gebhart/patrepeval huggingface dataset:
Structure and Expression of the Lactococcus lactis Gene for Phospho- -galactosidase (lacG) in Escherichia coli and L. lactis (1989)

The Lactococcus lactis subsp. lactis 712 lacG gene encoding phospho-beta-galactosidase was isolated from the lactose mini-plasmid pMG820 and cloned and expressed in Escherichia coli and L. lactis. The low phospho-beta-galactosidase activity in L. lactis transformed with high-copy-number plasmids containing the lacG gene contrasted with the high activity found in L. lactis containing the original, low-copy-number lactose plasmid pMG820, and indicated that the original lactose promoter was absent from the cloned DNA. In E. coli the phospho-beta-galactosidase could be overproduced using the strong inducible lambda PL promoter, which allowed a rapid purification of the active enzyme. The complete nucleotide sequence of the L. lactis lacG gene and its surrounding regions was determined. The deduced amino acid sequence was confirmed by comparison with the amino acid composition of the purified phospho-beta-galactosidase and its amino-terminal sequence. This also allowed the exact positioning of the lacG gene and identification of its characteristic Gram-positive translation initiation signals. The homologous expression data and the sequence organization of the L. lactis lacG gene indicate that the gene is organized into a large lactose operon which contains an intergenic promoter located in an inverted repeat immediately preceding the lacG gene. The organization and sequence of the L. lactis lacG gene were compared with those of the highly homologous lacG gene from Staphylococcus aureus. A remarkable bias for leucine codons was observed in the lacG genes of these two species. Heterogramic homology was observed between the deduced amino acid sequence of the L. lactis phospho-beta-galactosidase, that of the functionally analogous E. coli phospho-beta-glucosidase, and that of an Agrobacterium beta-glucosidase (cellobiase).
IPS-1 Is Essential for the Control of West Nile Virus Infection and Immunity (2010)

The innate immune response is essential for controlling West Nile virus (WNV) infection but how this response is propagated and regulates adaptive immunity in vivo are not defined. Herein, we show that IPS-1, the central adaptor protein to RIG-I-like receptor (RLR) signaling, is essential for triggering of innate immunity and for effective development and regulation of adaptive immunity against pathogenic WNV. IPS-1(-/-) mice exhibited increased susceptibility to WNV infection marked by enhanced viral replication and dissemination with early viral entry into the CNS. Infection of cultured bone-marrow (BM) derived dendritic cells (DCs), macrophages (Macs), and primary cortical neurons showed that the IPS-1-dependent RLR signaling was essential for triggering IFN defenses and controlling virus replication in these key target cells of infection. Intriguingly, infected IPS-1(-/-) mice displayed uncontrolled inflammation that included elevated systemic type I IFN, proinflammatory cytokine and chemokine responses, increased numbers of inflammatory DCs, enhanced humoral responses marked by complete loss of virus neutralization activity, and increased numbers of virus-specific CD8+ T cells and non-specific immune cell proliferation in the periphery and in the CNS. This uncontrolled inflammatory response was associated with a lack of regulatory T cell expansion that normally occurs during acute WNV infection. Thus, the enhanced inflammatory response in the absence of IPS-1 was coupled with a failure to protect against WNV infection. Our data define an innate/adaptive immune interface mediated through IPS-1-dependent RLR signaling that regulates the quantity, quality, and balance of the immune response to WNV infection.
USHERSYNDROME: From Genetics to Pathogenesis (2001)

Usher syndrome (USH) is defined by the association of sensorineural deafness and visual impairment due to retinitis pigmentosa. The syndrome has three distinct clinical subtypes, referred to as USH1, USH2, and USH3. Each subtype is genetically heterogeneous, and 12 loci have been detected so far. Four genes have been identified, namely, USH1B, USH1C, USH1D, and USH2A. USH1B, USH1C, and USH1D encode an unconventional myosin (myosin VIIA), a PDZ domain-containing protein (harmonin), and a cadherin-like protein (cadherin-23), respectively. Mutations of these genes cause primary defects of the sensory cells in the inner ear, and probably also in the retina. In the inner ear, the USH1 genes, I propose, are involved in the same signaling pathway, which may control development and/or maintenance of the hair bundles of sensory cells via an adhesion force (a) at the junctions between these cells and supporting cells and (b) at the level of the lateral links that interconnect the stereocilia. In contrast, the molecular pathogenesis of USH2A, which is owing to a defect of a novel extracellular matrix protein, is likely to be different from that of USH1.
The leukocyte integrin LFA-1 reconstituted by cDNA transfection in a nonhematopoietic cell line is functionally active and not transiently regulated. (1990)

