gebhart/patrepeval huggingface dataset:
Monoclonal antibodies to a synthetic peptide homologous with the first 28 amino acids of Alzheimer's disease beta-protein recognize amyloid and diverse glial and neuronal cell types in the central nervous system. (1989)

Studies were conducted to identify neural cells that synthesize and/or process cerebral amyloid using antisera and monoclonal antibodies (MAbs) raised to synthetic peptides based on the first 28 amino acids of the amyloid beta-protein. Using rabbit and mouse antisera, and 7 MAbs, sections of neocortex, hippocampus, cerebellum, and spinal cord from Alzheimer's disease (AD), Down's syndrome (DS), and control cases were probed. The antibodies produced 3 distinct immunohistochemical patterns: 1) staining restricted to neuritic plaque and blood vessel amyloid only (antisera, 1 of 7 MAbs); 2) immunoreactivity confined to cytoplasmic granules in diverse neuronal, glial (astrocytes, ependyma) and other (leptomeningeal, perivascular, choroid plexus) cells (1 of 7 MAbs); 3) a summation of these 2 patterns (5 of 7 MAbs). Controls resembled the AD and DS cases, except for a paucity of immunoreactive plaques and blood vessels in the controls. Immunoreactivity was reduced or removed by the peptides used to produce these antibodies. Formalin- and Bouins-fixed tissues reacted weakly or not at all with these antibodies while microwave denatured tissues reacted very intensely with them. Specific staining was enhanced by treatment of the tissue sections with Triton X-100, NaDodSO4, or trypsin. These studies significantly extend earlier studies that localized amyloid beta-protein precursor mRNA to human brain cells, and they suggest that the beta-protein, its precursor, and/or fragments thereof may exist in diverse neural cell types in AD, DS, and control brains.
High throughput sequencing methods for microbiome profiling: application to food animal systems (2012)

Analysis of microbial communities using high throughput sequencing methods began in the mid 2000s permitting the production of 1000s to 10,000s of sequence reads per sample and megabases of data per sequence run. This then unprecedented depth of sequencing allowed, for the first time, the discovery of the 'rare biosphere' in environmental samples. The technology was quickly applied to studies in several human subjects. Perhaps these early studies served as a reminder that though the microbes that inhabit mammals are known to outnumber host cells by an order of magnitude or more, most of these are unknown members of our second genome, or microbiome (as coined by Joshua Lederberg), because of our inability to culture them. High throughput methods for microbial 16S ribosomal RNA gene and whole genome shotgun (WGS) sequencing have now begun to reveal the composition and identity of archaeal, bacterial and viral communities at many sites, in and on the human body. Surveys of the microbiota of food production animals have been published in the past few years and future studies should benefit from protocols and tools developed from large-scale human microbiome studies. Nevertheless, production animal-related resources, such as improved host genome assemblies and increased numbers and diversity of host-specific microbial reference genome sequences, will be needed to permit meaningful and robust analysis of 16S rDNA and WGS sequence data.
The Escherichia coli Citrate Carrier CitT: a Member of a Novel Eubacterial Transporter Family Related to the 2-Oxoglutarate/Malate Translocator from Spinach Chloroplasts (1998)

Under anoxic conditions in the presence of an oxidizable cosubstrate such as glucose or glycerol, Escherichia coli converts citrate to acetate and succinate. Two enzymes are specifically required for the fermentation of the tricarboxylic acid, i.e., a citrate uptake system and citrate lyase. Here we report that the open reading frame (designated citT) located at 13.90 min on the E. coli chromosome between rna and the citrate lyase genes encodes a citrate carrier. E. coli transformed with a plasmid expressing citT was capable of aerobic growth on citrate, which provides convincing evidence for a function of CitT as a citrate carrier. Transport studies with cell suspensions of the transformed strain indicated that CitT catalyzes a homologous exchange of citrate or a heterologous exchange against succinate, fumarate, or tartrate. Since succinate is the end product of citrate fermentation in E. coli, it is likely that CitT functions in vivo as a citrate/succinate antiporter. Analysis of the primary sequence showed that CitT (487 amino acids, 53.1 kDa) is a highly hydrophobic protein with 12 putative transmembrane helices. Sequence comparisons revealed that CitT is related to the 2-oxoglutarate/malate translocator (SODiT1 gene product) from spinach chloroplasts and five bacterial gene products, none of which has yet been functionally characterized. It is suggested that the E. coli CitT protein is a member of a novel family of eubacterial transporters involved in the transport of di- and tricarboxylic acids.
A Variable-Length PCR Target Protein of Ehrlichia chaffeensis Contains Major Species-Specific Antibody Epitopes in Acidic Serine-Rich Tandem Repeats (2008)

