gebhart/patrepeval huggingface dataset:
Biochemical characterization of the extracellular domain of the 75-kilodalton tumor necrosis factor receptor (1993)

An expression plasmid encoding the extracellular domain of the 75-kDa human tumor necrosis factor (TNF) type 2 receptor (TNF-R2) was constructed and used to generate a stable cell line secreting soluble TNF-R2 (sTNF-R2). Purified sTNF-R2 was resolved by SDS-PAGE into one band of approximate M(r) 43,000, consistent with a molecular weight of 36,000 +/- 4800 obtained by sedimentation equilibrium analysis. The apparent molecular weight observed by gel filtration chromatography was approximately 136,000. Glycosylation analysis revealed that Asn-149 is fully glycosylated, while Asn-171 is incompletely glycosylated (approximately 50%), and that a proline-, serine-, and threonine-rich region (residues 175-234) contains O-linked carbohydrate structures. Scatchard analysis of [125I]TNF-alpha and [125I]TNF-beta binding to sTNF-R2 gave dissociation constants (Kd) of 0.3 and 0.75 nM, respectively, comparable to those observed for intact cell-surface TNF-R2. The sTNF-R2 was found to block the cytotoxicity of both TNF-alpha and TNF-beta in a murine L-M cell assay. The sizes of the sTNF-R2.TNF-alpha and sTNF-R2.TNF-beta complexes determined by gel filtration chromatography were approximately 322 and 204 kDa, respectively. The stoichiometry of the sTNF-R2.TNF-alpha and sTNF-R2.TNF-beta complexes were examined by size-exclusion chromatography, sedimentation equilibrium, and cross-linking. The data from these studies suggest that at least two molecules of sTNF-R2 can bind to a single TNF-alpha or TNF-beta trimer.
In vitro antimicrobial susceptibility testing of Borrelia burgdorferi: a microdilution MIC method and time-kill studies (1992)

The susceptibility of Borrelia burgdorferi, the causative agent of Lyme borreliosis, to various antimicrobial agents varies widely among published studies. These differences are probably due in part to variations in susceptibility testing techniques and growth endpoint determinations. We developed a microdilution method for determining the MICs of antibiotics against B. burgdorferi. The method incorporated BSK II medium, a final inoculum of 10(6) cells per ml, and a 72-h incubation period and was found to be simple and highly reproducible. A variety of antibiotics and strains of B. burgdorferi and one strain of Borrelia hermsii were examined by this method. MICs of penicillin, ceftriaxone, and erythromycin for the B31 strain of B. burgdorferi were 0.06, 0.03, and 0.03 microgram/ml, respectively. We compared the MICs obtained by the microdilution method with those obtained by a macrodilution method using similar criteria for endpoint determinations and found the values obtained by both methods to be in close agreement. To further investigate the bactericidal activities of penicillin, ceftriaxone, and erythromycin against strain B31, we used subsurface plating to determine MBCs and we also performed time-kill studies. The MBCs of penicillin, ceftriaxone, and erythromycin were 0.125, 0.03, and 0.06 micrograms/ml, respectively. Time-kill curves demonstrated a greater than or equal to 3-log10-unit killing after 72 h with penicillin, ceftriaxone, and erythromycin; ceftriaxone provided the greatest reduction in CFU. The described methods offer a more standardized and objective approach to susceptibility testing of B. burgdorferi.
OT-CLL: a human T cell chronic lymphocytic leukemia that produces IL 2 in high titer. (1982)