The functional activity of lymphocyte function-associated antigen 1 (LFA-1) on leukocytes can be regulated by T-cell receptor (TCR) stimulation and pharmacologic agents. It was of interest to determine if functionally active LFA-1 could be reconstituted on a nonhematopoietic, LFA-1-negative cell line. We report the expression of LFA-1 and diethylaminoethyl (DEAE) Mac-1 alpha beta heterodimers on the cell surface of a fibroblastoid cell line, COS, by DEAE dextran cotransfection of the alpha and beta subunit cDNAs. Immunoprecipitation studies demonstrated that the alpha and beta subunit was expressed in heterodimers. The alpha or beta subunit was expressed at lower levels after transfection with the alpha or beta subunit cDNA alone. Cotransfection of the alpha and beta subunit cDNAs, but not transfection of alpha or beta alone, was sufficient to reconstitute intercellular adhesion molecule-1 (ICAM-1) binding activity. Consistent with this observation, LFA-1 on the fibroblastoid cells possesses the activation epitope defined by the L16 monoclonal antibody (mAb). This epitope marks the conversion of LFA-1 from the low to high avidity state on peripheral blood T lymphocytes (PBLs) and is constitutively present on activated cell lines. In contrast to LFA-1 on leukocytes, the functional activity of LFA-1 on fibroblastoid cells was not influenced by phorbol ester treatment. Furthermore, the use of agents that interfere with intracellular signaling, a protein kinase C inhibitor, cAMP analogue, or the combination of a phosphodiesterase inhibitor and adenyl cyclase activator, did not affect the binding of COS cells expressing LFA-1 to purified ICAM-1.
Modulation of the IgH enhancer's cell type specificity through a genetic switch. (1991)

Using defined regions of the immunoglobulin heavy-chain enhancer linked to minimal promoters and cDNAs that encode the two helix-loop-helix transcription factors ITF-1 and TFE3, we demonstrate that activity of an otherwise repressed enhancer can be stimulated in nonlymphoid cells. Repression in non-B cells is mediated by the microE5 motif. Derepression occurs at two levels. First, overexpression of ITF-1, and E12/E47-related protein that binds the microE5 motif, leads to transcriptional activation itself. Second, binding of ITF-1 physically displaces a repressor that normally blocks the stimulatory activity of TFE3, which binds the neighboring microE3 motif. TFE3 can only stimulate enhancer activity in the presence of ITF-1 or in the absence of a microE5 motif. Hence, one component of the enhancer's cell type specificity can be artificially modulated through a "genetic switch" in which activity is dictated by the relative levels of ITF-1 and a competing repressor.
Embedding of Bacterial Cellulose Nanofibers within PHEMA Hydrogel Matrices: Tunable Stiffness Composites with Potential for Biomedical Applications (2018)

Bacterial cellulose (BC) and poly(2-hydroxyethyl methacrylate) (PHEMA) hydrogels are both considered as biocompatible materials with potential use in various biomedical applications including cartilage, cardiovascular stent, and soft tissue engineering. In this work, the “ever-wet” process based on in situ UV radical polymerization of HEMA monomer in BC nanofibrous structure impregnated with HEMA was used, and a series of BC-PHEMA composites was prepared. The composite structures were characterized by ATR FT-IR spectroscopy, WAXD, SEM, and TEM techniques. The strategy of using densified BC material of various cellulose fiber contents was applied to improve mechanical properties. The mechanical properties were tested under tensile, dynamic shear, and relaxation modes. The final composites contained 1 to 20 wt% of BC; the effect of the reinforcement degree on morphology, swelling capacity, and mechanical properties was investigated. The biocompatibility test of BC-PHEMA composites was performed using mouse mesenchymal stem cells.
Fiber-optic confocal microscope: FOCON (1992)

