gebhart/patrepeval huggingface dataset:
Accelerated cell line development using two‐color fluorescence activated cell sorting to select highly expressing antibody‐producing clones (2007)

The success of engineered monoclonal antibodies as biopharmaceuticals has generated considerable interest in strategies designed to accelerate development of antibody expressing cell lines. Stable mammalian cell lines that express therapeutic antibodies at high levels typically take 6-12 months to develop. Here we describe a novel method to accelerate selection of cells expressing recombinant proteins (e.g., antibodies) using multiparameter fluorescence activated cell sorting (FACS) in association with dual intracellular autofluorescent reporter proteins. The method is co-factor-independent and does not require complex sample preparation. Chinese hamster ovary (CHO) clones expressing high levels of recombinant antibody were selected on the basis of a two-color FACS sorting strategy using heavy and light chain-specific fluorescent reporter proteins. We were able to establish within 12 weeks of transfection cell lines with greater than a 38-fold increase in antibody production when compared to the pool from which they were isolated, following a single round of FACS. The method provides a robust strategy to accelerate selection and characterization of clones and builds a foundation for a predictive model of specific productivity based upon on two-color fluorescence.
Free secretory component and lactoferrin of human milk inhibit the adhesion of enterotoxigenic Escherichia coli (1995)

The non-immunoglobulin component of human milk responsible for the inhibition of Escherichia coli cell adhesion (haemagglutination) mediated by colonisation factor antigen 1 (CFA1) was determined by chromatographic fractionation of human whey proteins with Sephadex G-200, DEAE cellulose and heparin-sepharose. Pure free secretory component (fSC) and pure lactoferrin (Lf) were isolated and both compounds inhibited the haemagglutination induced by E. coli CFA1+. The lowest concentrations of purified fSC and Lf able to inhibit the haemagglutination induced by E. coli strain TR50/3 CFA1+ were 0.06 mg/ml and 0.1 mg/ml respectively. Commercially available lactoferrin from human milk and transferrin from human serum, which has a great structural analogy to lactoferrin, also inhibited the haemagglutination. The lowest concentrations of the commercial lactoferrin and transferrin able to inhibit the haemagglutination induced by E. coli TR50/3 CFA1+ were 0.03 mg/ml and 0.4 mg/ml, respectively. These results indicate that fSC and Lf may be important non-specific defence factors against enterotoxigenic E. coli infections.
Fe−B Bonding in (Dibromoboryl)ferrocene:  A Structural and Theoretical Investigation (1996)

The geometry and electronic structure of borylferrocenes, FcBR2, have been investigated by X-ray structure analysis (R = Br) and density functional theory (DFT) calculations (R = H). An interaction between filled d-type orbitals at iron and the empty p orbital of boron causes bending of the BR2 substituent toward the central iron atom. The dip angle α* is 17.7° (18.9°) for FcBBr2 (X-ray structure). Slightly larger values were calculated for the sterically unhindered model system FcBH2 (α* = 21.6° [LDA/NL]). According to the DFT calculations, the Fe−B interaction in FcBH2 is considerably weaker than the Fe−Cexo bond of the isoelectronic cation FcCH2+ (α* = 41.0° [LDA/NL]). In 1,1‘-diborylated ferrocene no energetically preferred rotamer was detected by our DFT calculations.
Spatio-Temporally Adaptive Waiting Time for Cell Phone Sensor Networks (2011)

In cell phone sensor networks (CpSN), sensor-embedded cell phones communicate sensor data using Near Field Communication outlets such as Wi-Fi or Bluetooth. This paper considers a query dissemination application of CpSN, where sensor data belonging to a certain time window [[Formula: see text], [Formula: see text]] is needed from a region of interest. Existing approaches, such as ADAPT, use adaptive broadcast ranges at the Wireless Access Point (WAP) for query dissemination. This paper proposes the adaptation of waiting time at nodes for energy-efficient query dissemination. The design and analysis of the proposed Spatio-Temporally Adaptive Distributed Velocity Dependent (STA-DVD) waiting time is presented. The STA-DVD protocol is analytically compared with a Spatially Adaptive Distributed Velocity Dependent (SA-DVD) waiting time based protocol. Simulation results show that STA-DVD has a superior querying performance in terms of number of samples procured than SA-DVD, at a slightly higher energy cost. For the case of a Randomized Waiting (RW) time adopted by nodes in ADAPT, the ADAPT-RW protocol has the best querying performance, with significantly high energy costs. STA-DVD has a comparable querying performance with ADAPT-RW, for high residual times and a better performance for low residual times, with significantly low energy dissipation.
Synthesis of a kairomone and other chemicals from cardanol, a renewable resource (2012)

