gebhart/patrepeval huggingface dataset:
Activation of Human Acid Sphingomyelinase through Modification or Deletion of C-terminal Cysteine (2003)

One form of Niemann-Pick disease is caused by a deficiency in the enzymatic activity of acid sphingomyelinase. During efforts to develop an enzyme replacement therapy based on a recombinant form of human acid sphingomyelinase (rhASM), purified preparations of the recombinant enzyme were found to have substantially increased specific activity if cell harvest media were stored for several weeks at -20 degrees C prior to purification. This increase in activity was found to correlate with the loss of the single free thiol on rhASM, suggesting the involvement of a cysteine residue. It was demonstrated that a variety of chemical modifications of the free cysteine on rhASM all result in substantial activation of the enzyme, and the modified cysteine responsible for this activation was shown to be the C-terminal residue (Cys629). Activation was also achieved by copper-promoted dimerization of rhASM (via cysteine) and by C-terminal truncation using carboxypeptidase Y. The role of the C-terminal cysteine in activation was confirmed by creating mutant forms of rhASM in which this residue was either deleted or replaced by a serine, with both forms having substantially higher specific activity than wild-type rhASM. These results indicate that purified rhASM can be activated in vitro by loss of the free thiol on the C-terminal cysteine via chemical modification, dimerization, or deletion of this amino acid residue. This method of activation is similar to the cysteine switch mechanism described previously for matrix metalloproteinases and could represent a means of posttranslational regulation of ASM activity in vivo.
Bone morphogenetic protein encapsulated with a biodegradable and biocompatible polymer (1996)

To develop a controlled release system for bone morphogenetic protein (BMP), poly(DL-lactide-co-glycolide) (PLGA) capsules containing BMP were prepared by an interfacial precipitation method using a water-in-oil-in-water emulsion. The surface morphology, particle size distribution, and hydrolytic degradation rate of the PLGA capsules were examined. The encapsulation yield and release rate of BMP in vitro were measured using fluorescein isothiocyanate-labeled BMP. The amount of BMP released from PLGA capsules increased between days 3 and 5. In addition, the effectiveness of BMP encapsulated in PLGA to induce bone formation in vivo was also examined by subcutaneous implantation in rats. Complete digestion of the capsules and new bone formation including bone marrow were identified by histologic examination of harvested tissues at 3 weeks after implantation. These results demonstrated that encapsulation of BMP with PLGA could be a promising method to induce bone in clinics.
Reproductive Endocrinology: Physiology, Pathophysiology and Clinical Management. (1986)

Among those biomedical fields in which a virtual explosion of new knowledge and understanding has occurred over the past decade the physiology and pathophysiology of reproductive processes are prime examples. The neural and endocrine regulation of reproduction has been explored with new and sophisticated methods and with increasing comprehension of the important factors involved in the control of this important function. By extrapolation from animal models as well as by direct investigation involving humans new light has been shed on the operation of the human reproductive system in both health and disease. The overall purpose of this book is to provide contemporary factual information and new understanding of human reproductive processes keeping in mind the needs of students and investigators in reproductive endocrinology and biology as well as the needs of clinicians who face the problem of diagnosing and treating reproductive dysfunction. To accomplish these purposes the chapters range from the clinical and systemic to the cellular and molecular. Whenever possible cellular or molecular mechanisms for normal or disturbed function are presented. The elements of the reproductive system covered most extensively are various parts of the brain the pituitary gland and the gonads. Each of these obviously is a separate and distinguishable component of the system but in addition they have a number of common mechanistic features. The authors hope that these similarities and integrated modes of action will impress the reader and that some readers will be provoked into continued deeper study of this field.
A study of the susceptibility of three species of primate to vaginal colonization with Gardnerella vaginalis. (1984)

