gebhart/patrepeval huggingface dataset:
Impact of Rapid Susceptibility Testing and Antibiotic Selection Strategy on the Emergence and Spread of Antibiotic Resistance in Gonorrhea (2017)

Rapid diagnostics reporting antibiotic susceptibility may extend the usefulness of existing antibiotics for gonorrhea treatment, but ongoing monitoring of resistance patterns will be critical.
Cancer Chemopreventive Effects and Cytotoxic Activities of the Triterpene Acids from the Resin of Boswellia carteri (2006)

Fifteen triterpene acids, viz., seven of the β-boswellic acids (ursane-type) (1—7), two of the α-boswellic acids (oleanane-type) (8, 9), two of the lupeolic acids (lupane-type) (10, 11), and four of the tirucallane-type (12—14, 16), and two cembrane-type diterpenes (17, 18), isolated from the MeOH extract of the resin of Boswellia carteri (Burseraceae), together with a triterpene acid 15 (the acetyl derivative of 14), were examined for their inhibitory effects on the induction of Epstein–Barr virus early antigen (EBV-EA) by 12-O-tetradecanoylphorbol-13-acetate (TPA) in Raji cells and on activation of (±)-(E)-methyl-2[(E)-hydroxyimino]-5-nitro-6-methoxy-3-hexemide (NOR 1), a nitrogen oxide (NO) donor, and cytotoxic activities against three human neuroblastoma cell lines, IMR-32, NB-39, and SK-N-SH in vitro. On evaluation against the EBV-EA activation induced by TPA, seven compounds, 2, 10, 11, and 13—16, showed potent inhibitory effects on EBV-EA induction. Upon evaluation against activation of NOR 1, five compounds, 7, 13, and 14—16, showed potent inhibitory effects. Further, fifteen compounds, 1—7, 9—11, 13—15, 17, and 18, exhibited potent cytotoxic activities with IC50 values of 4.1—82.4 μM against all of the three human neuroblastoma cells tested.
The Assembly of Human Fibrinogen (1996)

Fibrinogen is a plasma protein consisting of six polypeptide chains which are linked by disulfide bonds. During protein synthesis, assembly of the molecule proceeds through the formation of alphagamma and betagamma heterodimers followed by the generation of alphabetagamma half-molecules and dimerizing to generate the mature six-chain molecule. In the present study, sequences required for the formation of the alphagamma and betagamma heterodimers were examined in stably transfected baby hamster kidney cells expressing combinations of normal as well as modified polypeptide chains. Deletion of the amino terminus and the proximal first half of the coiled-coil region of the three fibrinogen chains had little or no effect on heterodimer and half-molecule formation. These deletions, however, did prevent half-molecules from forming the six-chain molecule. Deletion of the distal second half of the coiled-coil region of each chain completely prevented the assembly process. Point mutations in the second half of the coiled-coil region also indicated that hydrophilic residues that form ion pairs between interacting chains were not critical in the formation of the heterodimeric complexes. These results suggest that the initial formation of the alphagamma and betagamma complexes depends primarily on hydrophobic interactions of amino acids located in the second half of the coiled-coil region of the molecule. These interactions occur in the rough endoplasmic reticulum in the presence of various chaperones such as BiP.
Intelligent patient monitoring and management systems: a review (1993)

The diversity of factors that take part in the design of intelligent patient monitoring and management systems is presented. Particular attention is given to intelligent monitoring and management interfaces, and to the use of knowledge-based systems in patient monitoring and management.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A rapid, colourimetric assay for cytotoxin activity in Campylobacter jejuni (1996)

Cell extracts and culture supernates of Campylobacter jejuni NCTC 11168 and three isolates from faecal samples from patients with enteritis were tested for cytotoxic activity on HeLa and Vero cells using a sensitive and rapid dye reduction assay which represents a simple assay for cytotoxin activity that can be assessed visually or spectrophotometrically in the wells of microplates. The assay was as sensitive as trypan blue exclusion and did not require the use of radioisotopes. A low level of cytotoxin activity, compared to that produced by a control verotoxin 2-producing Escherichia coli strain, was detected in cell extracts of all four strains, but no activity was detected in culture supernates. Production of an enterotoxin was evaluated by reverse passive latex agglutination with anti-cholera toxin antibody, a procedure which also represents a rapid and simple assay for this toxin. No enterotoxin activity was detected in cell extracts or culture supernates from any of the isolates.
An efficient algorithm for large-scale detection of protein families (2002)