Ehrlichia chaffeensis and E. canis have a small subset of tandem repeat (TR)-containing proteins that elicit strong host immune responses and are associated with host-pathogen interactions. In a previous study, we molecularly characterized a highly conserved 19-kDa major immunoreactive protein (gp19) of E. canis and identified the corresponding TR-containing ortholog variable-length PCR target (VLPT) protein in E. chaffeensis. In this study, the native 32-kDa VLPT protein was identified and the immunodeterminants defined in order to further understand the molecular basis of the host immune response to E. chaffeensis. Synthetic and/or recombinant polypeptides corresponding to various regions of VLPT were used to localize major antibody epitopes to the TR-containing region. Major antibody epitopes were identified in three nonidentical repeats (R2, R3, and R4), which reacted strongly with antibodies in sera from an E. chaffeensis-infected dog and human monocytotropic ehrlichiosis patients. VLPT-R3 and VLPT-R2 reacted most strongly with antibody, and the epitope was further localized to a nearly identical proximal 17-amino-acid region common between these repeats that was species specific. The epitope in R4 was distinct from that of R2 and R3 and was found to have conformational dependence. VLPT was detected in supernatants from infected cells, indicating that the protein was secreted. VLPT was localized on both reticulate and dense-core cells, and it was found extracellularly in the morula fibrillar matrix and associated with the morula membrane.
Selective cytokine gene expression in renal cell carcinoma tumor cells and tumor‐infiltrating lymphocytes (1995)

The progression of tumors such as renal cell carcinoma (RCC), despite the presence of substantial lymphocytic infiltrates (TIL), suggests that the ability of the local immune response to control tumor growth is impaired. Cytokine gene expression was examined to further investigate the nature of this response. Initial studies were performed with frozen tumors using PCR-assisted mRNA amplification with cytokine-specific primers for interleukin 10 (IL-10), interleukin 2 (IL-2) and interferon-gamma (IFN-gamma). IL-2 mRNA was not detected, despite the presence of T cells as defined by the expression of CD3 gamma mRNA. In contrast, mRNA for IFN-gamma was expressed in 4/9 and for IL-10 in 5/9 tumors. To confirm this, 5 fresh tumor specimens were examined, and PCR demonstrated that IL-10 mRNA was detectable in 4/5 tumors from which RNA was isolated at the time of nephrectomy. In these experiments multiple cycles and dilutions were employed to semi-quantitate the expression of IL-10. To identify potential sources of this cytokine in the tumor bed, IL-10 mRNA expression in freshly isolated lymphocytes and tumor cells, TIL lines, cultured RCC and established RCC lines was examined. Our studies demonstrate that within the tumor TIL may be one source of IL-10. Lymphocyte-enriched populations from 4/5 tumors expressed IL-10 mRNA as did 4/6 freshly isolated tumor cell preparations. IL-10 gene expression was not detected, however, in tumor cells after one passage in vitro in short-term cultured RCC tumor cells (passages 2-5) or in established RCC tumor cell lines. Finally, 4/9 CD4+ and 2/5 CD8+ TIL lines expressed IL-10 mRNA either constitutively or after stimulation with anti-CD3 antibody. This finding was associated with IL-10 production in vitro. Our studies demonstrate that IL-10 mRNA is frequently present in RCC tumors and may originate from the tumor-infiltrating mononuclear cell population.
High-gain, broad spectral bandwidth erbium-doped fibre amplifier pumped near 1.5μm (1989)

A small-signal gain exceeding 25 dB, and a 3dB spectral bandwidth of 35 nm around 1.545μm are obtained for an erbium-doped silica fibre amplifier pumped in the short wavelength wing of the 1.5μm absorption band.
Metric-based shape retrieval in large databases (2003)

