gebhart/patrepeval huggingface dataset:
A gentle method for preparing cyto- and nucleo-skeletons and associated chromatin (1988)

We describe a method for permeabilizing and extracting cells that preserves both structure and function whilst allowing the cell derivatives to be handled freely. Cells are encapsulated in microbeads of agarose; the coat of agarose, which is freely permeable to small molecules, forms a protective layer around fragile cell constituents. Cells are then permeabilized by the non-ionic detergent Triton X-100 or antibody and complement in a buffer whose ionic composition mimics that of the cytoplasm. The resulting structures have been characterized morphologically (by immunofluorescence and electron microscopy) and biochemically. Lysis with Triton removes both cell and nuclear membranes, and extracts most of the cytoplasm to leave chromatin surrounded by cytoskeleton; nucleus and cytoplasm then become accessible to triphosphates, enzymes and antibodies. Lysis with complement permeabilizes the cell membrane but leaves the nuclear membrane intact; triphosphates and restriction enzymes, but not antibodies, can then enter both nucleus and cytoplasm. Both types of lysis yield preparations whose chromatin template remains essentially intact, and which is replicated and transcribed at rates close to, or greater than, those found in vivo. Treatment of complement-lysed cells with Triton reduces the very efficient DNA synthesis, implying that the nuclear membrane is involved, directly or indirectly, in replication.
Reactivity of 2-Deoxy-2-iodoglycosyl Isothiocyanates with O-, S-, and N-Nucleophiles. Synthesis of Glycopyranoso-Fused Thiazoles (2003)

The reactivity of 2-deoxy-2-iodoglycosyl isothiocyanates toward O- and S-nucleophiles gives an easy access to 2-deoxy-2-iodoglycopyranosyl thiocarbamates and dithiocarbamates. Internal nucleophilic displacement of the iodine by the sulfur atom in these compounds allows the preparation of glycopyranoso[1,2-d]-1,3-thiazoles and glycopyranoso[1,2-d]-1,3-thiazolidin-2-one or -2-thione. Reaction with amines or polyamines as N-nucleophiles led directly to 2-aminoglycopyranoso[1,2-d]-1,3-thiazoles without isolation of the intermediate thioureas. Methyl 2-deoxy-2-iodoglycopyranosyl thiocarbamates also allow the synthesis of 2-deoxyglycopyranosyl thiocarbamates or 2-deoxy-2-iodoglycopyranosyl carbamates.
Near infra-red interactance for nutritional assessment of dialysis patients (1999)

We conclude that NIR, which can be performed within seconds, may serve as an objective indicator of nutritional status in haemodialysis patients. More comparative and longitudinal studies are needed to confirm the validity of NIR measurements in nutritional evaluation of dialysis patients.
Research notes: A partially male-sterile mutant in soybeans (1979)

An entry consisting mostly of plants having little to no seed set was found amidst the breeding material of Dr. Walter R. Fehr (Iowa State University) in 1975. The entry was descendent from germplasm population AP6(Sl)Cl, which was described by Fehr and Ortiz (1975). Investigations have revealed that partial male sterility was the primary cause leading to reduced seed set (Stelly, 1979).
A Sensitive Shock Index for Real-Time Patient Assessment During Simulated Hemorrhage (2013)

CRI provided a significantly earlier indicator of impending hemodynamic decompensation than SI > or = 0.9 during progressive LBNP. These results support the notion that the CRI represents an improved 'shock index' as an indicator of impending hemorrhagic shock compared to standard vital signs.
Activation of Human T Lymphocytes by Crosslinking of Anti-CD3 Monoclonal Antibodies (1989)

