gebhart/patrepeval huggingface dataset:
Microplate assay for denatured collagen using collagen hybridizing peptides (2018)

The purpose of this study was to develop a microplate assay for quantifying denatured collagen by measuring the fluorescence of carboxyfluorescein bound collagen hybridizing peptides (F-CHP). We have shown that F-CHP binds selectively with denatured collagen, and that mechanical overload of tendon fascicles causes collagen denaturation. Proteinase K was used to homogenize tissue samples after F-CHP staining, allowing fluorescence measurement using a microplate reader. We compared our new assay to our previous image analysis method and the trypsin-hydroxyproline assay, which is the only other available method to directly quantify denatured collagen. Relative quantification of denatured collagen was performed in rat tail tendon fascicles subjected to incremental tensile overload, and normal and ostoeoarthritic guinea pig cartilage. In addition, the absolute amount of denatured collagen was determined in rat tail tendon by correlating F-CHP fluorescence with percent denatured collagen as determined by the trypsin-hydroxyproline assay. Rat tail tendon fascicles stretched to low strains (<7.5%) exhibited minimal denatured collagen, but values rapidly increased at medium strains (7.5-10.5%) and plateaued at high strains (≥12%). Osteoarthritic cartilage had higher F-CHP fluorescence than healthy cartilage. Both of these outcomes are consistent with previous studies. With the calibration curve, the microplate assay was able to absolutely quantify denatured collagen in mechanically damaged rat tail tendon fascicles as reliably as the trypsin-hydroxyproline assay. Further, we achieved these results more efficiently than current methods in a rapid, high-throughput manner, with multiple types of collagenous tissue while maintaining accuracy. © 2018 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 37:431-438, 2019.
Pseudorandom Sequence Modifications for Ion Mobility Orthogonal Time-of-Flight Mass Spectrometry (2008)

Due to the inherently low duty cycle of ion mobility spectrometry (IMS) experiments that sample from continuous ion sources, a range of experimental advances have been developed to maximize ion utilization efficiency. The use of ion trapping and accumulation approaches prior to the ion mobility drift tube has demonstrated significant gains over discrete sampling from continuous sources but have traditionally relied upon a signal averaging (SA) to attain analytically useful signal-to-noise ratios (SNR). Multiplexed (MP) techniques based upon the Hadamard transform offer an alternative experimental approach by which ion utilization efficiency can be elevated from approximately 1 to approximately 50%. Recently, our research group demonstrated a unique multiplexed ion mobility time-of-flight (MP-IMS-TOF) approach that incorporates ion trapping and can extend ion utilization efficiency beyond 50%. However, the spectral reconstruction of the multiplexed signal using this experiment approach requires the use of sample-specific weighting designs. Such general weighting designs have been shown to significantly enhance ion utilization efficiency using this MP technique, but cannot be universally applied. By modifying both the ion trapping and the pseudorandom sequence (PRS) used for the MP experiment, we have eliminated the need for complex weighting matrices. For both simple and complex mixtures, SNR enhancements of up to 13 were routinely observed as compared to the SA-IMS-TOF approach. In addition, this new class of PRS provides a 2-fold enhancement in the number of ion gate pulses per unit time compared to the traditional HT-IMS experiment.
Evaluation of the Safety Profile of the ASFV Vaccine Candidate ASFV-G-ΔI177L (2022)

African swine fever (ASF) is the cause of a recent pandemic that is posing a threat to much of the world swine production. The etiological agent, ASF virus (ASFV), infects domestic and wild swine, producing a variety of clinical presentations depending on the virus strain and the genetic background of the pigs infected. No commercial vaccine is currently available, although recombinant live attenuated vaccine candidates have been shown to be efficacious. In addition to determining efficacy, it is paramount to evaluate the safety profile of a live attenuated vaccine. The presence of residual virulence and the possibility of reversion to virulence are two of the concerns that must be evaluated in the development of live attenuated vaccines. Here we evaluate the safety profile of an efficacious live attenuated vaccine candidate, ASFV-G-ΔI177L. Results from safety studies showed that ASFV-G-ΔI177L remains genetically stable and phenotypically attenuated during a five-passage reversion to virulence study in domestic swine. In addition, large-scale experiments to detect virus shedding and transmission confirmed that even under varying conditions, ASFV-G-ΔI177L is a safe live attenuated vaccine.
Foam : The future of effective cosmeceuticals (2006)

