gebhart/patrepeval huggingface dataset:
Control of the cell-specificity of σF activity in Bacillus subtilis (1996)

Sporulation in Bacillus subtilis is a simple developmental system involving the differentiation of two cell types that are formed by an asymmetric cell division. Major changes in the pattern of transcription during sporulation are brought about by the synthesis of new sigma factors (sigma), which are subunits of RNA polymerase that determine promoter specificity. Transcription in the smaller prespore cell type is initiated by a sigma factor called sigma F, the activity of which is subject to tight spatial and temporal control. It is negatively regulated by an anti-sigma factor, SpoIIAB, which is in turn controlled by an anti-anti-sigma factor, SpoIIAA. SpoIIAA and SpoIIAB participate in two contrasting reactions in vitro. In the presence of ATP, the proteins interact transiently and SpoIIAA is inactivated by phosphorylation on a specific serine residue; SpoIIAA then remains free to inhibit sigma F. In the presence of ADP, SpoIIAA binds tightly to SpoIIAB, and sigma F is set free. Release of sigma F activity in vivo might thus be effected by a prespore-specific reduction in the ATP/ADP ratio. Genetic experiments have implicated a fourth protein, called SpoIIE, in this system. It now appears that SpoIIE has two important and independent functions in the establishment of the prespore-specific transcription by sigma F. First it regulates sigma F activity, probably acting as a phosphatase to regenerate the active, non-phosphorylated form of SpoIIAA. Second it controls the formation of the septum that generates the prespore compartment. Combination of these two functions in a single polypeptide may provide a means of coupling gene expression with morphogenesis.
In Vitro Release Behavior of Dextran-Methacrylate Hydrogels Using Doxorubicin and other Model Compounds (2000)

In vitro drug release behavior of doxorubicin, Alizarin Red S, FITC-dextran from photocross-linked dextran-methacrylate hydrogel was studied. The effects of pH of media, degree of substitution (DS) of dextran-methacrylate hydrogel, and molecular weight of model compounds on their release profiles were investigated. Each model compound was successfully incorporated into dextran-methacrylate hydrogel matrix through photopolymerization of the hydrogel precursor. Delayed release of model compounds was observed with these hydrogels having a higher DS. Doxorubicin and Alizarin Red S showed pH-dependent release behavior because of the presence of ionizable groups in their structure. Different types of ionization of doxorubicin and Alizarin Red S resulted in more release into an acidic or alkaline media. As molecular weights of drugs increased, the total amount of released drug at the end of 240 hrs decreased significantly and reached a minimum level as the MW of drugs reached about 10,000. Release of these three model compounds followed simple Fickian diffusion at an early stage of release, i.e., cumulative release of model compounds was proportional to the square root of time. Dextran-methacrylate hydrogel effectively delayed and controlled the release of anticancer antibiotics, doxorubicin.
Co-channel interference modeling and analysis in a poisson field of interferers in wireless communications (2003)

The paper considers interference in a wireless communication network caused by users that share the same propagation medium. Under the assumption that the interfering users are spatially Poisson distributed and under a power-law propagation loss function, it has been shown in the past that the interference instantaneous amplitude at the receiver is /spl alpha/-stable distributed. Past work has not considered the second-order statistics of the interference and has relied on the assumption that interference samples are independent. In this paper, we provide analytic expressions for the interference second-order statistics and show that depending on the properties of the users' holding times, the interference can be correlated. We provide conditions under which the interference becomes m-dependent, /spl phi/-mixing, or long-range dependent. Finally, we present some implications of our theoretical findings on signal detection.
The frequency of hereditary large bowel cancer. (1983)

In brief, an unknown but small fraction of colorectal cancer in the United States is due to single gene traits that are usually easy to identify by the clinician who is aware of the many disorders which predispose to colorectal cancer. An additional, perhaps a larger fraction could be attributed to familial cancer syndromes which may arise from environmental or genetic factors or both. In any case, once a familial or mendelian trait is recognized, the risk to offspring and sibs tends to be 50%, since most predisposing traits behave in an autosomal dominant fashion. Easy means of surveillance and surgical prophylaxis are at hand. The largest hurdle, in my opinion, is to prod the health care system into thinking of and acting on the family history and to overcome the misconception that genetic disease is untreatable and unpreventable. Indeed, given poor control of the best known environmental carcinogens (sunlight and tobacco use), heritable colorectal cancer may well be the most manageable determinant of colorectal cancer--much more so, perhaps, than environmental factors like diet.
Regulation of thromboxane receptor activation in human platelets. (1989)

