due to its high mutation rate and its repertoire of immunoevasive strategies. To address these difficulties, a multivalent, proteasome-targeted, live genetic vaccine was recently developed against HIV-1 using the expression library immunization approach. In this HIV-1 vaccine all open reading frames of HIV-1 are expressed from 32 plasmids as Ag fragments fused to the ubiquitin protein to increase Ag targeting to the proteasome to enhance CTL responses. In this work we demonstrate the ability of the HIV-1 library vaccine to simultaneously provoke robust HLA-A*0201-restricted T cell responses against all 32 HIV-1 library vaccine Ags after single immunization by gene gun. These CD8 T cell responses included HLA-A*0201-restricted CTL activity, CD8/IFN-gamma T cell responses, and HLA tetramer binding against defined immunodominant epitopes in gag, pol, env, and nef as well as potent CD8/IFN-gamma responses against undefined HLA-A*0201-restricted epitopes in all remaining Ags of the library. CD8 responses mediated by single gag, pol, env, and nef plasmids from the vaccine demonstrated little reduction in specific T cell responses when these plasmids were diluted into the context of the full 32-plasmid library, suggesting that Ag dominance or immune interference is not an overt problem to limit the efficacy of this complex vaccine. Therefore, this work demonstrates the ability of the HIV-1 library vaccine to generate robust multivalent genome-wide T cell responses as one approach to control the highly mutable and immunoevasive HIV-1 virus.
Mitogenesis in normal human fibroblasts by polyinosinic · polycytidylic acid and other synthetic acidic polymers: Enhancement of action by glucocorticoids (1981)

The ability of specific synthetic polyelectrolytes to act as mitogens for quiescent normal human fibroblasts in cultures is described. Of several acidic polymers tested, polyinosinic acid .polycytidylic acid (poly I.poly C) and dextran sulfate were the most effective in stimulating 3H]thymidine incorporation (2-to 10-fold). The concentration for a half-maximal effect (ED50) was 0.4 microgram/ml (0.8 nM) for poly I.poly C, and 1.7 microgram/ml (3.4 nM) for dextran sulfate. Single-stranded polyinosinic acid or polycytidylic acid had no effect. The time course of stimulation of DNA synthesis by these acidic polymers was similar to that for naturally occurring mitogens such as epidermal growth factor, beginning at about 18 hours and reaching a maximum rate 26 to 30 hours after the addition of polymer. Glucocorticoids that have an 11-beta hydroxyl group (e.g., dexamethasone) had no effect on DNA synthesis alone, but enhanced several-fold the mitogenic activity of poly I.poly C or dextran sulfate; the ED50 for dexamethasone was 0.75 ng/ml (1.9 nM). Glucocorticoids with an 11-keto group were inactive in this respect. The labeling index following treatment of cultures with poly I.poly C and dexamethasone was 14%, compared with a labeling index of 25% following stimulation by fetal calf serum. The extent of stimulation of DNA synthesis by poly I.poly C and dexamethasone was comparable to that induced by epidermal growth factor. It appears that both the poly I.poly C and dexamethasone are required for only a short period of time (approximately 3 hours) in order to produce maximal stimulation of DNA synthesis 30 hours later.
Pushing the Envelope in the mTOR Pathway: The Second Generation of Inhibitors (2011)

The phosphatidylinositol-3-kinase (PI3K)/mTOR pathway has been a major focus of attention for cancer researchers in the past decade. A preliminary and incomplete understanding of the molecular biology of this complex network has importantly conditioned not only the development of the first generation of mTOR inhibitors, but also the biomarker studies designed to identify the best responders to these agents. Most recently, research in this pathway has focused on the dual nature of mTOR that is integrated by the mTOR complex 1 and complex 2. These two complexes are formed and regulated by different proteins and are also driven by multiple different compensatory feedback loops. This deeper understanding has allowed the development of a promising second generation of inhibitors, which are able to block simultaneously both complexes due to their catalytic activity over mTOR. Moreover, some of them also exert an inhibitory effect over PI3K that is a key player in the feedback loops. This article reviews the newest insights in the signaling of the mTOR pathway and then focuses on the development of the new wave of mTOR inhibitors.
Cellular Delivery of Doxorubicin via pH-Controlled Hydrazone Linkage Using Multifunctional Nano Vehicle Based on Poly(β-L-Malic Acid) (2012)