Abstract Synthesis of a tsetse fly kairomone component (3‐propylphenol), a detergent [sodium 2‐(dec‐8‐enyl)‐6‐hydroxybenzenesulfonate], a polymer additive (1‐octene), and a detergent precursor [3‐(non‐8‐enyl)phenol] using cardanol [3‐(pentadec‐8‐enyl)phenol], has been accomplished. Both carbon–carbon double bond isomerization and metathesis methodologies were employed in the syntheses of these target molecules. The kairomone component was obtained, albeit in low yield, in three steps starting with cardanol. Synthesis of a new detergent, sodium 2‐(dec‐8‐enyl)‐6‐hydroxybenzenesulfonate, was achieved by direct metathesis of cardanol with cis ‐2‐butene followed by sulfonation and basification. Finally, synthesis of 1‐octene and 3‐(non‐8‐enyl)phenol was accomplished in one pot by direct metathesis of cardanol with ethylene. These products have been characterized spectroscopically, especially using 1 H and 13 C NMR.
The Human Acrosome Reaction Is Highly Sensitive to Inhibition by Cyclodiene Insecticides (1997)

The mammalian sperm acrosome reaction (AR) is essential to fertilization. It can be initiated in vitro by progesterone, a putative physiological initiator that helps to activate sperm GABA(A) receptor/chloride channels and by glycine, a substitute for the egg zona pellucida, which activates sperm glycine receptor/chloride channels. Even at 1 nM (0.41 ng/ml or 0.41 ppb), chlordane and endosulfan, chlorinated cyclodiene blockers of insect neuronal GABA(A) receptor/chloride channels, strongly inhibited the AR initiated by progesterone or glycine. Inhibition of the latter was also seen at 0.1 nM chlordane and endosulfan, but neither cyclodiene inhibited either AR initiator at 0.01 nM. Inhibitory concentrations of these cyclodienes are well within the range detected in human and wildlife tissue and fluids as a result of environmental contamination.
Scid mouse model of epstein‐barr virus‐induced lymphomagenesis of immunodeficient humans (1991)

Immunodeficient humans are at very high risk of developing Epstein-Barr virus (EBV)-induced lymphomagenesis. Severe combined immunodeficient mice (SCID) have been shown to develop lymphoproliferative disease (LPD) following transfer of peripheral blood leukocytes (PBL) with latent EBV. To study mechanisms of lymphomagenesis, we compared results of engraftment of PBL from normal donors and immunodeficient donors with X-linked lymphoproliferative disease (XLP). Graft-versus-host disease (GVHD) developed in 6 of 10 SCID mice 4 to 8 weeks following transfer of PBL from normal donors. In contrast, none of 9 mice engrafted with PBL from XLP patients with T-cell defects showed GVHD. LPD developed in mice regardless of the immune competence of the donors. The expression of EBV-encoded proteins, results of immunophenotyping, and karyotyping of the LPD lesions revealed lethal oligoclonal LPD owing to transfer of latent EBV in B cells in mice engrafted with PBL from seropositive donors. Polyclonal LDP developed in mice engrafted with PBL from seronegative patients which were infected with B95-8 virus 6 weeks after transfer of the cells. This model is useful for investigating mechanisms of EBV-induced LDP in immunodeficient patients.
Microalgae as Sources of Carotenoids (2011)