Foam products are emerging as the future vehicle for the delivery of cosmetic and cosmeceutical active agents. They can deliver active ingredients for a variety of skin conditions such as wrinkles, hyperpigmentation, acne and cellulite. This review will highlight several advantages of foam.
Piezoelectric Crystal Biosensor System for Detection of Escherichia Coli (1989)

Abstract A piezoelectric crystal biosensor system was applied to the detection of Escherichia coli. the system consists of an oscillator, a frequency counter, a flow cell and a modified piezoelectric crystal. Anti-E. coli antibody is immobilized on the surface of the crystal. It is used as an E. coli detection by measuring its resonant frequency shift due to a mass change caused by specific binding of the micro organisms to the surface. the frequency shift correlates with an E. coli concentration in the range of 106−108 cells·cm−3. the resonant frequency shift is increased by further treatment to bind micro-particles modified with anti-E. coli antibody. This method allows us to improve the determination limit to 105 cells · cm−3.
Measuring human movement for biomechanical applications using markerless motion capture (2006)

Modern biomechanical and clinical applications require the accurate capture of normal and pathological human movement without the artifacts associated with standard marker-based motion capture techniques such as soft tissue artifacts and the risk of artificial stimulus of taped-on or strapped-on markers. In this study, the need for new markerless human motion capture methods is discussed in view of biomechanical applications. Three different approaches for estimating human movement from multiple image sequences were explored. The first two approaches tracked a 3D articulated model in 3D representations constructed from the image sequences, while the third approach tracked a 3D articulated model in multiple 2D image planes. The three methods are systematically evaluated and results for real data are presented. The role of choosing appropriate technical equipment and algorithms for accurate markerless motion capture is critical. The implementation of this new methodology offers the promise for simple, time-efficient, and potentially more meaningful assessments of human movement in research and clinical practice.
Impact of nicotine pathway downregulation on polyamine biosynthesis and leaf ripening in tobacco (2021)

Traditional breeding and molecular approaches have been used to develop tobacco varieties with reduced nicotine and secondary alkaloid levels. However, available low-alkaloid tobacco varieties have impaired leaf quality likely due to the metabolic consequences of nicotine biosynthesis downregulation. Recently, we found evidence that the unbalanced crosstalk between nicotine and polyamine pathways is involved in impaired leaf ripening of a low-alkaloid (LA) Burley 21 line having a mutation at the <i>Nic1</i> and <i>Nic2</i> loci, key biosynthetic regulators of nicotine biosynthesis. Since the <i>Nic1</i> and <i>Nic2</i> loci are comprised of several genes, all phenotypic changes seen in LA Burley 21 could be due to a mixture of genetics-based responses. Here, we investigated the commercial burley variety TN90 LC and its transgenic versions with only one downregulated gene, either putrescine methyl transferase (PMT-RNAi) or PR50-protein (PR50-RNAi). Nicotine levels of cured lamina of TN90 LC, TN90 PMT-RNAi and TN90 PR50-RNAi, were 70.5 ± 3.8, 2.4 ± 0.5, and 6.0 ± 1.1 mg/g dry weight, respectively. Low-alkaloid transgenic lines showed delayed leaf maturation and impaired leaf quality. We analyzed polyamine contents and ripening markers in wild-type TN90 control plants (WT) and the two transgenic lines. The ripening markers revealed that the PMT-RNAi line showed the most pronounced impaired leaf maturation phenotype at harvest, characterized by higher chlorophyll (19%) and glucose (173%) contents and more leaf mesophyll cells per area (25%), while the ripening markers revealed that maturation of PR50-RNAi plants was intermediate between PMT-RNAi and WT lines. Comparative polyamine analyses showed an increase in free and conjugated polyamines in roots of both transgenic lines, this being most pronounced in the PMT-RNAi plants. For PMT-RNAi plants, there were further perturbations of polyamine content in the leaves, which mirrored the general phenotype, as PR50-RNAi transgenic plants looked more similar to the WT than PMT-RNAi transgenic plants. Activity of ornithine decarboxylase, the enzyme that catalyzes the committing step of polyamine biosynthesis, was significantly higher in roots and mature leaves of PMT-RNAi plants in comparison to WT, while there was no increase observed for arginine decarboxylase. Treatment of both transgenic lines with polyamine biosynthesis inhibitors decreased the polyamine content and ameliorated the phenotype, confirming the intricate interplay of polyamine and nicotine biosynthesis in tobacco and the influence of this interplay on leaf ripening.
Preclinical evaluation of AFM24, a novel CD16A-specific innate immune cell engager targeting EGFR-positive tumors (2021)