Thromboxane A2 (TxA2) is a potent platelet agonist that serves as an amplifying signal after exposure of platelets to other stimulants, such as thrombin, in vitro. Exposure of platelets to the TxA2 receptor agonists U46619 and SQ 26,655 (1.4 microM) resulted in a 60-90% decrease in subsequent TxA2 receptor-stimulated aggregation, calcium release, and protein kinase C activation. The desensitization was rapid, with a half-time of 2-3 min. The sequence of events involved in TxA2 receptor desensitization involves initial uncoupling of the receptor from a guanine nucleotide binding (G) protein followed by eventual receptor down-regulation. Consistent with this hypothesis were (i) a 60-70% decrease in SQ 26,655-stimulated platelet GTPase activity, (ii) a shift to the right of the dose-response curve for U46619-stimulated release of calcium [EC50, 275 +/- 51 nM (control)] vs. 475 +/- 71 nM (desensitized); P less than 0.01], and (iii) a delayed loss of receptor sites. In summary, exposure of platelets to TxA2 receptor agonists results in rapid desensitization of the biochemical and functional responses to interaction with its receptor in human platelets. The kinetics of these events are consistent with the hypothesis that this icosanoid functions in the regulation as well as amplification of platelet activation in vivo.
Complete Nucleotide Sequence of the Escherichia coli Plasmid pBR322 (1979)

I have determined the 4362-nucleotide-pair sequence of the plasmid cloning vector pBR322 using the DNA-sequencing technique of Maxam and Gilbert (1977). The DNA structure has several interesting features that lead to testable predictions.
Detection of Mycobacterium avium subsp. paratuberculosis by a Sonicate Immunoassay Based on Surface-Enhanced Raman Scattering (2007)

A sandwich immunoassay for the rapid, low-level detection of Mycobacterium avium subsp. paratuberculosis has been developed. M. avium subsp. paratuberculosis is the causative agent of Johne's disease in cattle, and one of the major obstacles in controlling the spread of this disease is the inability to rapidly detect small amounts of bacteria or other diagnostic markers shed during the subclinical stage of infection. This paper details the development and performance of an assay for sonicated M. avium subsp. paratuberculosis lysate that is based on surface-enhanced Raman scattering (SERS). There are two key components of the assay: (i) an immobilized layer of monoclonal antibodies that target a surface protein on the microorganism; and (ii) extrinsic Raman labels (ERLs) that are designed to selectively bind to captured proteins and produce large SERS signals. By correlating the number of M. avium subsp. paratuberculosis bacilli present prior to sonication to the amount of total protein in the resulting sonicate, the detection limit determined for total protein can be translated to the microorganism concentration. These findings yield detection limits of 100 and 200 ng/ml (estimated to be 500 and 1,000 M. avium subsp. paratuberculosis bacilli/ml) for sonicate spiked in phosphate buffer and sonicate spiked in whole milk, respectively. Moreover, the time required to complete the assay, which includes sample preparation, antigen extraction, ERL incubation, and readout, is less than 24 h. The potential for incorporation of this novel assay into diagnostic laboratories is also briefly discussed.
MicroRNA Cluster 302–367 Enhances Somatic Cell Reprogramming by Accelerating a Mesenchymal-to-Epithelial Transition (2011)

