gebhart/patrepeval huggingface dataset:
IRX‐2 and Thymosin α1 (Zadaxin) Increase T Lymphocytes in T Lymphocytopenic Mice and Humans (2007)

Mouse studies showed a synergy of thymosin alpha1 (Talpha1) and a natural cytokine mixture (IRX-2) in increasing T lymphocyte number and responses. Clinical studies with IRX-2 showed increases of T lymphocytes in lymphocytopenic cancer patients but relatively little effect on irradiated, lymphocytopenic patients. The present phase 1 and 2 study shows that Talpha1 enhances the effect of IRX-2 in these lymphocytopenic patients. Patients (seven) were treated with subcutaneously injected IRX-2 (200 units IL-2 equivalence), Talpha1 (1.6 mg/day) (four patients), or the combination of IRX-2 and Talpha1 (seven patients) daily for 10 days. Peripheral blood lymphocytes (T, B, NK) and subsets (CD4, CD8) were measured at the start of treatment and on day 11. IRX-2 and Talpha1 had little or no significant effect. The combination markedly increased various lymphocyte populations (>350 cells/microL). Four patients followed for 6 weeks displayed sustained increases involving both naïve and memory T cells. Responses to persistent infections were observed in three of the four patients and no significant toxicity was observed. Talpha1 and IRX-2 synergize to increase safely T cells in lymphocytopenic patients.
An Overview of Affinity Chromatography (2000)

Affinity chromatography is pervasively accepted and used as a tool in biomedical research and biotechnology; yet its origins only 30 years ago sometimes seem dimmed in history. However, the potential of this technology continues to stimulate continued development and new applications. Having a new book on this methodology is eminently appropriate today. And being able to introduce this book is our pleasure.
Detection of T‐Lymphocyte Subpopulations in the Peripheral Blood and the Synovium of Patients with Rheumatoid Arthritis and Juvenile Rheumatoid Arthritis Using Monoclonal Antibodies (1982)

Monoclonal antibodies with specificities for various human T-cell antigens were used in direct immunofluorescence to quantify the proportions of T lymphocytes with suppressor/cytotoxic-cell markers and with helper/inducer-cell markers and of T lymphocytes with HLA-DR antigens. Normal percentages of lymphocytes with suppressor/cytotoxic-cell markers were detected in the peripheral blood synovial fluid and synovial tissue lymphocytes from patients with juvenile rheumatoid arthritis (JRA) and rheumatoid arthritis (RA), respectively. Normal percentages of T lymphocytes with helper/inducer-cell markers were seen in the peripheral blood of RA and JRA patients and in the synovial tissues of RA patients. Slightly decreased percentages of cells with the helper/inducer-cell marker were detected in the synovial fluids of JRA patients. The proportions of HLA-DR-positive T lymphocytes were highly increased in the synovial fluid and synovial tissue, whereas the numbers of these cells in the peripheral blood were normal. No significant differences in T gamma cells were detected between peripheral blood, synovial fluid and synovial tissue of JRA patients or between peripheral blood and synovial tissue of RA patients.
Participation of c-met in the progression of human gastric cancers: anti-c-met oligonucleotides inhibit proliferation or invasiveness of gastric cancer cells. (1997)

The protooncogene c-met encodes the receptor for hepatocyte growth factor (HGF), a potent epithelial cell mitogen with scattering activity. In this study, we first screened c-met expression in human gastric carcinomas. Twenty-eight of 154 tumors (18%) were positively stained for MET proteins. The incidence of c-met expression increased with higher histopathological stages of the cancer. Second, we examined functional roles of c-met in cultured gastric carcinoma cells, using an antisense strategy. Cell lines used were MKN-45, TMK-1, and MKN-28. Among them, MKN-45 cells exhibited the highest c-met expression and grew in response to HGF, whereas TMK-1 cells had an ability to invade in an HGF-dependent manner. When antisense oligodeoxyribonucleotides complementary to c-met messenger RNA (mRNA) were administered to the culture medium, the content of MET protein was selectively decreased in either MKN-45 or TMK-1 cells, indicating that the antisense molecules did inhibit the translation of c-met mRNA. The growth of MKN-45 cells was markedly inhibited by the antisense c-met oligonucleotides in a dose-dependent manner, but not by sense or scrambled controls. The antisense oligonucleotides also effectively inhibited the migration of TMK-1 cells. These results indicate that c-met gene products may be causally related to the proliferation or invasion of gastric cancer cells, and that antisense c-met DNA has the potential to help circumvent the progression of gastric cancers.
Human retinopathy-associated ciliary protein retinitis pigmentosa GTPase regulator mediates cilia-dependent vertebrate development (2009)