The proliferation of human T lymphocytes induced by anti-CD3 monoclonal antibodies (mAb) is used as a model for antigen-induced activation via the T cell receptor-CD3 complex. Since both systems are accessory cell (AC)-dependent, an understanding of the role of AC in anti-CD3-induced proliferation may provide an understanding of physiological activation via the T cell receptor. Previous work has implicated receptor crosslinking as an important AC function. To determine its necessity in anti-CD3-induced lymphocyte proliferation, we prepared highly purified T lymphocytes and found that these cells did not respond to the anti-CD3 mAb UCHT1, either alone or with interleukin 1 (IL1), interleukin 2 (IL2), or tetradecanoyl phorbol acetate (TPA). However, the response, as measured by appearance of IL2 receptors and proliferation, was restored by crosslinking with immobilized goat anti-mouse antibodies (GAM) and did not require the addition of IL1, IL2, or TPA. Thus, crosslinking of CD3 receptors was a sufficient signal for proliferation of these cells. Cyclosporine A (CsA) inhibited the activation induced by immobilized UCHT1. Since macrophages are the principle targets of CsA-mediated suppression of mitogen-induced proliferation, but macrophages do not participate in the response to immobilized anti-CD3, this may indicate that CsA was inhibiting crosslinking or a signal generated by it.
Integrative model of genomic factors for determining binding site selection by estrogen receptor‐α (2010)

A major question in transcription factor (TF) biology is why a TF binds to only a small fraction of motif eligible binding sites in the genome. Using the estrogen receptor-α as a model system, we sought to explicitly define parameters that determine TF-binding site selection. By examining 12 genetic and epigenetic parameters, we find that an energetically favorable estrogen response element (ERE) motif sequence, co-occupancy by the TF FOXA1, the presence of the H3K4me1 mark and an open chromatin configuration in the pre-ligand state provide specificity for ER binding. These factors can model estrogen-induced ER binding with high accuracy (ROC-AUC=0.95 and 0.88 using different genomic backgrounds). Moreover, when assessed in another estrogen-responsive cell line, this model was highly predictive for ERα binding (ROC-AUC=0.86). Variance in binding site selection between MCF-7 and T47D resides in sites with suboptimal ERE motifs, but modulated by the chromatin configuration. These results suggest a definable interplay between sequence motifs and local chromatin in selecting TF binding.
Quaternary optical ASK-DPSK and receivers with direct detection (2003)

We present a novel quaternary optical-modulation scheme based on the combination of amplitude and phase modulation. The modulator has a simple structure and can be realized by using standard components. We present two simple receivers, each one using photodiodes for direct detection. The performance of the modulation scheme is investigated.
HIV-2 link to AIDS in West Africa. (1990)

To date, very little is known concerning the clinical spectrum of human immunodeficiency virus type 2 (HIV-2) infection, and the question as to whether HIV-2 will ultimately prove to be as pathogenic as human immunodeficiency virus type I (HIV-1) remains, as yet, unanswered. We reviewed the currently available reports of HIV-2 infection to assess what is known about the extent of HIV-2 pathogenicity as it compares to HIV-1 pathogenicity. There is evidence that HIV-2 is associated with AIDS. Most of this evidence, however, comes from descriptive case-report type data that do not meet the basic requirements for defining causality. The most significant problems are the lack of control groups and the absence of a documented temporal relationship with HIV-2 infection preceding the development of AIDS. Comparisons of the epidemiology and disease association between HIV-1 and HIV-2 in Africa may suggest relative pathogenic effects. Although certain comparisons between HIV-2 and HIV-1 are difficult to make, we conclude on the basis of existing data that the pathogenic effects and the natural history of HIV-2 are distinct from those of HIV-1.
Evaluation of the Infectivity, Immunogenicity, and Efficacy of Live Cold-Adapted Influenza B/Ann Arbor/1/86 Reassortant Virus Vaccine in Adult Volunteers (1990)