Marine microalgae constitute a natural source of a variety of drugs for pharmaceutical, food and cosmetic applications-which encompass carotenoids, among others. A growing body of experimental evidence has confirmed that these compounds can play important roles in prevention (and even treatment) of human diseases and health conditions, e.g., cancer, cardiovascular problems, atherosclerosis, rheumatoid arthritis, muscular dystrophy, cataracts and some neurological disorders. The underlying features that may account for such favorable biological activities are their intrinsic antioxidant, anti-inflammatory and antitumoral features. In this invited review, the most important issues regarding synthesis of carotenoids by microalgae are described and discussed-from both physiological and processing points of view. Current gaps of knowledge, as well as technological opportunities in the near future relating to this growing field of interest, are also put forward in a critical manner.
Magnetic anisotropy in arrays of Ni, CoFeB, and Ni/Cu nanowires (2007)

An effective field model based on intrawire and interwire dipolar interactions has been developed in order to describe the magnetic anisotropy in arrays of homogeneous and multilayer nanowires. Variable angle ferromagnetic resonance (FMR) and vibrating sample magnetometry (VSM) characterization techniques were used to determine the effective interaction field acting on Ni, CoFeB, and Ni/Cu nanowires. FMR spectra are well described by a rigid magnetization model and VSM data are in rough agreement with a mean longitudinal field model. FMR and VSM values of the effective fields are mutually consistent and in fair agreement with the values calculated with the model. The results show that the anisotropy of our arrays is strongly dominated by the dipolar interactions.
Field access bubble-to-bubble logic operations (1972)

Bubble-to-bubble logic operations can greatly enhance the versatility of bubble memory devices. Our experience to date, however, has shown us that logic operations reduce the device operating margins to a degree that would allow logic only where the ratio of memory sites to logic gates is greater than one hundred. For example, quasistatic rotating field operation of exclusive OR, AND/OR, and replicate gates was obtained for a ± 3.5 percent bias margin at 45 to 55 Oe rotating field drive for an AND/OR gate to a ± 1.5 percent bias field margin at 50 to 60 Oe rotating field drive for an exclusive OR gate. In all cases these devices were prepared by ion milling or chemical etching T-bar, Y-bar, or chevron patterns in 3000 to 5000 Å thick Permalloy films on glass. The pattern feature sizes ranged from 3 to 7.5 μm. The Permalloy on glass patterns were placed on epitaxially grown magnetic garnet wafers with bubble diameters ranging from 8 to 17 μm. Circuit operation was determined by visual observation. In all cases, the results are from either the first design of the circuits or the first iteration design.
ASSESSMENT OF BACTERIAL PATHOGENESIS BY ANALYSIS OF GENE EXPRESSION IN THE HOST (2000)

A number of techniques have been developed to assess the expression of microbial virulence genes within the host (in vivo). These studies have shown that bacteria employ a wide variety of mechanisms to coordinately regulate the expression of these genes during infection. Two tenets have emerged from these studies: bacterial adaptation responses are critical to growth within the host, and interactions between microorganisms and the microenvironments of their hosts cannot be revealed from in vitro studies alone. Results that support these tenets include (i) the prevalent class of in vivo expressed genes are involved in adaptation to environmental stresses, (ii) pathogens recovered from host tissues (versus laboratory growth) are often more resistant to host killing mechanisms, and (iii) virulence gene expression can differ in the animal compared to laboratory media. Thus, pathogenicity comprises the unique ability to adapt to the varied host milieus encountered as the infection proceeds.
A Modular Benchmarking Infrastructure for High-Performance and Reproducible Deep Learning (2019)

We introduce Deep500: the first customizable benchmarking infrastructure that enables fair comparison of the plethora of deep learning frameworks, algorithms, libraries, and techniques. The key idea behind Deep500 is its modular design, where deep learning is factorized into four distinct levels: operators, network processing, training, and distributed training. Our evaluation illustrates that Deep500 is customizable (enables combining and benchmarking different deep learning codes) and fair (uses carefully selected metrics). Moreover, Deep500 is fast (incurs negligible overheads), verifiable (offers infrastructure to analyze correctness), and reproducible. Finally, as the first distributed and reproducible benchmarking system for deep learning, Deep500 provides software infrastructure to utilize the most powerful supercomputers for extreme-scale workloads.
Purification and characterization of a rabbit bone metalloproteinase that degrades proteoglycan and other connective-tissue components (1983)