MicroRNAs (miRNAs) are emerging critical regulators of cell function that frequently reside in clusters throughout the genome. They influence a myriad of cell functions, including the generation of induced pluripotent stem cells, also termed reprogramming. Here, we have successfully delivered entire miRNA clusters into reprogramming fibroblasts using retroviral vectors. This strategy avoids caveats associated with transient transfection of chemically synthesized miRNA mimics. Overexpression of 2 miRNA clusters, 106a-363 and in particular 302-367, allowed potent increases in induced pluripotent stem cell generation efficiency in mouse fibroblasts using 3 exogenous factors (Sox2, Klf4, and Oct4). Pathway analysis highlighted potential relevant effectors, including mesenchymal-to-epithelial transition, cell cycle, and epigenetic regulators. Further study showed that miRNA cluster 302-367 targeted TGFβ receptor 2, promoted increased E-cadherin expression, and accelerated mesenchymal-to-epithelial changes necessary for colony formation. Our work thus provides an interesting alternative for improving reprogramming using miRNAs and adds new evidence for the emerging relationship between pluripotency and the epithelial phenotype.
Digital libraries, value, and productivity (1995)

A digital library is popularly viewed an electronic version of a public library. But replacing paper by electronic storage leads to three major differences: storage in digital form, direct communication to obtain material, and copying from a master version. These differences in turn lead to a plethora of further differences, so that eventually the digital library no longer mimics the traditional library. Furthermore, a library is only element in the process of creating, storing, culling, accessing, selecting, and distributing information to customers. While the technical focus of digital library research is on the central functions of storage and access, major changes will occur in the interaction within the new systems.
Inhibition of Respiration in Prototheca zopfii by Light (1970)

Irradiation of cells of Prototheca zopfii with blue light inhibited the respiratory capacity of the cells. The inhibition of respiration was correlated with a photodestruction of cytochrome c(551), cytochrome b(559), and cytochrome a(3). Cytochrome c(549), cytochrome b(555), and cytochrome b(564) were unaffected by the irradiation treatment. The alpha-band of reduced cytochrome a was shifted from 599 to 603 nm by irradiation, an effect similar to that observed when methanol was added to nonirradiated cells. The presence of oxygen was required during irradiation for both photoinhibition of respiration and photodestruction of the cytochromes. Cytochrome a(3) was protected against photodestruction by cyanide. Photodestruction of these same cytochromes also occurred when washed mitochondria of P. zopfii were irradiated.
The theory of super-resolution electron microscopy via Wigner-distribution deconvolution (1992)

Abstract The theory of deconvolving the microdiffraction data-set available in a scanning transmission electron microscope or, equivalently, the set of all bright- and dark-field images available in a conventional transmission electron microscope to obtain super- resolution micrographs (which are not limited by the transfer function of the objective lens) is developed and described with reference to holography and other phase-retrieval schemes. By the use of a Wigner distribution, influences of the instrument function can be entirely separated from the information pertaining to the specimen. The final solution yields an unambiguous estimate of the complex value of the specimen function at a resolution which in theory is only limited by the electron wavelength. The faithfulness of the image processing is shown to be not seriously affected by specimen thickness or partial coherence in the illuminating beam. The inversion procedure is remarkably noise insensitive, implying that it should result in a robust and practicable experimental technique, though one that will require very large computing facilities.
A geometric invariant for visual recognition and 3D reconstruction from two perspective/orthographic views (2002)

The author addresses the problem of reconstructing 3D space in a projective framework from two views, and the problem of artificially generating novel views of the scene from two given views. He shows that with the correspondences coming from four non-coplanar points in the scene and the corresponding epipoles, one can define and reconstruct (using simple linear methods) a projective invariant, referred to as projective depth, that can be used later to reconstruct the projective or affine structure of the scene, or directly to generate novel views of the scene. The derivation has the advantage that the viewing transformation matrix need not be recovered in the course of computations (i.e., he computes structure without motion).< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Vgr-1/BMP-6 induces osteoblastic differentiation of pluripotential mesenchymal cells. (1995)