A cold-adapted (ca) influenza B reassortant that derived two genes encoding the hemagglutinin and neuraminidase from influenza B/Ann Arbor/1/86 wild-type virus and six internal RNA segments from ca influenza B/Ann Arbor/1/66 virus was evaluated in 66 adult volunteers having a serum hemagglutination inhibition antibody titer less than or equal to 1:8. The ca reassortant was attenuated and elicited the production of systemic and local antibodies; the 50% human infectious dose was 10(6.4) TCID50. Six weeks after vaccination, 12 unvaccinated volunteers and 13 recipients of ca virus (10(7.5) TCID50) were challenged experimentally with homologous wild-type influenza B virus. The ca vaccine completely protected against illness, and the magnitude of shedding was 50-fold less in vaccinees than in unimmunized controls, five of whom became ill. These findings indicate that the six internal RNA segments of the ca influenza B/Ann Arbor/66 donor virus confer desirable properties of a live virus vaccine to a reassortant derived from a virulent virus. Such reassortants may be suitable vaccines for healthy adults.
Stromelysin‐1: Three‐dimensional structure of the inhibited catalytic domain and of the C‐truncated proenzyme (1995)

The proteolytic enzyme stromelysin-1 is a member of the family of matrix metalloproteinases and is believed to play a role in pathological conditions such as arthritis and tumor invasion. Stromelysin-1 is synthesized as a pro-enzyme that is activated by removal of an N-terminal prodomain. The active enzyme contains a catalytic domain and a C-terminal hemopexin domain believed to participate in macromolecular substrate recognition. We have determined the three-dimensional structures of both a C-truncated form of the proenzyme and an inhibited complex of the catalytic domain by X-ray diffraction analysis. The catalytic core is very similar in the two forms and is similar to the homologous domain in fibroblast and neutrophil collagenases, as well as to the stromelysin structure determined by NMR. The prodomain is a separate folding unit containing three alpha-helices and an extended peptide that lies in the active site of the enzyme. Surprisingly, the amino-to-carboxyl direction of this peptide chain is opposite to that adopted by the inhibitor and by previously reported inhibitors of collagenase. Comparison of the active site of stromelysin with that of thermolysin reveals that most of the residues proposed to play significant roles in the enzymatic mechanism of thermolysin have equivalents in stromelysin, but that three residues implicated in the catalytic mechanism of thermolysin are not represented in stromelysin.
Correction: Collective Instance-Level Gene Normalization on the IGN Corpus (2014)

A high proportion of life science researches are gene-oriented, in which scientists aim to investigate the roles that genes play in biological processes, and their involvement in biological mechanisms. As a result, gene names and their related information turn out to be one of the main objects of interest in biomedical literatures. While the capability of recognizing gene mentions has made significant progress, the results of recognition are still insufficient for direct use due to the ambiguity of gene names. Gene normalization (GN) goes beyond the recognition task by linking a gene mention to a database ID. Unlike most previous works, we approach GN on the instance-level and evaluate its overall performance on the recognition and normalization steps in abstracts and full texts. We release the first instance-level gene normalization (IGN) corpus in the BioC format, which includes annotations for the boundaries of all gene mentions and the corresponding IDs for human gene mentions. Species information, along with existing co-reference chains and full name/abbreviation pairs are also provided for each gene mention. Using the released corpus, we have designed a collective instance-level GN approach using not only the contextual information of each individual instance, but also the relations among instances and the inherent characteristics of full-text sections. Our experimental results show that our collective approach can achieve an Fscore of 0.743. The proposed approach that exploits section characteristics in full-text articles can improve the F-scores of information lacking sections by up to 1.8%. In addition, using the proposed refinement process improved the F-score of gene mention recognition by 0.125 and that of GN by 0.03. Whereas current experimental results are limited to the human species, we seek to continue updating the annotations of the IGN corpus and observe how the proposed approach can be extended to other species.
Expression of Mmp9 and related matrix metalloproteinase genes during axolotl limb regeneration (1999)