Dysfunction of primary cilia is associated with tissue-specific or syndromic disorders. RPGR is a ciliary protein, mutations in which can lead to retinitis pigmentosa (RP), cone-rod degeneration, respiratory infections and hearing disorders. Though RPGR is implicated in ciliary transport, the pathogenicity of RPGR mutations and the mechanism of underlying phenotypic heterogeneity are still unclear. Here we have utilized genetic rescue studies in zebrafish to elucidate the effect of human disease-associated mutations on its function. We show that rpgr is expressed predominantly in the retina, brain and gut of zebrafish. In the retina, RPGR primarily localizes to the sensory cilium of photoreceptors. Antisense morpholino (MO)-mediated knockdown of rpgr function in zebrafish results in reduced length of Kupffer's vesicle (KV) cilia and is associated with ciliary anomalies including shortened body-axis, kinked tail, hydrocephaly and edema but does not affect retinal development. These phenotypes can be rescued by wild-type (WT) human RPGR. Several of the RPGR mutants can also reverse the MO-induced phenotype, suggesting their potential hypomorphic function. Notably, selected RPGR mutations observed in XLRP (T99N, E589X) or syndromic RP (T124fs, K190fs and L280fs) do not completely rescue the rpgr-MO phenotype, indicating a more deleterious effect of the mutation on the function of RPGR. We propose that RPGR is involved in cilia-dependent cascades during development in zebrafish. Our studies provide evidence for a heterogenic effect of the disease-causing mutations on the function of RPGR.
Orange-curd High Carotene Cauliflower Inbreds, NY 156, NY 163, and NY 165 (1988)

Abstract The orange curd mutant in cauliflower ( Brassica oleracea L. var. botrytis ) Snowball’ (1). Orange curd was controlled by a single dominant gene, or , but the intensity of orange color varied in homozygous ( OrOr ) and heterzygous ( Oror ) plants, due to modifying genes. Curd of OrOr plants were generally more intense colored than curds of Oror plants. The OrOr plants are stunted, and produce small curds, ≈30 to 40 mm or less in diameter, compared to Oror or oror curd plants, which have curds 150 to 200 mm in diameter.
3D eye model-based gaze estimation from a depth sensor (2016)

In this paper, we address the 3D eye gaze estimation problem using a low-cost, simple-setup, and non-intrusive consumer depth sensor (Kinect sensor). We present an effective and accurate method based on 3D eye model to estimate the point of gaze of a subject with the tolerance of free head movement. To determine the parameters involved in the proposed eye model, we propose i) an improved convolution-based means of gradients iris center localization method to accurately and efficiently locate the iris center in 3D space; ii) a geometric constraints-based method to estimate the eyeball center under the constraints that all the iris center points are distributed on a sphere originated from the eyeball center and the sizes of two eyeballs of a subject are identical; iii) an effective Kappa angle calculation method based on the fact that the visual axes of both eyes intersect at a same point with the screen plane. The final point of gaze is calculated by using the estimated eye model parameters. We experimentally evaluate our gaze estimation method on five subjects. The experimental results show the good performance of the proposed method with an average estimation accuracy of 3.78°, which outperforms several state-of-the-arts.
Maximizing productivity of CHO cell‐based fed‐batch culture using chemically defined media conditions and typical manufacturing equipment (2010)