Doxorubicin (DOX) is currently used in cancer chemotherapy to treat many tumors and shows improved delivery, reduced toxicity and higher treatment efficacy when being part of nanoscale delivery systems. However, a major drawback remains its toxicity to healthy tissue and the development of multi-drug resistance during prolonged treatment. This is why in our work we aimed to improve DOX delivery and reduce the toxicity by chemical conjugation with a new nanoplatform based on polymalic acid. For delivery into recipient cancer cells, DOX was conjugated via pH-sensitive hydrazone linkage along with polyethylene glycol (PEG) to a biodegradable, non-toxic and non-immunogenic nanoconjugate platform: poly(β-l-malic acid) (PMLA). DOX-nanoconjugates were found stable under physiological conditions and shown to successfully inhibit in vitro cancer cell growth of several invasive breast carcinoma cell lines such as MDA-MB-231 and MDA-MB- 468 and of primary glioma cell lines such as U87MG and U251.
HLA class I heavy-chain gene promoter elements mediating synergy between tumor necrosis factor and interferons. (1994)

The cytokines tumor necrosis factor (TNF), beta interferon (IFN-beta), and IFN-gamma increase major histocompatibility complex class I molecule expression. A greater than additive (i.e., synergistic) induction of class I heavy-chain mRNA is observed in HeLa cells treated with TNF in combination with either type of IFN. To define the cis-acting elements mediating cytokine synergy, the promoter of a human major histocompatibility complex class I heavy-chain gene (HLA-B7) was placed in front of a reporter gene and transfected into HeLa cells. Deletion analysis mapped the elements required for synergy to a 40-bp region containing a kappa B-like element, which is necessary for the response to TNF, and an interferon consensus sequence (ICS), which is necessary for the responses to IFNs. When the orientation of these elements was reversed or their normal 20-bp spacing was reduced by 5 or 10 bp, i.e., one half or one full turn of the DNA helix, essentially equivalent responses were obtained, suggesting that these parameters are not critical. In electromobility shift assays, a p50-containing NF-kappa B nuclear factor from TNF-treated cells binds kappa B-containing probes, and ISGF-2 from IFN-gamma-treated cells binds ICS-containing probes. A probe containing both the kappa B and ICS elements (kappa B-ICS) forms a novel complex with nuclear factors isolated from cells treated with both TNF and IFN-gamma; this complex also forms when nuclear factors from individually cytokine-treated cells are mixed in vitro. The natural variant ICS found in HLA-A responds to IFN-gamma and can mediate synergy with TNF. However, the variant kappa B found in HLA-C does not respond to TNF, nor can it mediate synergy between TNF and IFN-gamma. These observations suggest that synergy between TNF and IFNs in the induction of HLA class I gene expression results from the sum of individual interactions of cytokine-activated enhancer-binding factors with the transcription initiation complex.
Restoration of CSF [HCO3-] after its experimental lowering in normocapnic conditions (1979)

It is accepted that in hypercapnia the rise in cerebrospinal fluid bicarbonate concentration (CSF [HCO3-]) occurs because of local HCO3--generating mechanisms, dependent on carbonic anhydrase, as well as on diffusion of HCO3- from plasma. To investigate further the regulation of CSF [HCO3-], CSF HCO3- formation was studied under conditions of pure isocapnic CSF "metabolic" acidosis. In anesthetized normocapnic dogs CSF [HCO3-] was lowered to approximately 15 mmol/l by perfusing the brain ventricles with a low HCO3- solution for 45 min. In dogs with normal plasma [HCO3-], CSF [HCO3-] rose by approximately 7 mmol/l in 2 h after the end of the perfusion. Lowering plasma [HCO3-] to 10 mmol/l by infusing HCl, limited the CSF [HCO3-] rise to 2 mmol/l, indicating the importance of plasma HCO3- for the restoration of CSF [HCO3-]. The small and persistent rise of CSF [HCO3-] at low plasma [HCO3-] occurred against a concentration gradient with blood. Intraventricular injection of acetazolamide had no further effect on this small rise. It is concluded that under the conditions of our experiments the CSF [HCO3-] rise is significantly dependent on plasma [HCO3-] and the caronic anhydrase-dependent HCO3- generation in the CNS is less important.
CENP-F is a protein of the nuclear matrix that assembles onto kinetochores at late G2 and is rapidly degraded after mitosis. (1995)