In an attempt to develop an animal model of Gardnerella-associated vaginitis, several strains of Gardnerella vaginalis were inoculated into the lower genital tract of female pig-tailed macaques, tamarins and chimpanzees. G. vaginalis was not recovered from either tamarins or chimpanzees, but was recovered from each of 1O pig-tailed macaques inoculated with either of two freshly isolated Gardnerella strains, colonization persisting for 11-39 days. Examination of Gram-stained vaginal smears obtained from infected pig-tailed macaques failed to demonstrate clue cells, a feature which is pathognomonic of Gardnerella-associated vaginitis in humans. Other features characteristic of non-specific vaginitis, namely an increase in vaginal pH, and an increase in the ratio of succinate to lactate (S/L ratio) in vaginal fluid were not found. However, the physiology of the macaque vagina was found to be different from that of the human, the vaginal pH and S/L ratio of uninfected macaques both being higher than that seen in humans. The physiological differences between the macaque and human vagina may be due, in part, to a difference in their anaerobic vaginal flora. While these inter-species differences in vaginal physiology and microbiology limit the relevance of the pig-tailed macaque as a model of Gardnerella-associated vaginitis, the ease with which macaques are colonized with G. vaginalis may prove useful in studying bacterial adhesion and local immunity.
Estimates of the prevalence of arthritis and selected musculoskeletal disorders in the United States (1998)

Given the limitations of the data on which they are based, this report provides the best available prevalence estimates for arthritis and other rheumatic conditions overall, and for selected musculoskeletal disorders, in the US population.
Simulations of Lipid Vesicle Adsorption for Different Lipid Mixtures (2008)

Numerous experimental studies of lipid vesicle adsorption on solid surfaces show that electrostatic interactions play an important role for the kinetics and end result. The latter can, e.g., be intact vesicles or supported lipid bilayers (SLB). Despite an accumulated quite large experimental data base, the understanding of the underlying processes is still poor, and mathematical models are scarce. We have developed a phenomenological model of a vesicle adsorbing on a substrate, where the charge of the surface and the charge and polar state of the lipid headgroup can be varied. With physically reasonable assumptions and input parameters, we reproduce many key experimental observations, clarify the details of some experiments, and give predictions and suggestions for future experiments. Specifically, we have investigated the influence of different lipid mixtures (different charges of the headgroups) in the vesicle on the outcome of a vesicle adsorption event. For different mixtures of zwitterionic lipids with positive and negative lipids, we investigated whether the vesicle adsorbs or not, and--if it adsorbs--to what extent it gets deformed and when it ruptures spontaneously. Diffusion of neutral vesicles on different types of negatively charged substrates was also simulated. The mean surface charge density of the substrate was varied, including or excluding local fluctuations in the surface charge density. The simulations are compared to available experiments. A consistent picture of the influence of different lipid mixtures in the vesicle on adsorption, and the influence of different types of substrates on vesicle diffusion, appear as a result of the simulation data.
Synthesis and Screening of a Haloacetamidine Containing Library To Identify PAD4 Selective Inhibitors (2011)

Protein arginine deiminase activity (PAD) is increased in cancer, rheumatoid arthritis, and ulcerative colitis. Although the link between abnormal PAD activity and disease is clear, the relative contribution of the individual PADs to human disease is not known; there are 5 PAD isozymes in humans. Building on our previous development of F- and Cl-amidine as potent pan-PAD irreversible inhibitors, we describe herein a library approach that was used to identify PAD-selective inhibitors. Specifically, we describe the identification of Thr-Asp-F-amidine (TDFA) as a highly potent PAD4 inactivator that displays ≥15-fold selectivity for PAD4 versus PAD1 and ≥50-fold versus PADs 2 and 3. This compound is active in cells and can be used to inhibit PAD4 activity in cellulo. The structure of the PAD4·TDFA complex has also been solved, and the structure and mutagenesis data indicate that the enhanced potency is due to interactions between the side chains of Q346, R374, and R639. Finally, we converted TDFA into a PAD4-selective ABPP and demonstrated that this compound, biotin-TDFA, can be used to selectively isolate purified PAD4 in vitro. In total, TDFA and biotin-TDFA represent PAD4-selective chemical probes that can be used to study the physiological roles of this enzyme.
Fracture behaviour of nanoplatelet reinforced polymer nanocomposites (2006)