One of the earliest events in limb regeneration is the extensive remodeling of the extracellular matrix (ECM). Matrix metalloproteinases (MMPs) are a family of matrix degrading enzymes that have been identified in both normal and disease states. Using RT-PCR and cDNA library screening, we have isolated sequences homologous to four different Mmp genes. The spatial and temporal expression of one of these, Mmp-9, has been analyzed during axolotl limb regeneration. Northern blot analysis identifies a 3.8 kb transcript that is abundantly expressed during regeneration, and whole-mount in situ hybridization has uncovered an unusual bi-phasic expression pattern. The first phase begins at 2 hours after amputation, and expression is confined to the healed wound epithelium. This phase continues for 2 days, showing peak expression at 14 hours after amputation. This early phase may be needed to retard reformation of the basal lamina of the epidermis, and thereby facilitate the epidermal-mesenchymal interactions required for successful regeneration. The second phase begins a few days later when a small blastema has formed. During this phase, expression is in the mesenchyme, localized to cells around the tips of the cut skeletal elements. This expression is maintained through several stages until redifferentiation begins. The timing and position of the second phase of expression is consistent with a role for Mmp-9 in the removal of damaged cartilage matrix. We have also discovered that the time of onset of Mmp-9 expression is sensitive to denervation, which causes a delay of several hours. Finally, retinoids, known for their dramatic effects on the pattern of regenerating limbs, can cause a down regulation of Mmp-9 expression. Dev Dyn 1999;216:2–9. © 1999 Wiley-Liss, Inc.
Atomic Force Microscopy and Dissection of Gap Junctions (1991)

An atomic force microscope (AFM) was used to study the structure of isolated hepatic gap junctions in phosphate-buffered saline (PBS). The thickness of these gap junctions appears to be 14.4 nanometers, close to the dimensions reported by electron microscopy (EM). When an increasing force is applied to the microscope tip, the top membrane of the gap junction can be "dissected" away, leaving the extracellular domains of the bottom membrane exposed. When such "force dissection" is performed on samples both trypsinized and fixed with glutaraldehyde, the hexagonal array of gap junction hemichannels is revealed, with a center-to-center spacing of 9.1 nanometers.
Reservoir seismology : geophysics in nontechnical language (1994)

Real-life case histories with actual costs and benefits highlight this text on the methods and applications of oil exploration, development, and exploitation. Gadallah shows you how to transfer a raw image of seismic data into a meaningful subsurface geological picture of a given reservoir. He explains time-tested applications and technical buzz words, and introduces the latest technology in practical terms. Contents: Overview of geophysical techniques Basic seismic principles Acquisition of seismic data. Seismic data processing Migration Modeling Verticle seismic profiling Amplitude versus offset Analysis (AVO) 3-D seismic survey Tomography Seismic interpretation Case histories Conclusions.
Photosensitivity in optical fiber waveguides: Application to reflection filter fabrication (1978)

The observation of photosensitivity in Ge-doped core optical fibers is reported. The photosensitivity is manifested by light-induced refractive-index changes in the core of the waveguide. Narrowband reflectors in a guide structure have been fabricated using this photosensitivity and the resulting DFB reflectors employed as laser mirrors in a cw gas laser in the visible.
Syndecan‐1 and angiogenic cytokines in multiple myeloma: correlation with bone marrow angiogenesis and survival (2004)

Angiogenesis is a complex process involved in the proliferation and metastasis of malignant tumours, and partly triggered by the secretion of various angiogenic factors by tumour cells or cells in the stromal environment. We investigated the correlation between bone marrow angiogenesis, estimated as microvessel density (MVD), and interleukin-6 (IL-6), basic fibroblastic growth factor (bFGF), hepatocyte growth factor (HGF) and syndecan-1 in 67 patients with newly diagnosed multiple myeloma, and evaluated the prognostic value of these parameters. Circulating levels of IL-6, bFGF, HGF and syndecan-1 were significantly higher in patients than in controls. Moreover, in patients, bone marrow levels of bFGF, HGF and syndecan-1 were higher than peripheral blood levels. Positive correlations were found between MVD and syndecan-1 blood levels (r = 0.33, P = 0.017), syndecan-1 bone marrow levels (r = 0.49, P = 0.046) and HGF blood levels (r = 0.36, P = 0.008) respectively. High MVD and high blood levels of IL-6, HGF and syndecan-1 were predictive of a shorter survival. In a multivariate survival analysis MVD and blood levels of IL-6 retained independent prognostic significance, while in a survival analysis without MVD the peripheral blood levels of HGF and syndecan-1 were strong independent prognostic factors.
Expression of FOXA1 and GATA-3 in breast cancer: the prognostic significance in hormone receptor-negative tumours (2009)