This report identifies and describes a human T cell chronic lymphocytic leukemia, OT-CLL, which can be triggered by selected mitogens (either PHA or Con A) to produce IL 2 in high titer. Optimal IL 2 production requires culturing OT-CLL cells at 2 to 5 X 10(6)/ml for 24 hr in the presence of 1 to 2% PHA-M. Under these conditions, the titer of IL 2 generated is greater than 20-fold that obtained from conventional sources, e.g., from mitogen-activated tonsillar lymphocytes. Two lines of experimental evidence suggest that the tumor cell product(s) is IL 2. First, in functional assays, suprenatants derived from cultures of PHA-activated OT-CLL cells trigger the proliferation and long-term growth of IL 2-dependent human TCL cells. Second, a partial biochemical purification of the active moiety(ies) derived from OT-CLL demonstrates marked similarity to conventional human IL 2. Thus, the biologically active material(s) precipitates in 50 to 70% saturated (NH4)2 SO4 solutions; elutes from DEAE-Sepharose in the presence of 0.04-0.08 M NaCl; and has an apparent m.w. of approximately 14,000, as determined by Sephadex G-100 gel filtration. In addition, analysis of OT-CLL cells by indirect immunofluorescence, utilizing a panel of monoclonal antibodies, confirms not only that these tumor cells are of T cell lineage but that they display surface antigens that define the normal human peripheral T cell subset subserving helper or inducer function: OKT3+, OKT4+ , OKT8-.
Minireview: Update on Incretin Biology: Focus on Glucagon-Like Peptide-1 (2010)

The incretin hormone, glucagon-like peptide-1 (GLP-1), is now being used in the clinic to enhance insulin secretion and reduce body weight in patients with type 2 diabetes. Although much is already known about the biology of GLP-1, much remains to be understood. Hence, this review will consider recent findings related to the potential for enhancing endogenous levels of GLP-1 through selective use of secretagogues and the beneficial cardiovascular, neuroprotective, and immunomodulatory effects of GLP-1, as well as the possible effects of GLP-1 to enhance beta-cell growth and/or to induce pancreatitis or thyroid cancer. Finally, the potential for molecular medicine to enhance the success of GLP-1 therapy in the clinic is considered. A better understanding of the fundamental biology of GLP-1 may lead to new therapeutic modalities for the clinical use of this intestinal hormone.
Theoretical and experimental studies on active Y-junctions in optical waveguides (1978)

Theoretical and experimental results are presented on single-mode <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Y</tex> -junction switching devices in Ti-diffused LiNbO <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</inf> waveguides. The operation of these devices relies on a redistribution, by means of the elcctrooptic effect, of the power in the input waveguide before it is transmitted to the output waveguides of the <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Y</tex> -junction. Measured performance is shown to be predicted satisfactorily by a theoretical model of a <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Y</tex> -junction in homogeneous, planar waveguide. Transmission losses of less than 1 dB and extinction ratios of about 15 dB have been obtained in a device with a junction half-angle of 0.57°.
InGaAs quantum wells on wafer-bonded InP∕GaAs substrates (2005)

Wafer bonding and hydrogen implantation exfoliation techniques have been used to fabricate a thin InP template layer on GaAs with intermediate silicon nitride bonding layers. This template layer was used to directly compare subsequent metal organic vapor phase epitaxial growth of InGaAs∕InAlAs quantum-well structures on these wafer-bonded templates to growth on a standard InP substrate. Chemical mechanical polishing of the bonded structure and companion InP substrates was assessed. No effects from the coefficient of thermal mismatch are detected up to the growth temperature, and compositionally equivalent structures are grown on the wafer-bonded InP template and the bare InP substrate. However, after growth dislocation, loops can be identified in the InP template layer due to the ion implantation step. These defects incur a slight mosaic tilt but do not yield any crystalline defects in the epitaxial structure. Low-temperature photoluminescence measurements of the InGaAs grown on the template structure and the InP substrate exhibit near-band-edge luminescence on the same order; this indicates that ion implantation and exfoliation is a viable technique for the integration of III-V materials.
Structural and affinity studies of IgM polyreactive natural autoantibodies (1997)