A new design for a reflecting fiber-optic confocal microscope, FOCON, is presented in which the beam splitter of a conventional confocal microscope is replaced by a fiber-optic splitter, and the core of a single-mode fiber takes the place of both the source and detector pinholes. It is shown that FOCON has the same resolution characteristics as a conventional confocal microscope, and requires fewer optical components and only rough alignment. The microscope is robust and can be rapidly scanned in the x, y, and z directions through the simple movement of the end of an optical fiber.
Imaging in Prostate Cancer Staging: Present Role and Future Perspectives (2012)

Despite recent improvements in detection and treatment, prostate cancer continues to be the most common malignancy and the second leading cause of cancer-related mortality. Thus, although survival rate continues to improve, prostate cancer remains a compelling medical health problem. The major goal of prostate cancer imaging in the next decade will be more accurate disease characterization through the synthesis of anatomic, functional, and molecular imaging information in order to plan the most appropriate therapeutic strategy. No consensus exists regarding the use of imaging for evaluating primary prostate cancer. However, conventional and functional imaging are expanding their role in detection and local staging and, moreover, functional imaging is becoming of great importance in oncologic management and monitoring of therapy response. This review presents a multidisciplinary perspective on the role of conventional and functional imaging methods in prostate cancer staging.
Inhibition of Hepatitis B Virus Replication by the Host Zinc Finger Antiviral Protein (2013)

The zinc finger antiviral protein (ZAP) is a mammalian host restriction factor that inhibits the replication of a variety of RNA viruses, including retroviruses, alphaviruses and filoviruses, through interaction with the ZAP-responsive elements (ZRE) in viral RNA, and recruiting the exosome to degrade RNA substrate. Hepatitis B virus (HBV) is a pararetrovirus that replicates its genomic DNA via reverse transcription of a viral pregenomic (pg) RNA precursor. Here, we demonstrate that the two isoforms of human ZAP (hZAP-L and -S) inhibit HBV replication in human hepatocyte-derived cells through posttranscriptional down-regulation of viral pgRNA. Mechanistically, the zinc finger motif-containing N-terminus of hZAP is responsible for the reduction of HBV RNA, and the integrity of the four zinc finger motifs is essential for ZAP to bind to HBV RNA and fulfill its antiviral function. The ZRE sequences conferring the susceptibility of viral RNA to ZAP-mediated RNA decay were mapped to the terminal redundant region (nt 1820-1918) of HBV pgRNA. In agreement with its role as a host restriction factor and as an innate immune mediator for HBV infection, ZAP was upregulated in cultured primary human hepatocytes and hepatocyte-derived cells upon IFN-α treatment or IPS-1 activation, and in the livers of hepatitis B patients during immune active phase. Knock down of ZAP expression increased the level of HBV RNA and partially attenuated the antiviral effect elicited by IPS-1 in cell cultures. In summary, we demonstrated that ZAP is an intrinsic host antiviral factor with activity against HBV through down-regulation of viral RNA, and that ZAP plays a role in the innate control of HBV replication. Our findings thus shed light on virus-host interaction, viral pathogenesis, and antiviral approaches.
Increase of synaptic density and memory retention by a peptide representing the trophic domain of the amyloid beta/A4 protein precursor. (1994)

The secreted form (sAPP) of the Alzheimer amyloid beta/A4 protein precursor (APP) has been shown to be involved in the in vitro regulation of fibroblast growth and neurite extension from neuronal cells. The active site of sAPP responsible for these functions is within a small domain just C-terminal to the Kunitz-type protease inhibitor (KPI) insertion site. We report here that a 17-mer peptide, containing this active domain of sAPP, can induce cellular and behavioral changes when infused into rat brains. After 2 weeks of APP 17-mer peptide infusion, the animals were tested for reversal learning and memory retention and were sacrificed for morphological examination of brains. We found that administration of the APP 17-mer peptide resulted in an 18% increase in the number of presynaptic terminals in the frontoparietal cortex. At the behavioral level, 17-mer-infused animals with nonimpaired learning capability showed an increased memory retention that seemed to interfere with reversal learning performance. This APP 17-mer effect on memory retention was not observed in animals with impaired initial learning capacity. These results suggest that APP is involved in memory retention through its effect on synaptic structure.
Highly Efficient, General Procedure for the Preparation of Alkylzinc Reagents from Unactivated Alkyl Bromides and Chlorides (2003)