A metalloproteinase, 'proteoglycanase', that degrades proteoglycan and insoluble type IV collagen as well as casein was purified to homogeneity from rabbit bone culture medium. The major form of this proteinase had a final specific activity of 2400 micrograms of casein degraded/min per mg of enzyme protein, and Mr 24 500 by sodium dodecyl sulphate/polyacrylamide-gel electrophoresis or 12 500 by gel-filtration chromatography. It was active over the pH range 5.0-9.0 against a number of substrates, and the rates of degradation were almost constant over the whole of this range. The products generated from proteoglycan-aggregate degradation by this enzyme indicated cleavage at multiple chondroitin sulphate-binding sites along the protein core. In a new assay to detect degradation of insoluble type IV collagen, the proteoglycanase generated large fragments, probably by cleavage in the non-helical regions. The enzyme degraded laminin, fibronectin and procollagen, removing the extension peptides of the last-mentioned. It also cleaved the 'weak region' of the type III collagen helix in a manner analogous to trypsin. The synthetic substrate 2,4-dinitrophenyl-Pro-Leu-Gly-Ile-Ala-Gly-Arg-NH2 was cleaved exclusively at the Gly-Ile bond. The proteoglycanase was inhibited by tissue inhibitors of metalloproteinases from rabbit bone culture medium, human amniotic fluid and bovine nasal-cartilage extracts, forming essentially irreversible inactive complexes. The importance of this tissue-derived enzyme, with such a wide-ranging degradative capacity, in normal and pathological connective-tissue matrix degradation is discussed.
Dose dependence of tolerance during treatment with mononitrates. (1983)

In order to test the clinically supposed development of tolerance during chronic high-dose nitrate therapy, we studied a total of 24 patients with angiographically proven coronary heart disease at rest and during ergometric exercise (supine position, 50 w for 3 min). Pulmonary arterial pressure (PAP, floating catheter), arterial blood pressure (cuff method), cardiac output (Fick principle), heart rate, and exercise capacity (w X min) were measured at rest and exercise before and during chronic (4 weeks) oral therapy with 5-isosorbide mononitrate (5-ISMN), 3 X 20 mg/day (n = 14) and 3 X 50 mg/day (n = 10). After acute administration, both doses of 5-ISMN decreased mean PAP at rest and during exercise (rest: by 25% with 20 mg and by 29% with 50 mg; exercise: by 30% with 20 mg and by 45% with 50 mg), whereas cardiac output and stroke volume were only reduced by 5-ISMN at rest. During chronic treatment with 60 mg and 150 mg 5-ISMN, and additional administration of 20 mg or 50 mg respectively lowered PAP at rest by 15% and 19%; during ergometric exercise PAP was 22% and 14% lower than during ergometry before any drug treatment. The exercise capacity slightly increased during treatment to 60 mg 5-ISMN, whereas it decreased by 25% on chronic treatment with 150 mg 5-ISMN per day. Our results show that acute administration of 5-ISMN in either dose (20 mg and 50 mg) exerts unloading effects on the heart and will increase the exercise tolerance. In contrast to the higher dose of 150 mg 5-ISMN per day, chronic treatment with the lower dose of 60 mg 5-ISMN daily will not result in drug tolerance.
LightCycler consensus PCR for rapid and differential detection of human erythrovirus B19 and V9 isolates (2004)

Until recently, B19 virus was considered to be the only human pathogen of the genus erythrovirus. However, other non-B19 virus strains, such as V9, have now been isolated and are thought to cause infections clinically and serologically indistinguishable from those caused by B19 virus. Whereas B19 virus related isolates have a low genetic diversity of only 1-2%, nucleotide disparity of up to 12% was found for the new isolates, suggesting that non-B19 virus isolates may not be detectable using B19 virus specific PCR methods. To overcome this problem, we designed consensus primers and probes to enable the simultaneous detection of both B19 and non-B19 virus and subsequent discrimination of the two lineages by melting temperature (T(m)) analysis. A total of 196 clinical specimens, from 185 patients with a history of or an anamnesis resembling B19 virus infection, were analyzed using the consensus PCR test. Erythrovirus DNA was detected in 37 of these samples and was found to be B19 virus specific in each case, confirming previous results using B19 virus specific PCR. Although no non-B19 virus DNA was detected in any of the clinical samples tested in this study, more extensive studies are warranted. The routine use of erythrovirus consensus PCR in the diagnosis of B19 virus infection should provide valuable information on the epidemiology and clinical role of non-B19 virus isolates; its use in screening would increase the safety of blood products.
A40926, a new glycopeptide antibiotic with anti-Neisseria activity (1987)