Epidermal growth factor receptor (EGFR)-targeted cancer therapy such as anti-EGFR monoclonal antibodies and tyrosine kinase inhibitors have demonstrated clinical efficacy. However, there remains a medical need addressing limitations of these therapies, which include a narrow therapeutic window mainly due to skin and organ toxicity, and primary and secondary resistance mechanisms of the EGFR-signaling cascade (e.g., RAS-mutated colorectal cancer). Using the redirected optimized cell killing (ROCK®) antibody platform, we have developed AFM24, a novel bispecific, IgG<sub>1</sub>-scFv fusion antibody targeting CD16A on innate immune cells, and EGFR on tumor cells. We herein demonstrate binding of AFM24 to CD16A on natural killer (NK) cells and macrophages with <i>K<sub>D</sub></i> values in the low nanomolar range and to various EGFR-expressing tumor cells. AFM24 was highly potent and effective for antibody-dependent cell-mediated cytotoxicity via NK cells, and also mediated antibody-dependent cellular phagocytosis via macrophages <i>in vitro</i>. Importantly, AFM24 was effective toward a variety of EGFR-expressing tumor cells, regardless of EGFR expression level and KRAS/BRAF mutational status. <i>In vivo</i>, AFM24 was well tolerated up to the highest dose (75 mg/kg) when administered to cynomolgus monkeys once weekly for 28 days. Notably, skin and other toxicities were not observed. A transient elevation of interleukin-6 levels was detected at all dose levels, 2-4 hours post-dose, which returned to baseline levels after 24 hours. These results emphasize the promise of bispecific innate cell engagers as an alternative cancer therapy and demonstrate the potential for AFM24 to effectively target tumors expressing varying levels of EGFR, regardless of their mutational status.<b>Abbreviations:</b> ADA: antidrug antibody; ADCC: antibody-dependent cell-mediated cytotoxicity; ADCP: antibody-dependent cellular phagocytosis; AUC: area under the curve; CAR: chimeric-antigen receptor; CD: Cluster of differentiation; CRC :colorectal cancer; ECD: extracellular domain; EGF: epidermal growth factorEGFR epidermal growth factor receptor; ELISA: enzyme-linked immunosorbent assay; FACS: fluorescence-activated cell sorting; Fc: fragment, crystallizableFv variable fragment; HNSCC: head and neck squamous carcinomaIL interleukinm; Ab monoclonal antibody; MOA: mechanism of action; NK :natural killer; NSCLC: non-small cell lung cancer; PBMC: peripheral blood mononuclear cell; PBS: phosphate-buffered saline; PD: pharmacodynamic; ROCK: redirected optimized cell killing; RSV: respiratory syncytial virus; SABC: specific antibody binding capacity; SD: standard deviation; TAM: tumor-associated macrophage; TKI: tyrosine kinase inhibitor; WT: wildtype.
A glycoengineered anti‐CD19 antibody with potent antibody‐dependent cellular cytotoxicity activity <i>in vitro</i> and lymphoma growth inhibition <i>in vivo</i> (2011)

Human cluster of differentiation (CD) antigen 19 is a B cell-specific surface antigen and an attractive target for therapeutic monoclonal antibody (mAb) approaches to treat malignancies of B cell origin. MEDI-551 is an affinity-optimized and afucosylated CD19 mAb with enhanced antibody-dependent cellular cytotoxicity (ADCC). The results from in vitro ADCC assays with Natural Killer cells as effector cells, demonstrate that MEDI-551 is effective at lower mAb doses than rituximab with multiple cell lines as well as primary chronic lymphocytic leukaemia and acute lymphoblastic leukaemia samples. Targeting CD19 with MEDI-551 was also effective in several severe combined immunodeficiency lymphoma models. Furthermore, the combination of MEDI-551 with rituximab resulted in prolonged suppression of tumour growth, demonstrating that therapeutic mAbs with overlapping effector function can be combined for greater tumour growth inhibition. Together, the data demonstrate that MEDI-551 has potent antitumour activity in preclinical models of B cell malignancies. The results also suggest that the combination of the ADCC-enhanced CD19 mAb with an anti-CD20 mAb could be a novel approach for the treatment of B cell lymphomas.
A Packet Forwarding Method for the ISCSI Virtualization Switch (2007)