The transforming growth factor-beta (TGF-beta) superfamily is a group of secreted growth factors that appears to play a central role in mesenchymal differentiation, including cartilage and bone formation. The present study examines the role of one member of this family, vgr-1, also called bone morphogenetic protein-6, in mesenchymal cell differentiation. This factor may be considered as a prototype for the largest subgroup of related factors within the TGF-beta superfamily, the function of which has as yet been poorly defined. vgr-1 has been localized previously to hypertrophic cartilage and has been shown to induce endochondral bone formation in vivo. To further characterize the role of vgr-1 in bone and cartilage differentiation, we stably transfected the pluripotent mesenchymal cell line ROB-C26 with a vector to overexpress vgr-1. Overexpression of this factor did not affect cell shape or morphology, but it enhanced osteoblastic differentiation in vitro and altered cellular responsiveness to retinoic acid. Furthermore, the extracellular matrix produced by these vgr-1-overexpressing cells induced ectopic bone formation in vivo and osteoblastic differentiation in vitro, similar to the matrix produced by C26 cells treated with retinoic acid. The osteoinductive effect of the matrix from vgr-1-overexpressing cells was blocked using a neutralizing vgr-1 antibody but not with a neutralizing TGF-beta 1 antibody, indicating that vgr-1 alone was required for this osteogenic effect. In contrast, the osteoinductive effect of matrix from retinoic acid-treated cells was blocked with both vgr-1 and TGF-beta 1 antibodies, suggesting that TGF-beta 1 may act prior to vgr-1 during osteoblastic differentiation. We further demonstrated that osteoinduction by vgr-1 was dependent on presentation of vgr-1 within the matrix, because the osteoinductive effect of matrix from vgr-1-overexpressing cells could not be mimicked with the addition of soluble vgr-1 to parental C26 cells. Finally, overexpression of MyoD within the C26 cells overexpressing vgr-1 converted the cells to myoblasts, indicating that vgr-1 had induced early osteoblastic.
A simple microcontroller based digital lock-in amplifier for the detection of low level optical signals (2003)

Traditionally digital lock-in amplifiers sample the input signal at a rate much higher than the lock-in reference frequency and perform the lock-in algorithm with high-speed processors. We present a small and simple digital lock-in amplifier that uses a 20 bit current integrating analogue-to-digital converter interfaced to a microcontroller. The sample rate is set to twice the reference frequency placing the sampled lock-in signal at the Nyquist frequency allowing the lock-in procedure to be performed with one simple algorithm. This algorithm consists of a spectral inversion technique integrated into a highly optimised low-pass filter. We demonstrate a system with a dynamic range of 103 dB recovering signals up to 85 dB below the interference.
Role of Neuraminidase in Lethal Synergism between Influenza Virus andStreptococcus pneumoniae (2003)

A lethal synergism exists between influenza virus and Streptococcus pneumoniae, accounting for excess mortality during influenza epidemics. Using a model of viral-bacterial synergism, we assessed the role that the influenza virus neuraminidase (NA) has in priming mice for pneumococcal infection. Administration of the selective NA inhibitor oseltamivir improved survival, independent of viral replication and morbidity from influenza. Both pathologic examination of the lungs and live imaging of pneumonic lesions, using a bioluminescent pneumococcus, suggested that the effect of NA inhibition was to limit the extent of pneumococcal pneumonia during early infection. Adherence assays and immunohistochemical staining for sialic acids in lungs from infected mice demonstrated that the influenza virus NA potentiates development of pneumonia by stripping sialic acid from the lung, thus exposing receptors for pneumococcal adherence. Selective NA inhibitors may be useful clinically to interrupt this novel mechanism of synergism and to prevent excess mortality from secondary bacterial pneumonia.
Age‐associated memory impairment: Proposed diagnostic criteria and measures of clinical change — report of a national institute of mental health work group (1986)

(1986). Age‐associated memory impairment: Proposed diagnostic criteria and measures of clinical change — report of a national institute of mental health work group. Developmental Neuropsychology: Vol. 2, No. 4, pp. 261-276.
Potent and Selective Inhibition of HIV and SIV by Prostratin Interacting with Viral Entry (2003)