This paper examines the problem of database organization and retrieval based on computing metric pairwise distances. A low-dimensional Euclidean approximation of a high-dimensional metric space is not efficient, while search in a high-dimensional Euclidean space suffers from the curse of dimensionality. Thus, techniques designed for searching metric spaces must be used. We evaluate several such existing exact metric-based indexing techniques, and show that they require extensive computational effort. This motivates the development of an approximate nearest neighbor search technique where the k nearest neighbors are used to approximate the local neighborhood of a point. The resulting kNN graph is searched in a best-first fashion producing excellent indexing efficiency.
Non-linear optoelectronic phase-locked loop for stabilization of opto-millimeter waves: towards a narrow linewidth tunable THz source (2011)

We propose an optoelectronic phase-locked loop concept which enables to stabilize optical beat notes at high frequencies in the mm-wave domain. It relies on the use of a nonlinear-response Mach-Zehnder modulator. This concept is demonstrated at 100 GHz using a two-axis dual-frequency laser turned into a voltage controlled oscillator by means of an intracavity electrooptic crystal. A relative frequency stability better than 10⁻¹¹ is reported. This approach of optoelectronic down conversion opens the way to the realization of continuously tunable ultra-narrow linewidth THz radiation.
Characterization of Insulin Secretion and Resistance in Type 2 Diabetes of Adolescents (2006)

These data emphasize that together with marked insulin resistance, the failure of beta-cell function is a major component in the course of T2D in childhood.
A pneumatic pressure-driven multi-throughput microfluidic circulation culture system (2016)

Here, we report a pneumatic pressure-driven microfluidic device capable of multi-throughput medium circulation culture. The circulation culture system has the following advantages for application in drug discovery: (i) simultaneous operation of multiple circulation units, (ii) use of a small amount of circulating medium (3.5 mL), (iii) pipette-friendly liquid handling, and (iv) a detachable interface with pneumatic pressure lines via sterile air-vent filters. The microfluidic device contains three independent circulation culture units, in which human umbilical vein endothelial cells (HUVECs) were cultured under physiological shear stress induced by circulation of the medium. Circulation of the medium in the three culture units was generated by programmed sequentially applied pressure from two pressure-control lines. HUVECs cultured in the microfluidic device were aligned under a one-way circulating flow with a shear stress of 10 dyn cm(-2); they exhibited a randomly ordered alignment under no shear stress and under reciprocating flow with a shear stress of 10 dyn cm(-2). We also observed 2.8- to 4.9-fold increases in expression of the mRNAs of endothelial nitric oxide synthase and thrombomodulin under one-way circulating flow with a shear stress of 10 dyn cm(-2) compared with conditions of no shear stress or reciprocating flow.
Androgen Receptor Length Polymorphism Associated with Prostate Cancer Risk in Hispanic Men (2002)

To our knowledge, our study represents the first case-control study of the androgen receptor gene in a Hispanic population and provides evidence of the increased prostate cancer risk associated with short CAG repeats. Our results suggest that short CAG repeats are associated with an increased prostate cancer risk in Hispanic men.
New pentafluorothio(SF5) alkylsulfonic acids (1989)

New pentafluorothioalkylsulfonic acids, F 5 SCXHCY 2 SO 3 H (X, Y = H, F), and the corresponding salts have been prepared from pentafluorothioalkyl bromides or olefins with sodium sulfite or sodium bisulfite. The compounds are characterized by ir, nmr ( 1 H, 19 F, 13 C), and mass spectra. Keywords: new pentafluorothioalkylsulfonic acids.
Induction of differentiation in murine myelomonocytic leukemia cells by the serum of patients with acute myeloid leukemia and other diseases (1981)

Sera from patients with leukemia, lymphomas or other diseases were tested for their capacity to induce differentiation in colonies produced in semi-solid agar by the mouse myelomonocytic leukemia, WEHI-3B. Of 949 samples tested, higher than normal differentiating activity was detected in patients with infections (31% of sera tested) and with acute myeloid leukemia in relapse (35% of sera tested). The higher activity of the latter sera was correlated with the concurrent presence of infections in the relapse leukemic patients. Elevated differentiating activity was also observed in sera from patients with neutrophil levels below 1,000/microliter even if infections were not present. The study indicates that patients with acute myeloid leukemia are able to elevate serum differentiating activity in response to infections or neutropenia and that the serum differentiating factors could play a role in suppressing myeloid leukemic populations by enforcing differentiation in the leukemic cells.
Intercellular communication between vascular smooth muscle and endothelial cells mediated by heparin‐binding epidermal growth factor‐like growth factor and vascular endothelial growth factor (1998)

