gebhart/patrepeval huggingface dataset:
Networks of energetic and metabolic interactions define dynamics in microbial communities (2015)

Microorganisms form diverse communities that have a profound impact on the environment and human health. Recent technological advances have enabled elucidation of community diversity at high resolution. Investigation of microbial communities has revealed that they often contain multiple members with complementing and seemingly redundant metabolic capabilities. An understanding of the communal impacts of redundant metabolic capabilities is currently lacking; specifically, it is not known whether metabolic redundancy will foster competition or motivate cooperation. By investigating methanogenic populations, we identified the multidimensional interspecies interactions that define composition and dynamics within syntrophic communities that play a key role in the global carbon cycle. Species-specific genomes were extracted from metagenomic data using differential coverage binning. We used metabolic modeling leveraging metatranscriptomic information to reveal and quantify a complex intertwined system of syntrophic relationships. Our results show that amino acid auxotrophies create additional interdependencies that define community composition and control carbon and energy flux through the system while simultaneously contributing to overall community robustness. Strategic use of antimicrobials further reinforces this intricate interspecies network. Collectively, our study reveals the multidimensional interactions in syntrophic communities that promote high species richness and bolster community stability during environmental perturbations.
HER-2/neu (c-erb-B2) gene and protein in breast cancer. (1999)

The HER-2/neu oncogene encodes a transmembrane tyrosine kinase receptor with extensive homology to the epidermal growth factor receptor. The association of HER-2/neu gene and protein abnormalities with prognosis in breast cancer is presented by considering a series of 52 published studies including more than 16,000 patients. The relative advantages and disadvantages of Southern blot testing, polymerase chain reaction amplification, and fluorescence in situ hybridization assays designed to detect HER-2/neu gene amplification are compared with HER-2/neu protein overexpression assays performed with immunohistochemical techniques applied to frozen and paraffin-embedded tissues and enzyme immunoassays performed on tumor cytosols. The importance of HER-2/neu protein overexpression in ductal carcinoma in situ, and HER-2/neu protein status in uncommon breast diseases in female patients and breast cancer in male patients are also considered. The potential value of HER-2/neu protein status for the prediction of response to therapy in breast cancer is presented for standard hormonal therapy, cytotoxic chemotherapy, and radiation therapy. Also evaluated is the status of serum-based testing for circulating HER-2/neu receptor protein and its ability to predict disease outcome and therapy response. Finally, preliminary data concerning use of antibody-based therapies directed against HER-2/neu protein and their potential use in breast cancer treatment are considered.
Aging and lung injury repair: A role for bone marrow derived mesenchymal stem cells (2008)

The incidence of lung fibrosis increases with age. Aging is associated with modifications in the intracellular and extracellular environment including alteration of the extracellular matrix, imbalance of the redox state, accumulation of senescent cells and potential alteration of the recruitment of bone marrow mesenchymal stem cells. The combination of these senescence-related alterations in the lung and in bone marrow progenitor cells might be responsible of the higher susceptibility to lung fibrosis in elderly individuals. The understanding of these age related changes must be considered in the rationale for the development of therapeutic interventions to control lung injury and fibrosis.
Under-three minute PCR: Probing the limits of fast amplification (2011)

Nucleic acid amplification is enormously useful to the biotechnology and clinical diagnostic communities; however, to date point-of-use PCR has been hindered by thermal cycling architectures and protocols that do not allow for near-instantaneous results. In this work we demonstrate PCR amplification of synthetic SARS respiratory pathogenic targets and bacterial genomic DNA in less than three minutes in a hardware configuration utilizing convenient sample loading and disposal. Instead of sample miniaturization techniques, near-instantaneous heating and cooling of 5 μL reaction volumes is enabled by convective heat transfer of a thermal fluid through porous media combined with an integrated electrical heater. This method of rapid heat transfer has enabled 30 cycles of PCR amplification to be completed in as little as two minutes and eighteen seconds. Surprisingly, multiple enzymes have been shown to work at these breakthrough speeds on our system. A tool for measuring enzyme kinetics now exists and can allow polymerase optimization through directed evolution studies. Pairing this instrument technology with modified polymerases should result in a new paradigm for high-throughput, ultra-fast PCR and will hopefully improve our ability to quickly respond to the next viral pandemic.
An infrared spectroscopic study of the interactions of carbohydrates with dried proteins (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAn infrared spectroscopic study of the interactions of carbohydrates with dried proteinsJohn F. Carpenter and John H. CroweCite this: Biochemistry 1989, 28, 9, 3916–3922Publication Date (Print):May 2, 1989Publication History Published online1 May 2002Published inissue 2 May 1989https://pubs.acs.org/doi/10.1021/bi00435a044https://doi.org/10.1021/bi00435a044research-articleACS PublicationsRequest reuse permissionsArticle Views1799Altmetric-Citations608LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
New Approach of Anti-VEGF Agents for Age-Related Macular Degeneration (2012)