Centromere protein-F (CENP-F) is mammalian kinetochore protein that was recently identified by an autoimmune serum (Rattner, J. B., A. Rao, M. J. Fritzler, D. W. Valencia, and T. J. Yen. Cell Motil. Cytoskeleton. 26:214-226). We report here the human cDNA sequence of CENP-F, along with its expression and localization patterns at different stages of the HeLa cell cycle. CENP-F is protein of the nuclear matrix that gradually accumulates during the cell cycle until it reaches peak levels in G2 and M phase cells and is rapidly degraded upon completion of mitosis. CENP-F is first detected at the prekinetochore complex during late G2, and is clearly detectable as paired foci that correspond to all the centromeres by prophase. During mitosis, CENP-F is associated with kinetochores from prometaphase until early anaphase and is then detected at the spindle midzone throughout the remainder of anaphase. By telophase, CENP-F is concentrated within the intracellular bridge at either side of the mid-body. The predicted structure of the 367-kD CENP-F protein consists of two 1,600-amino acid-long coil domains that flank a central flexible core. A putative P-loop nucleotide binding site (ADIPTGKT) is located within the globular carboxy terminus. The structural features deduced from our sequence studies and the spatial and temperal distribution of CENP-F revealed in our cytological and biochemical studies suggest that it may play a role in several mitotic events.
Amplification of snap-back DNA synthesis reactions by the uvsX recombinase of bacteriophage T4 (1991)

The uvsX protein of bacteriophage T4 is a recA-type recombinase. This protein has previously been shown to help initiate DNA replication on a double-stranded DNA template by catalyzing synapsis between the template and a homologous DNA single strand that serves as primer. Here, we demonstrate that this replication-initiating activity of the uvsX protein greatly amplifies the snap-back (hairpin-primed) DNA synthesis that is catalyzed by the T4 DNA polymerase holoenzyme on linear, single-stranded DNA templates. Amplification requires the presence of uvsX protein, the DNA polymerase holoenzyme, T4 gene 32 protein, and a T4 DNA helicase, in a reaction that is modulated by the T4 uvsY protein (an accessory protein to the uvsX recombinase). The reaction products consist primarily of large networks of double-stranded and single-stranded DNA. With alkali or heat treatment, these networks resolve into dimer-length single-stranded DNA chains that renature instantaneously to reform a monomer-length double helix. A simple model can explain this uvsX protein-dependent amplification of snap-back DNA synthesis; the mechanism proposed makes several predictions that are confirmed by our experiments.
T‐Fix endoscopic meniscal repair: Technique and approach to different types of tears (1995)

Endoscopic meniscus repair using the T-Fix suture device (Acufex Microsurgical, Inc, Mansfield, MA) allows ease of suture placement for meniscus stability without the problems associated with ancillary incisions such as neurovascular compromise. It is ideal for the central posterior horn tears that are difficult using conventional techniques. Vertical tears, bucket handle tears, flap tears, and horizontal tears can be approached using a temporary "anchor stitch" to stabilize the meniscus before T-Fix repair. The basic method of repair and our approach to these different types of tears is presented.
MEMS post-packaging by localized heating and bonding (2000)