In the course of a search for glycopeptide antibiotics having novel biological properties, we isolated A40926. Produced by an actinomycete of the genus Actinomadura, A40926 is a complex of four main factors which contain a fatty acid as part of a glycolipid attached to the peptide backbone. Its activity was, in most respects, similar to that of other glycopeptides, such as vancomycin and teicoplanin. However, in addition to inhibiting gram-positive bacteria, A40926 was very active against Neisseria gonorrhoeae. A40926 was rapidly bactericidal for N. gonorrhoeae clinical isolates at concentrations equal to or slightly higher than the MIC. In mice, levels in serum were higher and more prolonged than those of an equivalent subcutaneous dose of teicoplanin. These properties suggest that A40926 may have potential in the therapy of gonorrhea.
Forebody vortex control with miniature, rotatable nose-boom strakes (1992)

Experiments have been conducted in water and wind tunnel facilities to investigate the effectiveness of using rotatable miniaturized forebody nose-boom strakes to manipulate and control fighter aircraft forebody vortices at moderate to high angles of attack to provide potential aerodynamic control power in yaw. Water tunnel tests including flow visualization and yaw moment measurements were conducted on several different models of the F-16 fighter. Wind tunnel force and moment tests investigated the effects of several nose-boom strake configurations on an isolated 1/8th-scale X-29A forebody model. The primary variables of interest were strake size, configuration and roll angle orientation on the nose-boom. Both experiments showed clearly that small nose-boom strakes can be very effective in controlling the forebody vortex flowfield. Different degrees of flow asymmetry can be obtained by rotating a single or a pair of small strakes located on the nose-boom. With large fixed forebody strakes, such as those on the X-29A configuration, the effectiveness of the nose-boom strakes is significantly reduced.
Metal-organic frameworks as biosensors for luminescence-based detection and imaging (2016)

Metal-organic frameworks (MOFs), formed by the self-assembly of metal centres or clusters and organic linkers, possess many key structural and chemical features that have enabled them to be used in sensing platforms for a variety of environmentally, chemically and biomedically relevant compounds. In particular, their high porosity, large surface area, tuneable chemical composition, high degree of crystallinity, and potential for post-synthetic modification for molecular recognition make MOFs promising candidates for biosensing applications. In this review, we separate our discussion of MOF biosensors into two categories: quantitative sensing, focusing specifically on luminescence-based sensors for the direct measurement of a specific analyte, and qualitative sensing, where we describe MOFs used for fluorescence microscopy and as magnetic resonance imaging contrast agents. We highlight several key publications in each of these areas, concluding that MOFs present an exciting, versatile new platform for biosensing applications and imaging, and we expect to see their usage grow as the field progresses.
Similarities and differences between insulin and IGF-I: Structures, receptors, and signalling pathways (2008)

Insulin and the insulin-like growth factors (IGF-I, IGF-II) are pleiotropic hormones that have multiple roles in regulating vital metabolic and developmental processes. Although most early data suggested that insulin is mainly involved in metabolic activities (e.g. control of sugar levels) and IGF-I/II control growth and differentiation events (e.g. bone elongation, cell division), today, it is clear that there is cross-talk between the various ligands and receptors of the IGF family. As a result of these complex interactions, the spectrum of activities that were classically assigned to insulin or IGF-I/II has greatly expanded, and the signalling events mediated by the insulin and IGF receptors is the subject of intensive research. This review provides a comparative analysis of the structures, receptors, and signalling pathways of insulin and IGF-I.
Human coronavirus 229E encodes a single ORF4 protein between the spike and the envelope genes (2006)

Thus, the genome organization of the group 1b coronaviruses HCoV-NL63, PEDV and HCoV-229E is identical. It is possible that extensive culturing of the HCoV-229E laboratory strain resulted in truncation of ORF4. This may indicate that the protein is not essential in cell culture, but the highly conserved amino acid sequence of the ORF4 protein among clinical isolates suggests that the protein plays an important role in vivo.