Detection of protein families in large databases is one of the principal research objectives in structural and functional genomics. Protein family classification can significantly contribute to the delineation of functional diversity of homologous proteins, the prediction of function based on domain architecture or the presence of sequence motifs as well as comparative genomics, providing valuable evolutionary insights. We present a novel approach called TRIBE-MCL for rapid and accurate clustering of protein sequences into families. The method relies on the Markov cluster (MCL) algorithm for the assignment of proteins into families based on precomputed sequence similarity information. This novel approach does not suffer from the problems that normally hinder other protein sequence clustering algorithms, such as the presence of multi-domain proteins, promiscuous domains and fragmented proteins. The method has been rigorously tested and validated on a number of very large databases, including SwissProt, InterPro, SCOP and the draft human genome. Our results indicate that the method is ideally suited to the rapid and accurate detection of protein families on a large scale. The method has been used to detect and categorise protein families within the draft human genome and the resulting families have been used to annotate a large proportion of human proteins.
Root Variations Induced by Carbon Dioxide Gas Additions to Soil (1918)

1. Plants respond differently to carbon dioxide gas added to the soil in which they are grown. 2. The roots of the Christmas pepper, head lettuce, radish, and string bean were all found to be affected by additions of carbon dioxide gas to the soil. 3. The effects of carbon dioxide on root development were greater than those on the aerial portions of the plants. 4. The intermittent and constant applications of the carbon dioxide gas did not affect the roots of all the plants to the same extent. 5. The effect of the gas was not the same for the different plants used, although a constant treatment of 650 Ccs. of carbon dioxidegas per hour was apparently preventative of normal root development. 6. Decaying organic matter is held to be beneficial to growing plants. Cases have been cited by others where turning under immense amounts of green material has hurt the land temporarily; therefore the results obtained in these experiments lead to the belief that the carbon dioxide content of garden soils is sometimes detrimental to the root development of some plants growing in the garden. 7. The conclusion of Cannon and Free that soil aeration must be a factor of no less importance in plant growth than water and temperature is supported.
Infrared Spectroscopy: Fundamentals and Applications (2004)

Provides an introduction to those needing to use infrared spectroscopy for the first time, explaining the fundamental aspects of this technique, how to obtain a spectrum and how to analyse infrared data covering a wide range of applications. Includes instrumental and sampling techniques Covers biological and industrial applications Includes suitable questions and problems in each chapter to assist in the analysis and interpretation of representative infrared spectra Part of the ANTS (Analytical Techniques in the Sciences) Series.
Solid-State Chemistry: a Rediscovered Chemical Frontier (1990)

Chemical bonding in solids is not completely understood, mainly because of the wide variation in the chemical properties of the elements. Many difficult challenges remain in predicting the composition, structure, and the properties of new materials. Consequently, the synthesis of novel solids is as much an art as a science. Discoveries of new compounds and structure types highlight the versatility that nature has allowed with the relatively small number of elements. This article explores the long-term challenges in solid-state chemistry and then focuses on efforts at Cornell to prepare new solids.
The composition of CD34 subpopulations differs between bone marrow, blood and cord blood. (1996)