Natural polyreactive autoantibodies (NAA) are an important component of the normal B cell repertoire. One intriguing characteristic of these Abs is their binding to various dissimilar Ags. It has been generally assumed that these Abs bind the Ags with low affinity, and are encoded by germline genes. We have used surface plasmon resonance to determine binding of avidities, and conducted a structural analysis of five murine monoclonal natural autoantibodies displaying a typical polyreactive binding pattern against cytoskeleton Ags and DNA. We show that 1) all the five Abs bind the different Ags with kinetic constants similar to those observed for immune Abs; 2) they express a restricted set of V(H) and V(L) genes, since the same V(H) gene is expressed by three out of the five, and one particular Vkappa gene was expressed twice. In addition, a single D gene segment was used by three of the five Abs; and 3) they express, in most cases, genes in a close germline configuration. Our amino acid sequence and modeling studies show that the distribution of exposed side chains in the NAA paratopes is close to the general pattern observed in the complementarity-determining regions (CDRs) of variable domains from immune Abs. Although CDR3 regions of the heavy chain have been postulated to play a major role in determining polyreactivity on the basis of recombinatorial experiments, our results failed to show any distinctive particularity of this region in terms of length or charge when compared with classical immune Abs.
Blood flow, oxygen and nutrient supply, and metabolic microenvironment of human tumors: a review. (1989)

The objective of this review article is to summarize current knowledge of blood flow and perfusion-related parameters, which usually go hand in hand and in turn define the cellular metabolic microenvironment of human malignancies. A compilation of available data from the literature on blood flow, oxygen and nutrient supply, and tissue oxygen and pH distribution in human tumors is presented. Whenever possible, data obtained for human tumors are compared with the respective parameters in normal tissues, isotransplanted or spontaneous rodent tumors, and xenografted human tumors. Although data on human tumors in situ are scarce and there may be significant errors associated with the techniques used for measurements, experimental evidence is provided for the existence of a compromised and anisotropic blood supply to many tumors. As a result, O2-depleted areas develop in human malignancies which coincide with nutrient and energy deprivation and with a hostile metabolic microenvironment (e.g., existence of severe tissue acidosis). Significant variations in these relevant parameters must be expected between different locations within the same tumor, at the same location at different times, and between individual tumors of the same grading and staging. Furthermore, this synopsis will attempt to identify relevant pathophysiological parameters and other related areas future research of which might be most beneficial for designing individually tailored treatment protocols with the goal of predicting the acute and/or long-term response of tumors to therapy.
Reduced skin tumor development in cyclin D1-deficient mice highlights the oncogenic ras pathway in vivo (1998)

Cyclin D1 is part of a cell cycle control node consistently deregulated in most human cancers. However, studies with cyclin D1-null mice indicate that it is dispensable for normal mouse development as well as cell growth in culture. Here, we provide evidence that ras-mediated tumorigenesis depends on signaling pathways that act preferentially through cyclin D1. Cyclin D1 expression and the activity of its associated kinase are up-regulated in keratinocytes in response to oncogenic ras. Furthermore, cyclin D1 deficiency results in up to an 80% decrease in the development of squamous tumors generated through either grafting of retroviral ras-transduced keratinocytes, phorbol ester treatment of ras transgenic mice, or two-stage carcinogenesis.
3D Geological Model Construction Using a 3D Grid (2002)

This paper describes new approach to modelling geological structuren, using a grid of pillars in 3D. This method allows the creation of faults, horizons and zones within a single 3D grid. The construction of the grid is performed step by step, using the original data directly, as seismic interpretation and well picks
Organization of the recA gene of Escherichia coli. (1980)

The restriction map of a BamHI DNA fragment that contains the recA gene of Escherichia coli has been established and a large portion of the fragment's nucleotide sequence has been determined. The coding region of the recA gene contains 1059 nucleotide residues and encodes a single protein of 353 amino acid residues. The amino acid sequence of the first five residues of the NH2 terminus of the recA protein agrees with the sequence predicted from the DNA sequence except for the absence of formylmethionine in the purified protein. Immediately after the coding sequence, there is a G+C-rich sequence with dyad symmetry followed by an A+T-rich sequence. These could signal termination of transcription. The site of initiation for synthesis in vitro of the recA messenger RNA has been determined by analysis of the 5' nucleotide sequence of [gamma-32P]ATP-labeled transcripts. The promoter region shos a high degree of symmetry and contains sequences commonly found in recognition and binding sites for RNA polymerase.
Sunlight-Induced Bromate Formation in Chlorinated Seawater (1977)