Heparin-binding epidermal growth factor-like growth factor (HB-EGF), a potent mitogen and migration factor for vascular smooth muscle cells (SMC), promoted neovascularization in vivo in the rabbit cornea. MRI demonstrated quantitatively the angiogenic effect of HB-EGF when introduced subcutaneously into nude mice. HB-EGF is not directly mitogenic to endothelial cells but it induced the migration of bovine endothelial cells and release of endothelial cell mitogenic activity from bovine vascular SMC. This mitogenic activity was specifically blocked by neutralizing anti-vascular endothelial growth factor (VEGF) antibodies. In contrast, EGF or transforming growth factor-alpha (TGF-alpha) had almost no effect on release of endothelial mitogenicity from SMC. In addition, RT-PCR analysis demonstrated that VEGF165 mRNA levels were increased in vascular SMC 4-10-fold by 0.35-2 nM of HB-EGF, respectively. Our data suggest that HB-EGF, as a mediator of intercellular communication, may play a new important role in supporting wound healing, tumor progression and atherosclerosis by stimulating angiogenesis.
Systematic Review of the Neurobiological Relevance of Chemokines to Psychiatric Disorders (2015)

Psychiatric disorders are highly prevalent and disabling conditions of increasing public health relevance. Much recent research has focused on the role of cytokines in the pathophysiology of psychiatric disorders; however, the related family of immune proteins designated chemokines has been relatively neglected. Chemokines were originally identified as having chemotactic function on immune cells; however, recent evidence has begun to elucidate novel, brain-specific functions of these proteins of relevance to the mechanisms of psychiatric disorders. A systematic review of both human and animal literature in the PubMed and Google Scholar databases was undertaken. After application of all inclusion and exclusion criteria, 157 references were remained for the review. Some early mechanistic evidence does associate select chemokines with the neurobiological processes, including neurogenesis, modulation of the neuroinflammatory response, regulation of the hypothalamus-pituitary-adrenal axis, and modulation of neurotransmitter systems. This early evidence however does not clearly demonstrate any specificity for a certain psychiatric disorder, but is primarily relevant to mechanisms which are shared across disorders. Notable exceptions include CCL11 that has recently been shown to impair hippocampal function in aging - of distinct relevance to Alzheimer's disease and depression in the elderly, and pre-natal exposure to CXCL8 that may disrupt early neurodevelopmental periods predisposing to schizophrenia. Pro-inflammatory chemokines, such as CCL2, CCL7, CCL8, CCL12, and CCL13, have been shown to drive chemotaxis of pro-inflammatory cells to the inflamed or injured CNS. Likewise, CX3CL has been implicated in promoting glial cells activation, pro-inflammatory cytokines secretion, expression of ICAM-1, and recruitment of CD4+ T-cells into the CNS during neuroinflammatory processes. With further translational research, chemokines may present novel diagnostic and/or therapeutic targets in psychiatric disorders.
Purification and Properties of a NADPH‐Dependent Erythrose Reductase from the Newly Isolated Torula corallina (2003)

Torula corallina (KCCM-10171) is a yeast strain that is currently used for the industrial production of erythritol and has the highest erythritol yield ever reported for an erythritol-producing microorganism. Production of erythritol in T. corallina is catalyzed by erythrose reductase, an enzyme that converts erythrose to erythritol using NADPH as a cofactor. In this study, NADPH-dependent erythrose reductase was purified to homogeneity from the newly isolated T. corallina. The relative molecular weight of the erythrose reductase as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and size exclusion chromatography was 35.4 and 71.0 kDa, respectively, indicating that the enzyme is dimeric. This enzyme catalyzed both erythrose reduction and erythritol oxidation; both enzyme activities required NADP(H). The pH and temperature optima for erythrose reduction and erythritol oxidation were 6.0, 40 degrees C and 8.0, 45 degrees C, respectively. The sequence of the first 10 amino acids of this enzyme was N-V-K-N-F-Y-Q-P-N-D. The affinity (K(m)( )()= 7.12 mM) of the enzyme for erythrose was comparable to that of other known erythrose reductases, and the specificity for erythrose was very high, resulting in no production of other polyols, which may explain the high erythritol yield observed in this strain.
Measuring Curvature of Mirrors Using Image Analysis (1998)