Age-related macular degeneration (AMD) is the leading cause of visual loss in older population. Angiogenesis is an important factor associated with the development of CNV due to AMD. Treatment of CNV with intravitreal anti-VEGF monotherapy is currently the standard of care. However, not all patients respond to monotherapy, and modified anti-VEGF treatment regimen and combination therapy may target reducing treatment frequency or improving visual outcome. This paper reviews the many clinical trials that have been performed utilizing several treatment regimens. While many trials have shown that this variable therapy is justifiable, further study is required to determine correct regimens and dosage.
Recombinant bispecific antibodies for the targeting of adenoviruses to CEA‐expressing tumour cells: a comparative analysis of bacterially expressed single‐chain diabody and tandem scFv (2004)

We have generated two distinct recombinant bispecific antibody molecules for the retargeting of adenoviral vectors to CEA-expressing tumour cells. These antibody molecules were produced by combining the antigen-binding sites of a neutralising anti-fibre knob scFv (S11) and an anti-CEA antibody either in a single-chain diabody format (scDb CEA-S11) or a tandem scFv format (taFv CEA-S11). In order to facilitate expression of taFv CEA-S11 in bacteria we selected from a phage display library taFv molecules with an optimised linker that connects the two scFv fragments. ScDb CEA-S11 and taFv CEA-S11 were expressed and purified in soluble form from the bacterial periplasm with yields of approximately 100 micro g per litre of bacterial culture. In vitro, both bispecific molecules mediated selective and enhanced transduction of CEA-expressing tumour cells by recombinant adenoviruses. These assays did not reveal any differences in efficiency of adenoviral transduction by the two antibody formats. However, compared with taFv CEA-S11, scDb CEA-S11 exhibited a 2- to 3-fold increased stability in human plasma at 37 degrees C. In summary, we could demonstrate that both formats are suitable for adenovirus targeting to tumour cells with similar biological activity in vitro.
The Semantic Model Based on BSCM for the Information Security (2007)

Semanteme identifying is very difficult problem in the information security. But if the semantic models have been set up for the mechanism of the information security, that's the easy way to identify the semanteme. A few semantic models have been set up based on the BSCM (basic semantic of character meaning). These models should be defined the basic semanteme unit and be defined the models of the semantic relativity. The content of information could be judged by these models. The most basic semantic unit should be defined as BSCM. Basing on the BSCM, the model of the relativity of semanteme for the relativity of semanteme has been set up.
Polymerase Chain Reaction Detection of the t(11,14) Translocation Involving the bcl-1 Major Translocation Cluster in Mantle Cell Lymphoma (1995)

The utility of polymerase-mediated assays in the detection of the t(11;14) involving the bcl-1 major translocation cluster (bcl-1 MTC) was evaluated by analyzing DNA from 33 patients with mantle cell lymphoma, 14 patients with other non-Hodgkin's lymphomas, and five patients with reactive lymphoid hyperplasia. The polymerase chain reaction (PCR) assay was performed using a consensus immunoglobin heavy-chain joining region primer in conjunction with a chromosome 11 specific oligonucleotide primer flanking the translocation site. The sensitivity and specificity of the assay were confirmed by correlation of the (PCR) assay data with restriction analysis. Rearrangements at the bcl-1 MTC were detected in 13 (39%) of 33 cases of mantle cell lymphoma by PCR and in 13 (48%) of 27 cases by restriction analysis. Amplicons were detectable by PCR in 85% (11 of 13) of the cases shown to be bcl-1 rearranged by restriction analysis. Failure to detect amplification products in DNA samples from non-mantle cell lymphomas and reactive follicular hyperplasia further confirmed the specificity of the assay. Sequential hybridization of the PCR products with oligonucleotide probes 3' to the bcl-1 MTC primer revealed that the breakpoints in the bcl-1 MTC were clustered around an Sst I restriction site over a range of 170 base pairs. The study demonstrates that PCR-mediated assay for the detection of the t(11;14) at the bcl-1 MTC is specific and sensitive and can be used as an adjunct to restriction analysis in routine diagnostics.
Study protocol for the randomised controlled trial: Ketamine augmentation of ECT to improve outcomes in depression (Ketamine-ECT study) (2015)

Current Controlled Trials: ISRCTN14689382 (assigned 30/07/2012); EudraCT Number: 2011-005476-41.
An enhanced U6 promoter for synthesis of short hairpin RNA (2003)