Prostratin, a non-tumour promoting phorbol ester, exhibit a potent anti-HIV activity against human immunodeficiency virus type 1 (HIV-1). However, the antiviral mechanism of prostratin is not well defined. In the present study, we report that prostratin exhibits potent antiviral activity against different strains of HIV-1 (subtypes B and D), a clinical HIV isolate (L1), HIV-2 (ROD and EHO) and SIV (MAC251) with EC50-values ranging from 0.02-0.09 microg/ml. Prostratin was equally active against HIV strains resistant to the polyanionic binding inhibitor dextran sulphate, the fusion inhibitor T-20 (enfuvirtide), nucleoside reverse transcriptase inhibitors (NRTIs) or protease inhibitors (PIs). In contrast, prostratin lost 4.4- and 6.8-fold of its effect against the HIV strains resistant to AMD3100 and the quaternary ammonium salt QAS10+, respectively. As shown by time-of-addition experiments, prostratin needs to be present at the time of viral adsorption to exert its antiviral activity. We selected an HIV strain (NL4.3/PROS) resistant to prostratin in MT-4 cells. The sensitivity of NL4.3/PROS towards prostratin, dextran sulphate and QAS10+ was reduced by 3.2, 4.1 and >50-fold, respectively. However, NL4.3/ PROS was still sensitive to AMD3100, T-20, NRTIs (zidovudine and nevirapine) and a PI (ritonavir). Recombination of the gp160-gene of the NL4.3/PROS strain in a NL4.3 wild-type molecular clone fully rescued its phenotypic resistance. DNA sequencing of the NL4.3/PROS strain revealed mutations throughout the gp120 gene previously associated with resistance towards other HIV entry inhibitors. We concluded that prostratin inhibits the entry step of the replication cycle of HIV by interacting with a cellular target necessary for viral entry.
16 channel phased array wavelength demultiplexeron InPwith low polarisation sensitivity (1994)

A waveguide grating demultiplexer on InP which resolves 16 channels in the 1535–1565 nm wavelength range is reported. The channels are spaced by 1.8 nm with a 3 dB bandwidth of 1.1 nm. Crosstalk is better than 9 dB and polarisation sensitivity is only 0.48 nm, which is the lowest value achieved with this demultiplexing approach.
Inclusion Bodies and Recovery of Proteins from the Aggregated State (1991)

In recent years protein folding has emerged as a central issue in cell physiology, immunology and biotechnology. In-vivo protein folding plays an important role in cellular responses such as the transport of polypeptides through membranes, cellular adaptation to extreme conditions, the assembly of viruses and multimeric enzymes and the destruction of aberrant polypeptides by proteases. Folding also appears to be directly related to certain disease states and immunosupression (1,2). In biotechnology the synthesis of biologically active recombinant proteins is the key issue for the production of commercially important polypeptides and when the expression of foreign genes is employed to manipulate the metabolism of the cell. Frequently, recombinant polypeptides are not able to fold properly within the host cell and form amorphous protein aggregates usually consisting of misfolded, often denatured polypeptides. These aggregates are known as inclusion bodies or refractile bodies since they appear as highly refractile areas when the cells
TLR-4 Signaling Promotes Tumor Growth and Paclitaxel Chemoresistance in Ovarian Cancer (2006)

Evidence suggests that an inflammatory profile of cytokines and chemokines persisting at a particular site would lead to the development of a chronic disease. Recent studies implicate bacterial infection as one possible link between inflammation and carcinogenesis; however, the crucial molecular pathways involved remain unknown. We hypothesized that one possible upstream signaling pathway leading to inflammation in carcinogenesis may be mediated by Toll-like receptors (TLR). We describe for the first time an adaptive mechanism acquired by ovarian cancer cells that allows them to promote a proinflammatory environment and develop chemoresistance. We propose that the TLR-4-MyD88 signaling pathway may be a risk factor for developing cancer and may represent a novel target for the development of biomodulators. Our work explains how bacterial products, such as lipopolysaccharide, can promote, directly from the tumor, the production of proinflammatory cytokines and the enhancement of tumor survival. In addition, we provide new evidence that links TLR-4 signaling, inflammation, and chemoresistance in ovarian cancer cells.
Kuzhikkanam (Tomb-fee & Land Tenure): A Re-Discovery from Historical Palm Leave Manuscripts (2013)

This article is an attempt to explore and analyse the practice of levying Kuzhikkanam (tomb fee) for the burial of dead bodies in the Syrian church cemeteries in Kerala. There are eighteenth and nineteenth century palm leaf records in the Syrian churches which provide a lot of interesting information on this practice. This term is borrowed from the secular practice of levying Kulikkanam (Kuzhikkanam), that is, rent paid for cultivating the land that was newly brought under cultivation by land improvements either through reclamation or deforestation.