&lt;div class="htmlview paragraph"&gt;This paper describes a method for measuring the radius of curvature of mirrors by measuring the size of the reflected image. The image is generated by a video camera, captured using an image grabber board and analyzed using custom software on a standard computer. The system is shown to be capable to higher resolution than the current SAE defined spherometer and capable of determining radius of curvature over a smaller area. The latter is particularly important in using the system for measuring aspheric mirrors.&lt;/div&gt;
INTRODUCTION OF FOREIGN GENES INTO THE SEED EMBRYO CELLS OF RICE BY ELECTRO-INJECTION AND THE REGENERATION OF TRANSGENIC RICE PLANTS (1991)

The NPTII gene has been successfully transferred to the seed embryo cells of two rice varieties (Oryza sativa L. subsp. indica cv. Sanerai and Qryza sativa L. subsp. japonica cv. Nonghu No. 6) by means of electroinjection. Resistant calli were screened out on MS medium with 100 μg/ml Km. Transgenic rice plants were regenerated via somatic embryogenesis. Both NPTII detection and Southern blot hybridization demonstrate that the foreign gene has integrated and expressed stably in the transformants.
Reoperation in a Jehovah's Witness 22 years after aortic allograft reconstruction of the right ventricular outflow tract. (2003)

We report the case of a 29-year-old male Jehovah's Witness who presented with hemolysis and right heart failure as a consequence of extreme calcification of an aortic valve-containing allograft and Dacron prosthesis that had been placed 22 years earlier to repair tetralogy of Fallot. Reoperation had been denied by several other centers, because of the patient's refusal to undergo blood transfusion. For 2 weeks preoperatively, we raised the patient's hemoglobin level by treating him with recombinant erythropoietin, oral iron, and folic acid. At surgery, under normothermic cardiopulmonary bypass, we replaced the aortic allograft in the right ventricular outflow tract with a cryopreserved pulmonary allograft, also containing a valve. The postoperative course was uneventful, and the patient was released from the hospital on the 13th postoperative day in excellent condition.
Novel Immunotherapies (2009)

Multiple myeloma is still a fatal disease. Despite advances in high-dose chemotherapy and stem-cell transplantation and the development of novel therapeutics, relapse of the underlying disease remains the primary cause of treatment failure. Strategies for posttransplantation immunomodulation are desirable for eradication of remaining tumor cells. To this end, immunotherapy aimed at inducing myeloma-specific immunity in patients has been explored. Idiotype protein, secreted by myeloma cells, has been the primary target for immunotherapy as it is the best defined tumor-specific antigen. This chapter focuses on novel immunotherapies that are being developed to treat patients with myeloma. I will discuss potential myeloma antigens, antigen-specific T cells, and their function on myeloma tumor cells, and T-cell-based and antibody-based immunotherapies for myeloma. Furthermore, clinical studies of T-cell-based immunotherapy in the form of vaccination, allogeneic stem-cell transplantation and donor lymphocyte infusions, with or without donor vaccination using patient-derived idiotype, and future application of donor-derived or patient-derived, antigen-specific T-cell infusion in this disease are also discussed. Based on the specificity of the immune effector molecules and cells, immunotherapies with specific T cells or therapeutic antibodies may represent novel strategies for the treatment of multiple myeloma in the near future.
Metal nano-dot memory for high-density non-volatile memory application (2005)

New nonvolatile memory with extremely high density metal nanodots, MND (metal nanodot) memory, is proposed for a future high density nonvolatile memory application (Takata et al., 2003). Fundamental characteristics of the MND memory were evaluated. MND film is used as a charge retention layer in the MND memory. The MND film consists of the thin oxide film that dispersively includes high density metal dots with nanoscale. The MND film is formed by using sputtering technique with a special sputtering target. The diameter and the density of the MND in the film are typically 2-3 nm and around 2 /spl times/ 10/sup 13//cm/sup 2/, respectively, which were superior to that of Si nanodot memory. Nonvolatile memory operation at a relatively low voltage and good endurance characteristic were confirmed in the MND memory fabricated according to the conventional MOS process.