Short hairpin RNAs (shRNAs) transcribed by RNA polymerase III (Pol III) promoters can trigger sequence-selective gene silencing in culture and in vivo and, therefore, may be developed to treat diseases caused by dominant, gain-of-function type of gene mutations. These diseases develop in people bearing one mutant and one wild-type gene allele. While the mutant is toxic, the wild-type performs important functions. Thus, the ideal therapy must selectively silence the mutant but maintain the wild-type expression. To achieve this goal, we designed an shRNA that selectively silenced a mutant Cu,Zn superoxide dismutase (SOD1(G93A)) allele that causes amyotrophic lateral sclerosis. However, the efficacy of this shRNA was relatively modest. Since the allele-specific shRNA has to target the mutation site, we could not scan other regions of SOD1 mRNA to find the best silencer. To overcome this problem, we sought to increase the dose of this shRNA by enhancing the Pol III promoter. Here we demonstrate that the enhancer from the cytomegalovirus immediate-early promoter can enhance the U6 promoter activity, the synthesis of shRNA and the efficacy of RNA interference (RNAi). Thus, this enhanced U6 promoter is useful where limited choices of shRNA sequences preclude the selection of a highly efficient RNAi target region.
Dehalogenation and deamination of L-2-amino-4-chloro-4-pentenoic acid by Proteus mirabilis. (1987)

Eighty-one strains of bacteria were tested for their ability to catalyze the release of chloride ion from DL-2-amino-4-chloro-4-pentenoic acid. A dehalogenating enzyme was obtained from the cells of Proteus mirabilis IFO 3849, which can use the L-isomer. The enzyme was constitutively produced. The conversion of L-2-amino-4-chloro-4-pentenoic acid to 2-keto-4-pentenoic acid, ammonia, and chloride ion was demonstrated. The reaction product, 2-keto-4-pentenoic acid, was isolated as its 2, 4-dinitrophenylhydrazone and identified by catalytic hydrogenolysis of the hydrazone to the corresponding amino acid, norvaline.
Glow discharge plasma deposition of tetraethylene glycol dimethyl ether for fouling‐resistant biomaterial surfaces (1992)

The glow discharge plasma deposition (GDPD) of tetraethylene glycol dimethyl ether is introduced as a novel method for obtaining surfaces that are resistant to protein adsorption and cellular attachment. Analysis of films by x-ray photoelectron spectroscopy and several biological assays indicate the formation of a fouling-resistant, PEO-like surface on several substrata (e.g., glass, polytetrafluoroethylene, polyethylene). Adsorption of 125I-radiolabelled proteins (fibrinogen, albumin and IgG) from buffer and plasma was very low (typically less than 20 ng/cm2) when compared to the untreated substrata, which exhibited much higher levels of protein adsorption. Not all coated substrata adsorbed equal amounts of protein (e.g., coated glass samples typically adsorbed more protein than coated polyethylene or coated polytetrafluoroethylene samples), suggesting that the substratum used may affect the amount of protein adsorbed. Measurement of dynamic platelet adhesion, using epifluorescent video microscopy, and endothelial cell attachment further demonstrates the short-term nonadhesiveness of these surfaces.
Assessment and In Vivo Scoring of Murine Experimental Autoimmune Uveoretinitis Using Optical Coherence Tomography (2013)

Despite advances in clinical imaging and grading our understanding of retinal immune responses and their morphological correlates in experimental autoimmune uveoretinitis (EAU), has been hindered by the requirement for post-mortem histology. To date, monitoring changes occurring during EAU disease progression and evaluating the effect of therapeutic intervention in real time has not been possible. We wanted to establish whether optical coherence tomography (OCT) could detect intraretinal changes during inflammation and to determine its utility as a tool for accurate scoring of EAU. EAU was induced in C57BL/6J mice and animals evaluated after 15, 26, 36 and 60 days. At each time-point, contemporaneous Spectralis-OCT scanning, topical endoscopic fundal imaging (TEFI), fundus fluorescein angiography (FFA) and CD45-immunolabelled histology were performed. OCT features were further characterised on retinal flat-mounts using immunohistochemistry and 3D reconstruction. Optic disc swelling and vitreous opacities detected by OCT corresponded to CD45+ cell infiltration on histology. Vasculitis identified by FFA and OCT matched perivascular myeloid and T-cell infiltrates and could be differentiated from unaffected vessels. Evolution of these changes could be followed over time in the same eye. Retinal folds were visible and found to encapsulate mixed populations of activated myeloid cells, T-cells and microglia. Using these features, an OCT-based EAU scoring system was developed, with significant correlation to validated histological (Pearson r(2) = 0.6392, P<0.0001, n = 31 eyes) and TEFI based scoring systems (r(2) = 0.6784, P<0.0001). OCT distinguishes the fundamental features of murine EAU in vivo, permits dynamic assessment of intraretinal changes and can be used to score disease severity. As a result, it allows tissue synchronisation with subsequent cellular and functional assessment and greater efficiency of animal usage. By relating OCT signals with immunohistochemistry in EAU, our findings offer the opportunity to inform the interpretation of OCT changes in human uveitis.
Raman spectroscopic evaluation of polyacrylonitrile‐based carbon nanofibers prepared by electrospinning (2004)