Our previous data obtained by flow cytometry and by clonogenic assay had consistently shown a lower cloning efficiency of hematopoietic progenitor cells in bone marrow (BM) compared to those in blood (PB) or in cord blood (CB). Also, recent clinical reports have described more rapid reconstitution after PB than after BM transplantation. We have applied two- or three-color flow cytometric analysis using monoclonal antibodies directed against the stem- and progenitor cell antigen CD34, in combination with other cell surface markers. We report significant differences in the composition of progenitor cells contained in BM (238 specimens from 53 healthy donors and from patients in remission), PB (301 samples from 92 patients with or without cytokine support) and CB (n = 37). Leukapheresis products (Pher, n = 69) were included in the study as well as positively selected CD34+ cells obtained from BM (BMsel, n = 2), PB (PBsel, n = 28) and CB (CBsel, n = 5). We used monoclonal antibodies directed against CD7, CD19, CD34, CD38, CD45RA and glycophorin A. The highest proportion of CD34+ cells (in % of the MNC) was found in BM (mean 5.37% +/- 4.5). In the other sources, the mean values were 1.79% +/- 2.46 (PB), 1.48% +/- 1.81 (Pher) and 1.1% +/- 1.69 (CB). However, BM was the only source in which a considerable proportion of the CD34+ cells coexpressed the B cell antigen CD19 (mean 30.1%, median 28, range 0 to 84%). The amount of earlier myeloid progenitors as determined by their non-expression of the CD45RA antigen was lowest among BM CD34+ cells (26.7% +/- 16.6). In the other sources, the respective values were 57.5% +/- 17.9 (PB), 63.6% +/- 13.9 (Pher) and 70.4% +/- 16.1 (CB). These results were confirmed by subtype analyses of the CD34+ cells positively selected from the three sources. Enrichment showed minor CD34+ subpopulations to be identified. The mean proportions of B cell progenitors were 0.11% +/- 0.24 (PBsel) and 1.3% +/- 1.42 (CBsel) of the CD34+ cells. The CD34+ cells from all cell sources coexpressed GPA (median 0.15%, range 0 to 1.8%) and CD7 (median 0.25%, range 0 to 1.2%). The proportion of CD38- cells ranged from 0.7 to 4% of the CD34+ MNC. Thus, despite higher CD34 counts in BM, the relative proportions of myeloid progenitors are higher in PB and in CB. This suggests that, if timely reconstitution depends on the number of CD34+ cells transplanted, the mean number of "stem cells' (SC) required is 1.4-fold (for myeloid cells) or 2.2-fold (for earlier myeloid cells) higher for BM than for PB.
Enhanced expression of mRNA for transforming growth factor-beta, type I and type III procollagen in human post-burn hypertrophic scar tissues. (1993)

To explore the possible role of locally synthesized transforming growth factor beta-1 (TGF-beta 1) and procollagen gene expression in postburn hypertrophic scars, we have compared mRNA levels for type I and type III procollagen and TGF-beta 1 in human hypertrophic scar tissue with normal dermis obtained from the same patients as a control. Northern blot analysis of total RNA extracted from hypertrophic scar tissue and normal skin demonstrated two transcripts for the pro-alpha 1(I) chain (5.8 kb and 4.8 kb) and for the pro-alpha 1(III) chain (5.4 kb and 4.8 kb) and one transcript (4.9 kb) for TGF-beta 1. Quantitative analysis of dot blot autoradiograms of mRNA from three samples of hypertrophic scar tissue and normal skin showed average increases of 102% (p < 0.05) for pro-alpha 1(I), 91% (p < 0.06) for pro-alpha 1(III), and 61% (p < 0.05) for TGF-beta 1. Three additional hypertrophic scar samples were quantitatively analyzed on Northern blots and showed increases of 246%, 102%, and 250% of the specific messages for pro-alpha 1(I), pro-alpha 1(III), and TGF-beta 1 relative to a normal skin control. Two transcripts (4.9 kb and 2.5 kb) for TGF-beta 1 were identified in cultured fibroblasts. In contrast to the results from tissue, the level of these transcripts in fibroblasts cultured from hypertrophic scar tissue and normal skin were not significantly different, suggesting that the synthesis of this growth factor is stimulated in tissue by a presently unknown mechanism.(ABSTRACT TRUNCATED AT 250 WORDS)
CD8+ T lymphocytes producing Th2-type cytokines (Tc2) in HIV-infected individuals. (1996)