The authors present a review of the recent research effort towards developing a fundamental understanding of fracture behaviour of polymer nanocomposites that contain nanoplatelet fillers. Various toughening mechanisms reported in the literature are summarized and discussed. Within this review, an emphasis is placed on the up to date understanding of how the nanofiller aspect ratio affects the fracture behaviour of polymer nanocomposites. Besides, the effect of nanoplatelet dispersion and exfoliation on the fracture behaviour of polymer nanocomposites will be addressed.
Guidelines to cell engineering for monoclonal antibody production (2009)

Monoclonal antibodies (mAbs) are currently used for many diagnostic and therapeutic applications. The high demand for these biopharmaceuticals has led to the development of large-scale manufacturing processes, with productivity improvements being mainly achieved by optimization of bioreactor systems. However, more recently, the early steps of production, previous to bioreactor culture, have been presented as alternative areas where productivity enhancements can be achieved. Thus, this review describes the progress made for the improvement of productivity in mammalian expression systems for the high production of mAbs. Advances in the development of mAb-producing cell lines are being made, particularly regarding expression vector design and methods used for transfection, with the intent to create a reproducible methodology. Selection of the most suitable clones is also a critical step that can be improved, by including variables other than the expression level, which is still the common practice. Furthermore, strategies of cell engineering, although still mostly based on trial-and-error experimentation and not in standard protocols, hold great interest to improve cell growth and productivity, as well as product quality in the future. Improvements of the initial steps of the production process would not only result in cells with higher expression ability, but would also speed-up the process development.
Fundus albipunctatus and retinitis punctata albescens in a pedigree with an R150Q mutation in RLBP1 (2001)

Fundus albipunctatus (FA; OMIM 136880) is a rare form of apparently stationary night blindness characterized by the presence of myriad symmetrical round white dots in the fundus with a greater concentration in the midperiphery. A distantly similar but distinct clinical entity, retinitis punctata albescens (RPA), is also characterized by aggregation of irregular white flecks but is progressive and evolves to generalized atrophy of the retina. We studied 4 consanguineous kindreds diagnosed with FA from Saudi Arabia. Given the substantial phenotypic variation and overlap between different flecked retinal dystrophies, we evaluated all known genes associated with such conditions by both genetic analysis and direct sequencing. In one kindred, KKESH-099, we identified a homozygous R150Q alteration in RLBP1, the gene encoding the cellular retinaldehyde binding protein, associated previously with both recessive retinitis pigmentosa (arRP) and RPA. Examination of several patients aged 3-20 years over a 9-year period presented no evidence for either RP or RPA. In contrast, clinical examination of individuals with the same mutation in their fourth and fifth decade revealed signs consistent with RPA. The data suggest that the R150Q mutation in RLBP1 may result in RPA with slow progression. More importantly, younger individuals diagnosed with the milder disorder FA thought to be stationary may evolve to a more devastating and progressive phenotype.
An automatic system for the assessment of complex medium additives under cultivation conditions (2001)

Complex medium additives such as yeast extract or peptone are often used in industrial cell culture processes to prolong cell growth and/or to improve product formation. The quality of those supplements is dependent on the preparation method and can differ from lot to lot. To guarantee consistent production these different lots have to be tested prior to use in fermentation processes. Because a detailed qualitative and quantitative analysis of all components of such a complex mixture is a very difficult task, another assessment method has to be chosen. The best way to evaluate the effect of such supplements is to monitor cell activity during real cultivation conditions with and without the added supplement lot. A bioreactor-based test system has been developed to determine the oxygen requirement of the cells as a response to the addition of a supplement to be tested under standardized conditions. Investigations were performed with a mouse-mouse hybridoma cell line and yeast extracts as an example for complex medium additives. The results showed differences in the impact between different extract lots and between different concentrations of an extract.
The Novel Enzymatic 3"-N-Acetylation of Arbekacin by an Aminoglycoside 3-N-Acetyltransferase of Streptomyces Origin and the Resulting Activity. (1998)