This work addresses important post-packaging issues for microsystems and recommends specific research directions by localized heating and bonding. Micropackaging has become a major subject for both scientific research and industrial applications in the emerging field of microelectromechanical systems (MEMS). Establishing a versatile post-packaging process not only advances the field but also speeds up the product commercialization cycle. A review of engineering bases describing current technologies of MEMS packaging and wafer bonding is followed by an innovative post-packaging approach by localized heating and bonding, process demonstrations by selective encapsulation are presented, including an integrated low pressure chemical vapor deposition (LPCVD) sealing process, localized silicon-gold eutectic bonding, localized silicon-glass fusion bonding, localized solder bonding and localized CVD bonding processes.
Syntheses, crystal structures and photophysics of organogold(III) diimine complexes (1993)

A series of luminescent organogold(III) diimine complexes have been synthesised and the crystal structures of [Au(bipy)(mes)2]ClO4(bipy = 2,2′-bipyridine, mes = mesityl) and [Au(phen)(CH2SiMe3)2]ClO2(phen = 1,10-phenanthroline) have been determined.
Boosted Convolutional Neural Networks (BCNN) for Pedestrian Detection (2017)

A boosted convolutional neural network (BCNN) system is proposed to enhance the pedestrian detection performance in this work. Being inspired by the classic boosting idea, we develop a weighted loss function that emphasizes challenging samples in training a convolutional neural network (CNN). Two types of samples are considered challenging: 1) samples with detection scores falling in the decision boundary, and 2) temporally associated samples with inconsistent scores. A weighting scheme is designed for each of them. Finally, we train a boosted fusion layer to benefit from the integration of these two weighting schemes. We use the Fast-RCNN as the baseline, and test the corresponding BCNN on the Caltech pedestrian dataset in the experiment, and show a significant performance gain of the BCNN over its baseline.
Improving Safety with Information Technology (2003)

ealth care is growing increasingly complex, and most clinical research focuses on new approaches to diagnosis and treatment. In contrast, relatively little effort has been targeted at the perfection of operational systems, which are partly responsible for the well-documented problems with medical safety. 1 If medicine is to achieve major gains in quality, it must be transformed, and information technology will play a key part, 2 especially with respect to safety.
Intraperitoneal Lymphokine-Activated Killer Cell/Interleukin-2 Therapy in Patients With Intra- abdominal Cancer: Immunologic Considerations (1989)

Lymphokine-activated killer (LAK) cells and interleukin-2 (IL-2) were administered by the ip route to patients with intra-abdominal malignancies. Pharmacokinetic studies of IL-2 revealed 10- to 100-fold higher concentrations of IL-2 in peritoneal fluid versus serum. Ip levels of IL-2 were maintained well above those required to generate and maintain LAK cells in vitro. LAK cell activity was detectable in the peritoneal fluid for the duration of each treatment cycle and did not disappear until IL-2 was discontinued. Detection of interferon-gamma (IFN-gamma) in the peritoneal fluid of all patients was consistent with production in situ by activated lymphocytes. In some patients, low but detectable levels of IFN-gamma were also found in the serum. In vivo activation of monocytes in the peritoneal fluid as measured by in vitro production of hydrogen peroxide was documented in the majority of patients. Neither interleukin-1 nor tumor necrosis factor-alpha was detected in the peritoneal fluid. We found no correlation between the presence or levels of IL-2, IFN-gamma, or LAK cell lytic activity in peritoneal fluid or serum and response or nonresponse to therapy.
Epidemiology of gout (2008)

The incidence and prevalence of gout are rising, likely as a result of a changing pattern of risk factors. At-risk populations are growing, due to the fact that people are living longer. Longevity and current dietary and lifestyle choices have also contributed to increased rates of comorbidities associated with hyperuricemia and gout. The use of medications to treat such comorbidities also plays a role in some cases of gout. While dietary and lifestyle modification may be useful as adjunctive measures, such changes do not replace pharmacologic treatments for gout or associated comorbidities.
A genomewide scan for quantitative trait loci underlying areal bone size variation in 451 Caucasian families (2006)

Together with previous findings, this study has further delineated the genetic basis of bone size and laid a foundation for future studies to eventually elucidate the mechanisms of bone size regulation and associated fracture risks.
Antibodies to cholesterol. (1988)