[reaction: see text] Alkylzinc bromides have been efficiently prepared by the direct insertion of zinc metal (dust, powder, granule, shot), activated with 1-5 mol % I(2), into alkyl bromides in a polar aprotic solvent. The zinc reagents thus formed undergo Ni- and Pd-catalyzed cross-coupling with aryl halides to produce functionalized alkylarenes in excellent yields.
Comparing Ammonium and Phosphonium Polymerized Ionic Liquids: Thermal Analysis, Conductivity, and Morphology (2013)

Conventional free radical polymerization and anion metathesis of ammonium and phosphonium styrenics successfully generates high‐molecular‐weight polymerized ionic liquids (PILs). Phosphonium polyelectrolytes containing Cl ‐ counterions display significantly higher thermal stabilities (&gt;370 °C) compared with ammonium analogs (&lt;220 °C). Anion exchange to BF 4 – , TfO – , and Tf 2 N – improves the thermal stability of all the PILs and depresses their T g . Impedance‐spectroscopy‐probed ionic conductivities of PILs containing Tf 2 N – , and phosphonium PILs exhibit higher values than ammonium analogs. Phosphonium PILs displayed many advantages over ammonium PILs for emerging applications that demand higher thermal stabilities and ionic conductivities. image
Ultrasound Cardiography: Contrast Studies in Anatomy and Function (1969)

Ultrasound cardiography has become established as a valuable clinical tool in the detection of pericardial effusion (1) and the study of mitral valve disease (2, 3). The tricuspid valve can also be detected (4), and studies have been made of left ventricular stroke volume (5) and wall thickness (6). On the other hand, the extension of the ultrasonic method to the study of other cardiac structures has been slow because of the difficulty in recognizing the source of the echoes. Even here, however, Edler (7) has gained useful knowledge in the recognition of the origin of these echoes by the passing of needles into cadavers in duplication of the path of the ultrasonic beam and by the study of excised hearts. The purpose of this presentation is to describe a method for the ultrasonic identification of the cardiac chambers in the living subject. It is based on the intracardiac injection of substances that produce echoes at the site of injection as well as downstream in the flow pattern and permit identification of the heart cavities. The identification of the cardiac chambers without contrast injection is a natural outcome of this study and depends on the distinguishing of key anatomic structures, the relationship of the chambers to them, and the recognition of movement patterns that may be specific for a structure or chamber. Background Ultrasound was developed during the period following World War I for depth-sounding and localization of submarines and schools of fish. The emergence of technics for the measurement of very short periods of time permitted Firestone, in 1945, to use ultrasound in the nondestructive testing of materials (8). These same principles were employed by Edler and Hertz in 1954 to study heart motion and to initiate echocardiography as a clinical tool (9). Their method is in general use today. To summarize, short bursts (one to two microseconds) of ultrasonic energy are emitted by a transducer held in close contact with the skin. As this sound energy passes through tissue, it is reflected at interfaces of differing acoustic impedance to the same transducer, which also acts as a receiver between pulses. The time that elapses between the generation of the pulse of ultrasound and the arrival of the echo is a measure of the depth of the reflecting surface. The high frequency of the pulses (200 to 2,000 per second) offers many determinations per cardiac cycle and permits accurate and detailed tracking of rapidly moving structures, such as heart-valve cusps the velocities of which are often in excess of 250 mm per second (2). The echo pattern is usually displayed on the face of an oscilloscope by either of two methods. "A" mode shows the returning signals as spikes that oscillate back and forth on the x-axis as the depth of the reflecting surface changes. The size of the peak is proportional to the intensity of the recording signal. "A" mode is useful primarily for identification and location of echoes.
Selection on Rapidly Evolving Proteins in the Arabidopsis Genome (2003)