Kanamycin group antibiotics were subjected to enzymatic acetylation by a cell free extract containing an aminoglycoside 3-N-acetyltransferase, AAC(3)-X, derived from Streptomyces griseus SS-1198PR. Characterization of the incubated reaction mixtures by TLC and antibiotic assay revealed that a product retaining activity was specifically formed from arbekacin, an anti-MRSA semisynthetic aminoglycoside. The structural determination demonstrated that acetylation occurred at the 3"-amino group in arbekacin and amikacin, and at the 3-amino group in dibekacin as in the case of kanamycin. These results should reflected the effect of the (S)-4-amino-2-hydroxybutyryl side chain which is present in arbekacin and amikacin, but absent in dibekacin and kanamycin. The 3"-N-acetylation is the first finding in the enzymatic modifications of aminoglycoside antibiotics. 3"-N-Acetylarbekacin showed antibiotic activity as high as that of 2'-N-acetylarbekacin reported previously, whereas 3"-N-acetylamikacin showed no substantial activity. Thus, our results illuminated a novel aspect of arbekacin distinct from the other aminoglycosides.
DNA Sequence Determination by Hybridization: a Strategy for Efficient Large-Scale Sequencing (1993)

The concept of sequencing by hybridization (SBH) makes use of an array of all possible n-nucleotide oligomers (n-mers) to identify n-mers present in an unknown DNA sequence. Computational approaches can then be used to assemble the complete sequence. As a validation of this concept, the sequences of three DNA fragments, 343 base pairs in length, were determined with octamer oligonucleotides. Possible applications of SBH include physical mapping (ordering) of overlapping DNA clones, sequence checking, DNA fingerprinting comparisons of normal and disease-causing genes, and the identification of DNA fragments with particular sequence motifs in complementary DNA and genomic libraries. The SBH techniques may accelerate the mapping and sequencing phases of the human genome project.
Turning images into 3-D models (2008)

In this article developments and performance analysis of image matching for detailed surface reconstruction of heritage objects is discussed. Three dimensional image-based modeling of heritages is a very interesting topic with many possible applications. In this article we propose a multistage image-based modeling approach that requires only a limited amount of human interactivity and is capable of capturing the fine geometric details with similar accuracy as close-range active range sensors. It can also cope with wide baselines using several advancements over standard stereo matching techniques. Our approach is sequential, starting from a sparse basic segmented model created with a small number of interactively measured points. This model, specifically the equation of each surface, is then used as a guide to automatically add the fine details. The following three techniques are used, each where best suited, to retrieve the details: 1) for regularly shaped patches such as planes, cylinders, or quadrics, we apply a fast relative stereo matching technique. 2) For more complex or irregular segments with unknown shape, we use a global multi-image geometrically constrained technique. 3) For segments unsuited for stereo matching, we employ depth from shading (DFS). The goal is not the development of a fully automated procedure for 3D object reconstruction from image data or a sparse stereo approach, but we aim at the digital reconstruction of detailed and accurate surfaces from calibrated and oriented images for practical daily documentation and digital conservation of wide variety of heritage objects.
Encoding a qubit with Majorana modes in superconducting circuits (2014)

Majorana fermions are long-sought exotic particles that are their own antiparticles. Here we propose to utilize superconducting circuits to construct two superconducting-qubit arrays where Majorana modes can occur. A so-called Majorana qubit is encoded by using the unpaired Majorana modes, which emerge at the left and right ends of the chain in the Majorana-fermion representation. We also show this Majorana qubit in the spin representation and its advantage, over a single superconducting qubit, regarding quantum coherence. Moreover, we propose to use four superconducting qubits as the smallest system to demonstrate the braiding of Majorana modes and show how the states before and after braiding Majoranas can be discriminated.
CD4+T-Cell- and Gamma Interferon-Dependent Protection against Murine Malaria by Immunization with Linear Synthetic Peptides from aPlasmodium yoelii17-Kilodalton Hepatocyte Erythrocyte Protein (1999)