Cholesterol-dependent complement activation has been proposed as a factor that might influence the pathogenesis of atherosclerosis. Although antibodies to cholesterol conjugates have been reported, cholesterol is widely regarded as a poorly immunogenic substance. Monoclonal IgM complement-fixing antibodies to cholesterol were obtained in the present study after immunizing mice with liposomes containing high amounts of cholesterol (71 mol % relative to phosphatidylcholine) and lipid A as an adjuvant. Clones were selected for the ability of secreted antibodies to react with liposomes containing 71% cholesterol but not with liposomes containing 43% cholesterol. The antibodies also reacted with crystalline cholesterol in a solid-phase enzyme-linked immunosorbent assay. Binding of monoclonal antibodies to the surface of crystalline cholesterol was demonstrated by electron microscopy by utilizing a second antibody (anti-IgM) labeled with colloidal gold. The immunization period required to induce monoclonal antibodies was very short (3 days) and a high fraction of the hybrid cells (at least 70%) were secreting detectable antibodies to cholesterol. The results demonstrate that cholesterol can be a highly immunogenic molecule and that complement-fixing antibodies to cholesterol can be readily obtained.
Fast and Near-Optimal Algorithms for Approximating Distributions by Histograms (2015)

Histograms are among the most popular structures for the succinct summarization of data in a variety of database applications. In this work, we provide fast and near-optimal algorithms for approximating arbitrary one dimensional data distributions by histograms.
Faraday Effect Current Sensing Using a Sagnac Interferometer with a 3x3 Coupler (1990)

We demonstrate a fiber optic current sensor based on a Sagnac interferometer with a 3 {times} 3 coupler. Compared to the more common Sagnac interferometer with a 2 {times} 2 coupler, this design offers the additional benefits of a greater response for small signals and the unambiguous interpretation of signals that exceed the period of the response function. 6 refs., 6 figs.
New nucleoside analogs in the treatment of hematological disorders. (2004)

Cytotoxic nucleoside analogs have a broad clinical use. They were among the first chemotherapeutic agents used in the treatment of malignant diseases. The anticancer nucleosides include analogs of physiologic pyrimidine and purine nucleosides. They are used in oncology in the treatment of both, solid tumors and hematological malignancies. These agents have many intracellular targets, e.g. they act as antimetabolites, competing with natural nucleosides during DNA or RNA synthesis and as inhibitors of key cell enzymes. Understanding of the mechanisms of action of these compounds and synthesis of new analogs provides the possibility to further expand the spectrum of their clinical use and enhance their antitumor activity. In this paper we describe mechanisms of action and possible clinical use in the treatment of hematological malignancies of these nucleoside analogs, which are now in different stages of clinical trials, namely tezacitabine, troxacitabine, clofarabine, nelarabine, decitabine, CNDAC and ECyD.
Current-induced magnetic vortex motion by spin-transfer torque (2006)

We investigate the dynamics of a magnetic vortex driven by spin-transfer torque due to spin current in the adiabatic case. The vortex core represented by collective coordinate experiences a transverse force proportional to the product of spin current and gyrovector, which can be interpreted as the geometric force determined by topological charges. We show that this force is just a reaction force of Lorentz-type force from the spin current of conduction electrons. Based on our analyses, we propose analytically and numerically a possible experiment to check the vortex displacement by spin current in the case of single magnetic nanodot.
Multiplier policies for digital signal processing (1990)

The successful design of digital signal processing (DSP) systems and subsystems is often predicated on realizing fast multiplication in digital hardware. This tutorial provides the reader with a broad perspective of this important field and the pedagogy needed to understand the basic principles of digital multiplication. Both conventional and nonconventional methods of implementing multiplication, representing a mix of speed/complexity tradeoffs, are presented. Some are based on traditional shift-add structures, whereas others strive for greater mathematical sophistication. Topics include stand-alone fixed-point multipliers, cellular arrays, memory intensive policies, homomorphic systems, and modular arithmetic.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>