Chlorinated waters are being introduced into estuarine and coastal areas in increasing quantities. In such systems, the chlorine reacts with the natural bromide and ammonia to produce the highly toxic hypobromous acid, hypobromite ion, and haloamines. Sunlight causes up to 50 percent conversion to bromate ion, which is persistent in natural waters and has an unknown toxicity.
An AAV-derived Apaf-1 dominant negative inhibitor prevents MPTP toxicity as antiapoptotic gene therapy for Parkinson's disease (2001)

Adeno-associated virus (AAV) vector delivery of an Apaf-1-dominant negative inhibitor was tested for its antiapoptotic effect on degenerating nigrostriatal neurons in a 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) model of Parkinson's disease. The wild-type caspase recruitment domain of Apaf-1 was used as a dominant negative inhibitor of Apaf-1 (rAAV-Apaf-1-DN-EGFP). An AAV virus vector was used to deliver it into the striatum of C57 black mice, and the animals were treated with MPTP. The number of tyrosine hydroxylase-positive neurons in the substantia nigra was not changed on the rAAV-Apaf-1-DN-EGFP injected side compared with the noninjected side. We also examined the effect of a caspase 1 C285G mutant as a dominant negative inhibitor of caspase 1 (rAAV-caspase-1-DN-EGFP) in the same model. However, there was no difference in the number of tyrosine hydroxylase-positive neurons between the rAAV-caspase-1-DN-EGFP injected side and the noninjected side. These results indicate that delivery of Apaf-1-DN by using an AAV vector system can prevent nigrostriatal degeneration in MPTP mice, suggesting that it could be a promising therapeutic strategy for patients with Parkinson's disease. The major mechanism of dopaminergic neuronal death triggered by MPTP seems to be the mitochondrial apoptotic pathway.
폐색성 동맥경화증에 대한 대퇴슬괵부 맥관재건술 1예보고 (1972)

A case of peripheral arterial sclerosis developed in a very young male who was treated at Capital 
Armed Forces General Hospital is presented. The literature on the subject is reviewed and the various surgical management for femoropopliteal occlusive disease are described. It is fairly well accepted today that autogenous saphenous vein bypass grafts offer the best results in the treatment of these lesions. There are many reports in the literatures that support this opinion and long term results of the autogenous saphenous bypass graft over the other procedures in the reconstructive surgery below the groin. The proper interpretation of the preoperative angiography is of utmost importance. This patient with recurrent infection on right great toe had a good distal run-off suited for bypass grafting . An aggressive surgical approach to this patient may avoid amputation. A good operative result was obtained from this patient with intermittent claudication and good distal run-off in angiography by means of saphenous vein bypass graft on right side and open thromboendarterectomy on left side.
Mobile Phone Based Clinical Microscopy for Global Health Applications (2009)

Light microscopy provides a simple, cost-effective, and vital method for the diagnosis and screening of hematologic and infectious diseases. In many regions of the world, however, the required equipment is either unavailable or insufficiently portable, and operators may not possess adequate training to make full use of the images obtained. Counterintuitively, these same regions are often well served by mobile phone networks, suggesting the possibility of leveraging portable, camera-enabled mobile phones for diagnostic imaging and telemedicine. Toward this end we have built a mobile phone-mounted light microscope and demonstrated its potential for clinical use by imaging P. falciparum-infected and sickle red blood cells in brightfield and M. tuberculosis-infected sputum samples in fluorescence with LED excitation. In all cases resolution exceeded that necessary to detect blood cell and microorganism morphology, and with the tuberculosis samples we took further advantage of the digitized images to demonstrate automated bacillus counting via image analysis software. We expect such a telemedicine system for global healthcare via mobile phone -- offering inexpensive brightfield and fluorescence microscopy integrated with automated image analysis -- to provide an important tool for disease diagnosis and screening, particularly in the developing world and rural areas where laboratory facilities are scarce but mobile phone infrastructure is extensive.
A classification for extant ferns (2006)

Abstract We present a revised classification for extant ferns, with emphasis on ordinal and familial ranks, and a synopsis of included genera. Our classification reflects recently published phylogenetic hypotheses based on both morphological and molecular data. Within our new classification, we recognize four monophyletic classes, 11 monophyletic orders, and 37 families, 32 of which are strongly supported as monophyletic. One new family, Cibotiaceae Korall, is described. The phylogenetic affinities of a few genera in the order Polypodiales are unclear and their familial placements are therefore tentative. Alphabetical lists of accepted genera (including common synonyms), families, orders, and taxa of higher rank are provided.
Prognostic significance of c-erbB-2 and estrogen receptor status in human breast cancer. (1991)