FOXA1 was a significant predictor of good outcome in breast cancer, whereas GATA-3 was an important luminal marker. The expression of FOXA1 may be used for risk stratification among ERalpha-negative patients.
A General Version of Crow's Shadow Volumes (1986)

In 1977 Frank Crow introduced a new class of algorithm for the generation of shadows. His technique, based on the concept of shadow volumes, assumes a polygonal database and a constrained environment. For example, polyhedrons must be closed, and polygons must be planar. This article presents a new version of Crow's algorithm, developed at the Universite de Montreal, which attempts a less constrained environment. The method has allowed the handling of both open and closed models and nonplanar polygons with the viewpoint anywhere, including any shadow volume. It does not, however, sacrifice the essential features of Crow's original version: penetration between polygons is allowed and any number of light sources can be defined anywhere in 3D space, including the view volume and any shadow volume. The method has been used successfully in the film Tony de Peltrie and is easily incorporated into an existing scan-line, hidden-surface algorithm.
Development of Preimplantation Embryos of the Golden Hamster in a Defined Culture Medium (1983)

Eight-cell embryos were recovered from mated golden hamsters that had been superovulated with pregnant mare's serum gonadotropin (PMSG) and human chorionic gonadotropin (hCG). Embryos were cultured for 24 or 32 h in a defined medium (modified Tyrode's solution) designed for fertilization of hamster oocytes in vitro. This medium was supplemented in some experiments with amino acids (glutamine, phenylalanine, methionine and isoleucine) and with vitamins (Eagle's Minimum Essential Medium vitamin supplement). At the end of the culture period, the numbers of embryos developing to the blastocyst stage were recorded. In other experiments, the effects of varying the osmotic pressure (225, 250, 275 and 300 m0smol/kg) and the pH (6.8 and 7.4) of the culture medium on blastocyst formation were examined. A difference was found between the ability of early 8-cell embryos (approx. 54 h post-egg activation) and late 8-cell embryos (approx. 62 h post-egg activation) to develop in culture. In the unsupplemented culture medium, only 2% of early 8-cell embryos developed to the blastocyst stage compared with 22% of late 8-cell embryos. A marked effect of the four amino acids on development was found. In the presence of amino acids 36% of early 8-cell embryos developed into blastocysts (18-fold increase). The amino acids also increased the percentage of late 8-cell embryos that developed into blastocysts from 22% to 66%. These data suggest that an important metabolic change may occur in hamster embryos during a critical period at the 8-cell stage of development. No additional effect on development was observed when vitamins were included in the culture medium. No significant effect of either osmotic pressure of pH of the culture medium on development was found. When blastocysts formed from cultured 8-cell embryos were transferred surgically to pseudopregnant hamsters, about 25% developed into normal-looking fetuses and 5 normal-looking young were born, 4 of which have survived. These results represent an approach towards achieving complete preimplantation development of hamster embryos in vitro.
Toll-like receptors in ocular immunity and the immunopathogenesis of inflammatory eye disease (2005)

Microbial agents have an important role in the pathogenesis of various inflammatory eye diseases, such as uveitis and keratitis. Microbial infections of the eye such as microbial keratitis, ocular onchocerciasis, bacterial endophthalmitis, viral retinitis, and other infectious uveitis are unfortunately common. In addition, microbial agents have been implicated in the pathogenesis of "non-infectious" immune mediated diseases such as HLA-B27 associated acute anterior uveitis. Toll-like receptors (TLR) are a family of pattern recognition receptors that initiates rapid host innate immune response to microbial components known as pathogen associated molecular patterns, which are unique to a given class of microbes, such as lipopolysaccharide of Gram negative bacteria. Recent in vitro and in vivo studies have demonstrated the expression and function of TLRs in the eye, with significant implications for better understanding of ocular immunity and the pathogenesis of inflammatory eye diseases affecting the cornea, uvea, and retina.