Unusual high proportions of CD8+ T-cell clones able to produce IL-4, but no IFN-gamma (Tc2 cells), were generated from both skin biopsies and peripheral blood of HIV-infected individuals in advanced phase of infection. Tc2 cells showed unusual phenotypic and functional features, such as CD30 expression, B-cell helper activity for IgE synthesis and reduced cytolytic potential. Cloning CD8+ T-cell from HIV-infected individuals in autologous feeder cells resulted in a marked increase of CD8+ T-cell clones showing a Tc2 profile. The addition in bulk culture before cloning of both IL-12 and a neutralizing anti-IL-4 antibody dramatically reversed the cytokine profile of CD8+ T-cell clones of HIV-infected individuals to the classic Tc1 pathway. Finally, cloning CD8+ T-cells from healthy HIV-seronegative donors in the presence of feeder cells from HIV-infected individuals resulted in the development of enhanced proportions of CD8+ T-cell clones able to produce IL-4. These data suggest that CD8+ T-cells from HIV-infected individuals can develop into Tc2 cells likely because of either the defective production of IL-12 by HIV-infected macrophages and/or other microenvironmental conditions favoring early IL-4 production. The Tc2 shift during HIV infection may play some role in the reduced defence against viral infections, including HIV itself, in patients with AIDS.
Transforming Growth Factor-α Null and Senescent Mice Show Decreased Neural Progenitor Cell Proliferation in the Forebrain Subependyma (1997)

The adult mammalian forebrain subependyma contains neural stem cells and their progeny, the constitutively proliferating progenitor cells. Using bromodeoxyuridine labeling to detect mitotically active cells, we demonstrate that the endogenous expression of transforming growth factor-alpha (TGFalpha) is necessary for the full proliferation of progenitor cells localized to the dorsolateral corner of the subependyma and the full production of the neuronal progenitors that migrate to the olfactory bulbs. Proliferation of these progenitor cells also is diminished with age (in 23- to 25-months-old compared with 2- to 4-months-old mice), likely because of a lengthening of the cell cycle. Senescence or the absence of endogenous TGFalpha does not affect the numbers of neural stem cells isolated in vitro in the presence of epidermal growth factor. These results suggest that endogenous TGFalpha and the effects of senescence may regulate the proliferation of progenitor cells in the adult subependyma, but that the number of neural stem cells is maintained throughout life.
Reprogramming of MLL-AF9 leukemia cells into pluripotent stem cells (2013)

The 'Yamanaka factors' (Oct4, Sox2, Klf4 and c-Myc) are able to generate induced pluripotent stem (iPS) cells from different cell types. However, to what degree primary malignant cells can be reprogrammed into a pluripotent state has not been vigorously assessed. We established an acute myeloid leukemia (AML) model by overexpressing the human mixed-lineage leukemia-AF9 (MLL-AF9) fusion gene in mouse hematopoietic cells that carry Yamanaka factors under the control of doxycycline (Dox). On addition of Dox to the culture, the transplantable leukemia cells were efficiently converted into iPS cells that could form teratomas and produce chimeras. Interestingly, most chimeric mice spontaneously developed the same type of AML. Moreover, both iPS reprogramming and leukemia reinitiation paths could descend from the same leukemia-initiating cell. RNA-seq analysis showed reversible global gene expression patterns between these interchangeable leukemia and iPS cells on activation or reactivation of MLL-AF9, suggesting a sufficient epigenetic force in driving the leukemogenic process. This study represents an important step for further defining the potential interplay between oncogenic molecules and reprogramming factors during MLL leukemogenesis. More importantly, our reprogramming approach may be expanded to characterize a range of hematopoietic malignancies in order to develop new strategies for clinical diagnosis and treatment.
Thrombin Activatable Fibrinolysis Inhibitor (TAFI) at the Interface between Coagulation and Fibrinolysis (2003)

The thrombin-catalysed conversion of plasma fibrinogen into fibrin and the development of an insoluble fibrin clot are the final steps of the coagulation cascade during haemostasis. A delicate balance between coagulation and fibrinolysis determines the stability of the fibrin clot. Thrombin Activatable Fibrinolysis Inhibitor (TAFI) plays an important role in this process. TAFI is activated by thrombin and protects the fibrin clot against lysis. The role of TAFI in bleeding and thrombotic disorders is discussed as well as its novel emerging role in wound healing and inflammation.
Pore formation in silicon by wet etching using micrometre-sized metal particles as catalysts (2008)