Using the 21N polyclonal antibody, we immunohistochemically stained 314 primary breast carcinomas to identify those tumors overexpressing the c-erbB-2 oncoprotein and to ascertain the prognostic significance of this expression on disease-free and overall survival. Positive membrane staining was present in 52 (17%) of these carcinomas of which 7 (13%) were ductal carcinomas in situ. There was no significant relationship between c-erbB-2 positivity and (a) age at diagnosis, (b) menopausal status, (c) tumor size, (d) lymph node status, (e) estrogen receptor status, or (f) whether or not the patient had disseminated disease outside the axillary fields. However, c-erbB-2-positive tumors were significantly associated with poorer grade (P = 0.02). Patients who were positive for this oncoprotein had a shorter disease-free survival (P = 0.002) and reduced overall survival (P = 0.0001). Overexpression of this oncoprotein was predictive of a worse prognosis in lymph node-positive disease (P = 0.003) and in patients presenting with grade II tumors (P = 0.001). Stratifying the patients on the basis of estrogen receptor status suggested that c-erbB-2+/estrogen receptor-negative status was predictive of a poorer prognosis when compared with the other subgroups (P less than 0.001). Primary and recurrent tumor tissues were available from 42 of the 314 patients. Identical patterns of c-erbB-2 expression occurred in 95% of cases, arguing against a direct role for c-erbB-2 expression in the process of tumor dissemination. The high incidence of staining in ductal carcinomas in situ suggests that expression of this oncoprotein is an early event in tumorigenesis. Finally, multivariate analysis indicated that the c-erbB-2 oncoprotein was an independent prognostic indicator for overall survival in breast carcinoma patients.
Probing cortical dopamine function in schizophrenia: what can D1 receptors tell us? (2003)

Schizophrenia is characterized by positive symptoms, negative symptoms and cognitive impairment. Positive symptoms may be related to excessive dopamine (DA) function, as suggested by the common antidopaminergic properties of antipsychotic medications, which are most effective at treating positive symptoms. Negative symptoms and impairment in higher cognitive functions are thought to be related to a dysfunction of the dorsolateral prefrontal cortex (DLPFC), possibly related to inappropriate stimulation of D1 receptors. In the last few years we have clearly demonstrated excess subcortical DA transmission and now have indirect evidence for cortical dopamine deficit. We studied 16 drug free patients with schizophrenia (7 drug naïve and 9 previously treated) and 16 matched controls, using positron emission tomography (PET) and [(11)C]NNC 112, a novel radiotracer for PET imaging of the D1 receptor, and the n-back task, a test of working memory. We observed a significant upregulation in D1 binding in the DLPFC in patients with schizophrenia compared to controls. This increase was present in both drug naïve and previously treated patients and was regionally selective. Furthermore, the increase was correlated with poor performance on the n-back task (r(2)=0.45, p=0.004). This upregulation of D1 receptors might be secondary to a sustained deficit in prefrontal DA function, as postmortem studies revealed deficits in DA innervation in the prefrontal cortex in schizophrenia.
Ultrafast optical imaging technology: principles and applications of emerging methods (2016)

Abstract High‐speed optical imaging is an indispensable technology for blur‐free observation of fast transient dynamics in virtually all areas including science, industry, defense, energy, and medicine. High temporal resolution is particularly important for microscopy as even a slow event appears to occur “fast” in a small field of view. Unfortunately, the shutter speed and frame rate of conventional cameras based on electronic image sensors are significantly constrained by their electrical operation and limited storage. Over the recent years, several unique and unconventional approaches to high‐speed optical imaging have been reported to circumvent these technical challenges and achieve a frame rate and shutter speed far beyond what can be reached with the conventional image sensors. In this article, we review the concepts and principles of such ultrafast optical imaging methods, compare their advantages and disadvantages, and discuss an entirely new class of applications that are possible using them.