A highly productive chemically defined fed-batch process was developed to maximize titer and volumetric productivity for Chinese hamster ovary cell-based recombinant protein manufacturing. Two cell lines producing a recombinant antibody (cell line A) and an Fc-fusion protein (cell line B) were used for development. Both processes achieved product titers of 10 g/L on day 18 under chemically defined conditions. For cell line B, the use of plant derived hydrolysates combined with the optimized chemically defined medium increased the titer to 13 g/L. Volumetric productivities were increased from a base line of about 200 mg/L/d to about 500 mg/L/d under chemically defined conditions and as high as 700 mg/L/d with cell line B using plant derived hydrolysates. Peak cell densities reached greater than 20E6 vc/mL, and cell viabilities were maintained above 80% on day 18 without the use of antiapoptotic genes or temperature shift. A rapid compound screening method was developed to effectively test positive factors within 72 h. Peak volumetric oxygen uptake rates (OUR) more than tripled from the baseline condition. Oxygen demand continued to increase after maximum cell density was reached with a maximal OUR of 3.7 mmol/L/h. The new process format was scaled up and verified at 100 L pilot scale using reactor equipment of similar configuration as used at manufacturing scale.
Acceleration of recombinant tissue-type plasminogen activator-induced reperfusion and prevention of reocclusion by recombinant antistasin, a selective factor Xa inhibitor, in a canine model of femoral arterial thrombosis. (1992)

Antistasin is a 119-amino acid protein initially isolated from salivary glands of the Mexican leech, Haementeria officinalis, that exhibits potent anticoagulant properties resulting from selective inhibition of blood coagulation factor Xa. The comparative antithrombotic efficacies of recombinant antistasin (rATS), standard heparin (Hep), and aspirin (ASA) administered adjunctly with recombinant tissue-type plasminogen activator (tPA) on thrombolytic reperfusion and reocclusion were determined in a canine model of femoral arterial thrombosis. An occlusive thrombus was formed by insertion of a thrombogenic copper coil into the femoral artery, and blood flow velocity was monitored directly and continuously by Doppler flowmetry. Sixty minutes after occlusion, dogs received an intravenous infusion of either saline (vehicle) or rATS (0.31, 1.25, or 2.5 micrograms/kg/min), intravenous boluses of Hep (100 units/kg + 50 units/kg/hr or 200 units/kg + 150 units/kg/hr), or a single intravenous bolus of ASA (2.0 mg/kg), followed 45 minutes later by tPA (0.8 mg/kg i.v. over 90 minutes). The saline and rATS infusions were discontinued 60 minutes after termination of tPA, and the last Hep boluses were given 105 minutes after termination of tPA. All dogs achieved reperfusion. The time to reperfusion in the ASA group was similar to that in the vehicle group (50 +/- 9 versus 50 +/- 6 minutes, respectively). Reperfusion times were slightly decreased by the low and high doses of Hep (34 +/- 6 and 31 +/- 4 minutes, respectively) and the rATS doses of 0.31 and 1.25 micrograms/kg/min (37 +/- 4 and 36 +/- 5 minutes, respectively). However, the time to reperfusion was dramatically reduced with the 2.5 micrograms/kg/min rATS dose (15 +/- 3 minutes, p less than 0.05).(ABSTRACT TRUNCATED AT 250 WORDS)
XYZeq: Spatially resolved single-cell RNA sequencing reveals expression heterogeneity in the tumor microenvironment (2021)

Single-cell RNA sequencing (scRNA-seq) of tissues has revealed remarkable heterogeneity of cell types and states but does not provide information on the spatial organization of cells. To better understand how individual cells function within an anatomical space, we developed XYZeq, a workflow that encodes spatial metadata into scRNA-seq libraries. We used XYZeq to profile mouse tumor models to capture spatially barcoded transcriptomes from tens of thousands of cells. Analyses of these data revealed the spatial distribution of distinct cell types and a cell migration-associated transcriptomic program in tumor-associated mesenchymal stem cells (MSCs). Furthermore, we identify localized expression of tumor suppressor genes by MSCs that vary with proximity to the tumor core. We demonstrate that XYZeq can be used to map the transcriptome and spatial localization of individual cells in situ to reveal how cell composition and cell states can be affected by location within complex pathological tissue.
PCR with an Expanded Genetic Alphabet (2009)