We present a packet forwarding method for the implementation of the iSCSI virtualization switch used in the SANs. Using the existing virtualization software plus network protocol stacks, first we build up a network-based storage virtualization switch model in the architecture of the symmetric approach. In compliance with the same functionality, our method can reduce the overheads of protocol processing by using a packet forwarding method based on caching the structure ID of the iSCSI session. With the Address Translator and Duplicating Handler, our design can also achieve the feature of storage virtualization management. From the result of our performance experiment, our forwarding system can achieve a higher performance on the READ/WRITE operations by 25% ~30% and reduce the CPU utilization by 10% ~15% compared to the conventional virtualization switch.
Molecularly cloned feline immunodeficiency virus NCSU1 JSY3 induces immunodeficiency in specific-pathogen-free cats (1996)

A full-length feline immunodeficiency virus NCSU1 (FIV-NCSU1) genome (JSY3) was cloned directly from FIV-NCSU1-infected feline CD4+ lymphocyte (FCD4E) genomic DNA and identified by PCR amplification with 5' long terminal repeat, gag, env, and 3' long terminal repeat primer sets. Supernatant from FCD4E cells cocultured with JSY3-transfected Crandell feline kidney (CrFK) cells was used as an inoculum. Cell-free JSY3 virus was cytopathogenic for FCD4E lymphocytes but did not infect CrFK cells in vitro. To determine in vivo infectivity and pathogenesis, six young adult specific-pathogen-free cats were inoculated with cell-free JSY3 virus. Provirus was detected at 2 weeks postinfection (p.i.) and was still detectable at 25 weeks p.i. as determined by gag region PCR-Southern blot analysis of peripheral blood mononuclear cell lysates. Infectious virus was recovered from peripheral blood mononuclear cells at 6 and 25 weeks p.i., and an antibody response to FIV was detected by 4 weeks. In the acute phase of infection, JSY3 provirus was found only in the CD4+ lymphocyte subset; however, by 14 weeks p.i., the greatest provirus burden was detected in B lymphocytes. All six cats were panlymphopenic at 2 weeks p.i., CD4+/CD8+ ratios were inverted by 6 weeks p.i., and five of the six cats developed lymphadenopathy by 10 weeks p.i. To determine if the JSY3 molecular clone caused immunodeficiency similar to that of the parental wild-type FIV-NCSU1, the cats were challenged with the low-virulence ME49 strain of Toxoplasma gondii at 29 weeks p.i. Five of six cats developed clinical signs consistent with generalized toxoplasmosis, and three of six cats developed acute respiratory distress and required euthanasia. Histopathologic examination of the severely affected cats revealed generalized inflammatory reactions and the presence of T. gondii tachyzoites in multiple tissues. None of the six age- and sex-matched specific-pathogen-free cats inoculated with only T. gondii developed clinical disease. Our results suggest that the pathogenesis of the molecularly cloned NCSU1 JSY3 is similar to that of wild-type FIV-NCSU1.
N-acetylneuraminyllactose-binding fibrillar hemagglutinin of Campylobacter pylori: a putative colonization factor antigen (1988)

Campylobacter pylori is the causative agent of gastritis and possibly of peptic and duodenal ulcers in adults. Histological observations show C. pylori attached to gastric epithelium as well as in the mucus layer of the stomach. We found that clinical isolates of C. pylori possess a cell-bound hemagglutinin detectable with human erythrocytes (all phenotypes tested) and those of a variety of animal species. The C. pylori hemagglutinin is antigenic, heat sensitive, and destroyed by pronase and papain but resistant to pepsin and trypsin. The hemagglutinin has fibrillar morphology; C. pylori-erythrocyte interaction displays very intimate contact, which is typical of fibrillae-mediated attachment. Fibrillae were removed from C. pylori by solubilization with N-octylglucose. After partial purification and removal of N-octylglucose by dialysis, the protein reaggregated, with the assembly of fibrillar structures. Hemagglutination inhibition was observed with the sialoproteins fetuin, alpha 2-macroglobulin, and glycophorin A but not with asialofetuin or asialoglycophorin A. The erythrocyte receptor was more sensitive to destruction by a neuraminidase specific for the N-acetylneuraminyl-alpha(2-3)-galactopyranosyl [NeuAc(2-3)Gal] sequence than one specific for NeuAc(2-6)Gal. Hemagglutination-inhibition assays with N-acetylneuraminyl-alpha(2-3)-lactose [NeuAc(2-3)-lactose] and NeuAc(2-6)-lactose confirmed that the C. pylori hemagglutinin preferentially binds to the NeuAc(2-3)Gal isomer of NeuAc-lactose. Based upon the above-described properties of the C. pylori fibrillar hemagglutinin, we conclude that this antigen should be designated as a putative colonization factor antigen.
Clinical predictors of recurrent <i><scp>C</scp>lostridium difficile</i> infection in out‐patients (2014)