Genes that have undergone positive or diversifying selection are likely to be associated with adaptive divergence between species. One indicator of adaptive selection at the molecular level is an excess of amino acid replacement fixed differences per replacement site relative to the number of synonymous fixed differences per synonymous site (omega = K(a)/K(s)). We used an evolutionary expressed sequence tag (EST) approach to estimate the distribution of omega among 304 orthologous loci between Arabidopsis thaliana and A. lyrata to identify genes potentially involved in the adaptive divergence between these two Brassicaceae species. We find that 14 of 304 genes (approximately 5%) have an estimated omega > 1 and are candidates for genes with increased selection intensities. Molecular population genetic analyses of 6 of these rapidly evolving protein loci indicate that, despite their high levels of between-species nonsynonymous divergence, these genes do not have elevated levels of intraspecific replacement polymorphisms compared to previously studied genes. A hierarchical Bayesian analysis of protein-coding region evolution within and between species also indicates that the selection intensities of these genes are elevated compared to previously studied A. thaliana nuclear loci.
Nextstep Programming: Concepts and Applications (1993)

1. NeXTSTEP Components. 2. Learning Objective-C. 3. Using the Application Kit. 4. Using InterfaceBuilder. 5. Processing Events. 6. Drawing with PostScript. 7. Processing Text. 8. Using Multiple Interface Files. 9. Customizing. NeXTSTEP. Appendix A: Using the Tools of the Trade. Appendix B: Further Troubleshooting. Appendix C: Taking the NeXT Step. Glossary.
A feasibility study on a single-unit wireless EEG sensor (2014)

The electroencephalography (EEG) is a widely used diagnostic tool for a number of clinical applications, such as diagnosis of epilepsy and study of sleep. Traditionally, to acquire a single channel of EEG signal, at least three electrodes must be installed on the skin separated at certain distances. They must also be connected to an amplifier by electrode leads. These basic requirements are acceptable in most clinical laboratories, but are unacceptable in certain point-of-care applications, such as during patient transportation. In order to remove these requirements, we are designing a single-unit EEG sensor in the size of a U.S. penny. It contains multiple closely spaced dry electrodes that can hook onto the skin, an electronic circuitry for signal amplification, digitization and wireless transmission, and a battery providing power. In this paper, we answer two key questions regarding the feasibility of the single-unit design: 1) can the closely-spaced electrodes obtain EEG signal reliably? and 2) will the electrodes orientated in certain ways improve signal quality? We conducted experiments utilizing closely spaced electrodes to record the alpha wave in the EEG. Our results have shown positive answers to the two feasibility questions.
Regenerating islet-derived 3-alpha is a biomarker of gastrointestinal graft-versus-host disease (2011)

There are no plasma biomarkers specific for GVHD of the gastrointestinal (GI) tract, the GVHD target organ most associated with nonrelapse mortality (NRM) following hematopoietic cell transplantation (HCT). Using an unbiased, large-scale, quantitative proteomic discovery approach to identify candidate biomarkers that were increased in plasma from HCT patients with GI GVHD, 74 proteins were increased at least 2-fold; 5 were of GI origin. We validated the lead candidate, REG3α, by ELISA in samples from 1014 HCT patients from 3 transplantation centers. Plasma REG3α concentrations were 3-fold higher in patients at GI GVHD onset than in all other patients and correlated most closely with lower GI GVHD. REG3α concentrations at GVHD onset predicted response to therapy at 4 weeks, 1-year NRM, and 1-year survival (P ≤ .001). In a multivariate analysis, advanced clinical stage, severe histologic damage, and high REG3α concentrations at GVHD diagnosis independently predicted 1-year NRM, which progressively increased with higher numbers of onset risk factors present: 25% for patients with 0 risk factors to 86% with 3 risk factors present (P < .001). REG3α is a plasma biomarker of GI GVHD that can be combined with clinical stage and histologic grade to improve risk stratification of patients.