Expansion of the genetic alphabet with a third base pair would lay the foundation for a semisynthetic organism with an expanded genetic code and also have immediate in vitro applications. Previously, the unnatural base pairs formed between d5SICS and either dNaM or dMMO2 were shown to be well-replicated by DNA polymerases under steady-state conditions and also transcribed by T7 RNA polymerase efficiently in either direction. We now demonstrate that DNA containing either the d5SICS-dNaM or d5SICS-dMMO2 unnatural base pair may be amplified by PCR with fidelities and efficiencies that approach those of fully natural DNA. These results further demonstrate that the determinants of a functional unnatural base pair may be designed into predominantly hydrophobic nucleobases with no structural similarity to the natural purines or pyrimidines. Importantly, the results reveal that the unnatural base pairs may function within an expanded genetic alphabet and make possible many in vitro applications.
Synthesis and Evaluation of RNA Transesterification Efficiency Using Stereospecific Serinol-Terpyridine Conjugates (2005)

Six novel artificial ribonucleases were synthesized employing a stereochemically pure abasic serinol backbone residue for attachment of the RNA transesterification agent copper(II) terpyridine. These stereochemically pure abasic residues were synthesized as phosphoramidite building blocks from the parent L-serine and D-serine starting building blocks and incorporated into oligonucleotides via solid-phase DNA synthesis. These artificial ribonucleases were constructed to determine if the stereochemistry of the alpha carbon of an abasic serinol residue has influence over RNA transesterification through selective placement of a pendant transesterification agent in either the major or minor groove. The novel artificial ribonucleases and previously synthesized artificial ribonucleases were challenged with a 28-mer and 159-mer RNA substrate. It was determined that the stereochemistry of the carbon atom derived from the alpha-carbon of serine did not influence the extent of cleavage in these studies using copper(II) terpyridine conjugated artificial ribonucleases.
Pathobiology of restenosis after angioplasty. (1993)

Restenosis is a consequence of a disturbed wound healing process after the vascular trauma of angioplasty or similar intervention. Mechanisms involve clotting, cell recruitment and activation (from the blood, the vascular wall, and the perivascular tissue), as well as cell proliferation, matrix synthesis, and tissue contraction. In more than half of the lesions, these events are coordinated and self-limited, leading to a remodeling of the vessel wall with more stable and viable tissue than the original necrotic and lipid-laden atherosclerotic plaque. This remodeling may be as important as the gain in lumen for long-term patency. However, this basically favorable healing process may be disturbed by predominantly local conditions such as poor resulting wound anatomy, necrotic debris, excessive old plaque material, continued movement and irritation, or poor flow, leading to repetitive activation of any of these mechanisms. It is this unpredictable chronic persistence of these essentially physiologic mechanisms rather than the mechanisms themselves that eventually lead to an exuberant proliferative and synthetic response, which builds up restenotic mass together with thrombotic material and the old plaque components.
A Case-Control Study of Alzheimer's Disease in Japan – Significance of Life-Styles (1994)

A case-control study of Alzheimer's disease was conducted in Japan; it involved 60 cases matched for sex and age with two resident controls each. Life-style was particularly highlighted in this study. Among many factors, 5 were accepted as significant risk factors: psychosocial inactivity, physical inactivity, head injury, loss of teeth and low education. A multiple logistic model was applied in order to evaluate synergism of major factors. Compared with those who have none of the factors, those who have all were 934.5 times more liable to develop Alzheimer's disease. Risk factors are not only useful for etiological studies but they give clues to identify high-risk individuals, and by eliminating these factors, the studies may also be applicable in the primary and the secondary prevention of this tragic disease.
Enrichment and detection of live antigen-specific CD4+ and CD8+ T cells based on cytokine secretion (1999)

Following appropriate antigen-specific stimulation, CD4(+) and CD8(+) T lymphocytes rapidly express cytokines. Based on this stimulation-induced cytokine secretion and using cell surface affinity matrix technology we have developed a new method that permits specific, rapid and efficient detection, isolation and characterization of live antigen-specific CD4(+) and CD8(+) T lymphocytes. The power of this technique is demonstrated here for HLA-A0201-restricted influenza matrix protein peptide 58-66-specific CD8(+) cytotoxic T lymphocytes, influenza A virus- and recombinant tetanus toxin C fragment-specific Th1 cells and tetanus toxoid-specific Th2 cells.
Low complexity schemes for the random access Gaussian channel (2017)