Antibiotic use was independently associated with a dramatic risk of recurrent Clostridium difficile infection in an out-patient cohort. It is important to avoid unnecessary systemic antibiotics in patients with Clostridium difficile infection, and patients with ongoing antibiotic use should be monitored closely for recurrent infection.
Mureidomycins E and F, minor components of mureidomycins. (1993)

Mureidomycins (MRDs) E and F were isolated from a culture filtrate of Streptomyces flavidovirens SANK 60486 which produces MRDs A approximately D. They possessed the same molecular formulae, C39H48N8O12S and very similar UV, IR and NMR spectra, but differed clearly from each other in HPLC profile. From the hydrolysates of MRDs E and F, 8-hydroxy-1,2,3,4-tetrahydro-3-isoquinoline carboxylic acid and 6-hydroxy-1,2,3,4-tetrahydro-3-isoquinoline carboxylic acid were detected, respectively, which were not detected from those of MRDs A approximately D. They showed strong anti-pseudomonal activity but less active than MRD A. MRDs E and F were synthesized from MRD A and formaldehyde through Pictet-Spengler reaction.
Towards 20-watt continuous wave quantum cascade lasers (2018)

Significant increase in continuous wave optical power from a single quantum cascade laser (QCL), beyond its current record of 5W, will likely require power scaling with active region lateral dimensions. Active region overheating presents a major technical problem for such broad area devices. Laser thermal resistance can be reduced and laser self-heating can be suppressed by significantly reducing active region thickness, i.e. by reducing number of active region stages and by reducing thickness of each stage in the cascade. The main challenge for quantum cascade lasers with a “thin” active region is to ensure that optical power emitted per active region unit area stays high despite the reduction in active region thickness, a condition critical for the power scaling. Experimental data demonstrating a multi-watt continuous wave operation for broad area QCLs, as well as various aspects of bandgap engineering, waveguide design, and thermal design pertinent to the broad area configuration, are discussed in this manuscript. The critical differences in broad-area laser design between mid-wave and long-wave QCLs is highlighted. Finally, semi-empirical model projections showing that the goal of reaching 20W from a single emitter is realistic is presented.
Functional Analysis of β‐Secretase Using Mutagenesis and Structural Homology Modeling (2001)

Beta-amyloid peptide, the major component of Alzheimer's disease plaques, is generated by proteolytic cleavage of the amyloid precursor protein by β- and γ-secretases. The recently identified β-secretase and its close homolog BACE2 form a new subclass of aspartic acid proteases, containing an ectodomain showing a high degree of homology to the pepsin family of proteases. Very little is known about this new subfamily. It displays distinct features from the pepsin family. We have used a combination of mutagenesis and structure homology modeling to investigate pro-protease processing and the role of disulfide bonds in β-secretase.
Amphotericin B Increases Influenza A Virus Infection by Preventing IFITM3-Mediated Restriction (2013)

The IFITMs inhibit influenza A virus (IAV) replication in vitro and in vivo. Here, we establish that the antimycotic heptaen, amphotericin B (AmphoB), prevents IFITM3-mediated restriction of IAV, thereby increasing viral replication. Consistent with its neutralization of IFITM3, a clinical preparation of AmphoB, AmBisome, reduces the majority of interferon's protective effect against IAV in vitro. Mechanistic studies reveal that IFITM1 decreases host-membrane fluidity, suggesting both a possible mechanism for IFITM-mediated restriction and its negation by AmphoB. Notably, we reveal that mice treated with AmBisome succumbed to a normally mild IAV infection, similar to animals deficient in Ifitm3. Therefore, patients receiving antifungal therapy with clinical preparations of AmphoB may be functionally immunocompromised and thus more vulnerable to influenza, as well as other IFITM3-restricted viral infections.