Au, Pt, or Ag particles with particle sizes of ca. 1 μm were used as catalysts for boring pores in p-type Si(100) wafers by wet etching in aqueous solutions containing hydrofluoric acid and hydrogen peroxide. Boring speed was fastest when Pt particles were used as the catalyst. However, the sidewalls of the pores and the surface of the wafer were covered with a nanoporous silicon layer of ca. 500 nm in thickness, and the pore showed a tapered structure. When micrometre-sized Ag particles were used, no deep pores were formed because the particles were unstable in the solution. In contrast to Pt and Ag particles, Au particles bored straight pores under some conditions. However, the morphology of pores depended on the shape of the Au particles. Spherical Au particles formed straight pores, whereas non-spherical Au particles formed pores with spiral sidewalls. When Au particles formed aggregates consisting of a small number of particles (<10 particles), crooked pores tended to be formed. In contrast, when the aggregates were composed of a larger number of particles, straight pores were formed and the boring speed was faster than the pores formed with isolated Au particles.
Salinibacter ruber gen. nov., sp. nov., a novel, extremely halophilic member of the Bacteria from saltern crystallizer ponds. (2002)

Five brightly red-pigmented, motile, rod-shaped, extremely halophilic bacteria were isolated from saltern crystallizer ponds in Alicante (two strains) and Mallorca (three strains), Spain. They grew optimally at salt concentrations between 20 and 30% and did not grow below 15% salts. Thus, these isolates are among the most halophilic organisms known within the domain Bacteria. The temperature optimum was 37-47 degrees C. A single, yet to be identified pigment was present, with an absorption maximum at 482 nm and a shoulder at 506-510 nm. The G+C content of the DNA was 66.3-67.7 mol% and, together, they formed a homogeneous genomic group with DNA-DNA similarities above 70%. The 16S rRNA gene sequences were almost identical to sequences recovered earlier from the saltern biomass by amplification of bacterial small-subunit rRNA genes from DNA extracted from the environment. This phylotype, earlier described as 'Candidatus Salinibacter', was shown by fluorescence in situ hybridization to contribute between 5 and 25% of the prokaryote community of the saltern crystallizers. We have therefore succeeded in isolating a bacterium from the natural environment that, although being a major component of the community, was previously known by its phylotype only. Isolation of the organism now allows formal description of a novel genus and species, for which we propose the name Salinibacter ruber gen. nov., sp. nov. The type strain is strain M31T (= DSM 13855T = CECT 5946T).
Polymersomes: nature inspired nanometer sized compartments (2009)

Provided the right hydrophilic/hydrophobic balance can be achieved, amphiphilic block copolymers are able to assemble in water into membranes. These membranes can enclose forming spheres with an aqueous core. Such structures, known as polymer vesicles or polymersomes (from the Greek “-some” = “body of”), have sizes that vary from tens to thousands of nanometers. The wholly synthetic nature of block copolymers affords control over parameters such as the molar mass and composition which ultimately determine the structure and properties of the species in solution. By varying the copolymer molecular mass it is possible to adjust the mechanical properties and permeability of the polymersomes, while the synthetic nature of copolymers allows the design of interfaces containing various biochemically-active functional groups. In particular, non-fouling and non-antigenic polymers have been combined with hydrophobic polymers in the design of biocompatible nano-carriers that are expected to exhibit very long circulation times. Stimulus-responsive block copolymers have also been used to exploit the possibility to trigger the disassembly of polymersomes in response to specific external stimuli such as pH, oxidative species, and enzyme degradation. Such bio-inspired ‘bottom-up’ supramolecular design principles offer outstanding advantages in engineering structures at a molecular level, using the same long-studied principles of biological molecules. Thanks to their unique properties, polymersomes have already been reported and studied as delivery systems for both drugs, genes, and image contrast agents as well as nanometer-sized reactors.
Phase II Clinical Investigation of Gemcitabine in Advanced Soft Tissue Sarcomas and Window Evaluation of Dose Rate on Gemcitabine Triphosphate Accumulation (2001)

Given the limited therapeutic armamentarium for STS, the activity of gemcitabine is encouraging. Its potential for combination therapy in the salvage setting should be studied with pharmacologically guided fixed dose-rate infusion.
Coherent Control of Quantum Dynamics: The Dream Is Alive (1993)

Current experimental and theoretical progress toward the goal of controlling quantum dynamics is summarized. Two key developments have now revitalized the field. First, appropriate ultrafast laser pulse shaping capabilities have only recently become practical. Second, the introduction of engineering control concepts has put the required theoretical framework on a rigorous foundation. Extrapolations to determine what is realistically possible are presented.