Abstract Poly(acrylonitrile) (PAN) solutions in N , N ‐dimethylformamide were electrospun into webs consisting of 350 nm ultra‐fine fibers. The webs were oxidatively stabilized and followed by heat treatment in the range of 700–1000°C. Characterization of the microstructure of PAN‐based carbon nanofibers was performed by x‐ray diffraction, field‐emission scanning electron microscopy, electrical conductivity and Raman spectroscopy. The L c (002) and L a (10) values were calculated to be 1.85–2.15 and 2.23–3.36 nm, respectively. The L c (002) and L a (10) values increased by about 86% and 66%, respectively, when the heat treatment temperature (HTT) was increased from 700 to 1000°C. The electrical conductivity of carbonized PAN nanofiber webs increased with increasing carbonization temperature, being 6.8 × 10 −3 and 1.96 S cm −1 at 700 and 1000°C, respectively. The D and G bands from Raman scattering were fitted into a Gaussian–Lorentzian hybridized function, and the crystallite sizes in the nanofibers were evaluated from the R ‐values determined from the ratios of the intensity of the G band to that of the D band. The domain size of the graphitic layers was in the range 1.6–3.2 nm with higher values at higher HTT. Copyright © 2004 John Wiley &amp; Sons, Ltd.
Production of interleukin-1 alpha, interleukin-1 beta and tumor necrosis factor by human mononuclear cells stimulated with granulocyte- macrophage colony-stimulating factor [see comments] (1988)

Abstract Recent studies have examined the synergistic effects of granulocyte- macrophage colony-stimulating factor (GM-CSF) and hematopoietin-1 (now identified as Interleukin-1, IL-1) on bone marrow colony formation. In the present report, human peripheral blood mononuclear cells (MNCs) were stimulated in vitro with recombinant human GM-CSF (rGM-CSF) and production of IL-1 alpha, IL-1 beta, and tumor necrosis factor (TNF) was measured by specific radioimmunoassays. In the MNCs of 20 individuals, rGM-CSF's ability to induce the three cytokines was variable. Nearly all donors responded to low-dose rGM-CSF (0.02 to 2 ng/mL) with production of TNF, whereas some individuals did not produce IL-1 alpha or IL-1 beta. The MNCs from some subjects stimulated with high-dose rGM-CSF (10 to 80 ng/mL) produced as much cytokine as in response to 10 ng/mL endotoxin. Localization (ie, extracellular or cell- associated cytokine) was specific for the cytokine rather than the stimulus. Indomethacin increased the amount of cytokine produced in response to rGM-CSF for IL-1 beta and TNF but not for IL-1 alpha. In addition, interferon-gamma (INF-gamma) upregulated the amount of TNF induced by rGM-CSF in all donors examined, with variable effect on IL-1 alpha and IL-1 beta. Suboptimal levels of endotoxin incubated with rGM- CSF did not alter the amount of IL-1 produced as compared with cells stimulated with rGM-CSF alone, whereas TNF production showed either no change or a slight decrease in production. These data suggest that GM- CSF may play an important role in the host defense response by stimulating production of these cytokines.
Skeletal Myogenic Progenitors Originating from Embryonic Dorsal Aorta Coexpress Endothelial and Myogenic Markers and Contribute to Postnatal Muscle Growth and Regeneration (1999)

Skeletal muscle in vertebrates is derived from somites, epithelial structures of the paraxial mesoderm, yet many unrelated reports describe the occasional appearance of myogenic cells from tissues of nonsomite origin, suggesting either transdifferentiation or the persistence of a multipotent progenitor. Here, we show that clonable skeletal myogenic cells are present in the embryonic dorsal aorta of mouse embryos. This finding is based on a detailed clonal analysis of different tissue anlagen at various developmental stages. In vitro, these myogenic cells show the same morphology as satellite cells derived from adult skeletal muscle, and express a number of myogenic and endothelial markers. Surprisingly, the latter are also expressed by adult satellite cells. Furthermore, it is possible to clone myogenic cells from limbs of mutant c-Met-/- embryos, which lack appendicular muscles, but have a normal vascular system. Upon transplantation, aorta-derived myogenic cells participate in postnatal muscle growth and regeneration, and fuse with resident satellite cells.The potential of the vascular system to generate skeletal muscle cells may explain observations of nonsomite skeletal myogenesis and raises the possibility that a subset of satellite cells may derive from the vascular system.