Most work on protective immunity against the pre-erythrocytic stages of malaria has focused on induction of antibodies that prevent sporozoite invasion of hepatocytes, and CD8(+) T-cell responses that eliminate infected hepatocytes. We recently reported that immunization of A/J mice with an 18-amino-acid synthetic linear peptide from Plasmodium yoelii sporozoite surface protein 2 (SSP2) in TiterMax adjuvant induces sterile protection that is dependent on CD4(+) T cells and gamma interferon (IFN-gamma). We now report that immunization of inbred A/J mice and outbred CD1 mice with each of two linear synthetic peptides from the 17-kDa P. yoelii hepatocyte erythrocyte protein (HEP17) in the same adjuvant also induces protection against sporozoite challenge that is dependent on CD4(+) T cells and IFN-gamma. The SSP2 peptide and the two HEP17 peptides are recognized by B cells as well as T cells, and the protection induced by these peptides appears to be directed against the infected hepatocytes. In contrast to the peptide-induced protection, immunization of eight different strains of mice with radiation-attenuated sporozoites induces protection that is absolutely dependent on CD8(+) T cells. Data represented here demonstrate that CD4(+) T-cell-dependent protection can be induced by immunization with linear synthetic peptides. These studies therefore provide the foundation for an approach to pre-erythrocytic-stage malaria vaccine development, based on the induction of protective CD4(+) T-cell responses, which will complement efforts to induce protective antibody and CD8(+) T-cell responses.
Active behavioral fingerprinting of wireless devices (2008)

We propose a simple active method for discovering facts about the chipset, the firmware or the driver of an 802.11 wireless device by observing its responses (or lack thereof) to a series of crafted non-standard or malformed 802.11 frames. We demonstrate that such responses can differ significantly enough to distinguish between a number of popular chipsets and drivers. We expect to significantly expand the number of recognized device types through community contributions of signature data for the proposed open fingerprinting framework. Our method complements known fingerprinting approaches, and can be used to interrogate and spot devices that may be spoofing their MAC addresses in order to conceal their true architecture from other stations, such as a fake AP seeking to engage clients in complex protocol frame exchange (e.g., in order to exploit a driver vulnerability). In particular, it can be used to distinguish rogue APs from legitimate APs before association.
Characterizing and measuring bias in sequence data (2013)

The assays presented in this paper provide a comprehensive view of sequencing bias, which can be used to drive laboratory improvements and to monitor production processes. Development guided by these assays should result in improved genome assemblies and better coverage of biologically important loci.
Nanopatterned Textile-Based Wearable Triboelectric Nanogenerator (2015)

Here we report a fully flexible, foldable nanopatterned wearable triboelectric nanogenerator (WTNG) with high power-generating performance and mechanical robustness. Both a silver (Ag)-coated textile and polydimethylsiloxane (PDMS) nanopatterns based on ZnO nanorod arrays on a Ag-coated textile template were used as active triboelectric materials. A high output voltage and current of about 120 V and 65 μA, respectively, were observed from a nanopatterned PDMS-based WTNG, while an output voltage and current of 30 V and 20 μA were obtained by the non-nanopatterned flat PDMS-based WTNG under the same compressive force of 10 kgf. Furthermore, very high voltage and current outputs with an average value of 170 V and 120 μA, respectively, were obtained from a four-layer-stacked WTNG under the same compressive force. Notably it was found there are no significant differences in the output voltages measured from the multilayer-stacked WTNG over 12 000 cycles, confirming the excellent mechanical durability of WTNGs. Finally, we successfully demonstrated the self-powered operation of light-emitting diodes, a liquid crystal display, and a keyless vehicle entry system only with the output power of our WTNG without any help of external power sources.