We consider an uncoordinated Gaussian multiple access channel with a relatively large number of active users within each block. A low complexity coding scheme is proposed, which is based on a combination of compute-and-forward and coding for a binary adder channel. For a wide regime of parameters of practical interest, the energy-per-bit required by each user in the proposed scheme is significantly smaller than that required by popular solutions such as slotted-ALOHA and treating interference as noise.
Magnetic field imaging with nitrogen-vacancy ensembles (2011)

We demonstrate a method of imaging spatially varying magnetic fields using a thin layer of nitrogen-vacancy (NV) centers at the surface of a diamond chip. Fluorescence emitted by the two-dimensional NV ensemble is detected by a CCD array, from which a vector magnetic field pattern is reconstructed. As a demonstration, ac current is passed through wires placed on the diamond chip surface, and the resulting ac magnetic field patterns are imaged using an echo-based technique with sub-micron resolution over a \\(140 \\mu m\\) x \\(140 \\mu m\\) field of view, giving single-pixel sensitivity \\(\\sim 100 nT / \\sqrt{Hz}\\). We discuss ongoing efforts to further improve the sensitivity, as well as potential bioimaging applications such as real-time imaging of activity in functional, cultured networks of neurons.
Long‐term amygdalohippocampal stimulation for refractory temporal lobe epilepsy (2002)

Short-term deep brain stimulation (DBS) recently has been shown to be efficacious in refractory temporal lobe epilepsy. We (1) evaluated long-term DBS in medial temporal lobe structures in patients with normal magnetic resonance imaging (MRI) findings and (2) investigated the use of chronic DBS electrodes for the localization of the ictal onset zone before DBS. In three patients with complex partial seizures (CPSs), DBS electrodes were implanted in the amygdalohippocampal region to identify and subsequently stimulate the ictal onset zone. CPSs were compared before and after chronic DBS. Side effects were carefully monitored. DBS electrodes yielded high-quality electroencephalogram recordings showing unilateral seizure onset in medial temporal lobe structures. For all patients, unilateral amygdalohippocampal stimulation was performed. After a mean follow-up of 5 months (range, 3-6 months), all patients had a greater than 50% reduction in seizure frequency. In two patients, antiepileptic drugs could be tapered. None of the patients reported side effects. This open study demonstrates the feasibility of consecutive electroencephalographic recordings and DBS in medial temporal lobe structures using DBS electrodes. These results prompt further studies in a larger patient population to establish the efficacy and safety of chronic DBS as an alternative treatment for refractory temporal lobe epilepsy.
Enzyme-Amplified Amperometric Detection of Hybridization and of a Single Base Pair Mutation in an 18-Base Oligonucleotide on a 7-μm-Diameter Microelectrode (1999)

A single base pair mismatch in an 18-base oligonucleotide was detected amperometrically with a 7-μm-diameter carbon microelectrode. The hybridization was followed directly and in real time by steady-state amperometry. The microelectrode was coated with a hybridization-sensing layer in a two-step electrophoretic process, which yielded microelectrodes with reproducible dimensions. In the first step, a thin film of an electron-conducting redox polymer was deposited electrophoretically at constant potential in a low ionic strength solution. In the second step, a carbodiimide-activated single-stranded probe was reactively electrophoretically deposited and covalently attached to the redox polymer film. The labeling enzyme, thermostable soybean peroxidase (SBP), was covalently bound to the 5‘-end of the target single-stranded oligonucleotide. When the redox polymer and the enzyme were brought to close proximity by hybridization of the target and probe oligonucleotides, the film on the electrode switched from being a noncatalyst to a catalyst for H2O2 electroreduction at −0.06 V vs Ag/AgCl. The current observed corresponded to that generated by ∼40 000 surface-bound and electrically connected SBP molecules.
On ordering color maps for lossless predictive coding (1996)

Linear predictive techniques perform poorly when used with color-mapped images where pixel values represent indices that point to color values in a look-up table. Reordering the color table, however, can lead to a lower entropy of prediction errors. In this paper, we investigate the problem of ordering the color table such that the absolute sum of prediction errors is minimized. The problem turns out to be intractable, even for the simple case of one-dimensional (1-D) prediction schemes. We give two heuristic solutions for the problem and use them for ordering the color table prior to encoding the image by lossless predictive techniques. We demonstrate that significant improvements in actual bit rates can be achieved over dictionary-based coding schemes that are commonly employed for color-mapped images.