gebhart/patrepeval huggingface dataset:
Fermentation, purification, formulation, and pharmacological evaluation of a prolyl endopeptidase from Myxococcus xanthus: Implications for Celiac Sprue therapy (2005)

Celiac Sprue is a multi-factorial disease characterized by an inflammatory response to ingested wheat gluten and similar proteins in rye and barley. Proline-rich gluten peptides from wheat, rye, and barley are relatively resistant to gastrointestinal digestion, and therefore persist in the intestinal lumen to elicit immunopathology in genetically susceptible individuals. In this study, we characterize the in vitro gluten detoxifying properties of a therapeutically promising prolyl endopeptidase from Myxococcus xanthus (MX PEP), and describe the development of a prototypical enteric-coated capsule containing a pharmacologically useful dose of this enzyme. A high-cell density fed-batch fermentation process was developed for overproduction of recombinant MX PEP in E. coli, yielding 0.25-0.4 g/L purified protein. A simple, scalable purification and lyophilization procedure was established that yields >95% pure, highly active and stable enzyme as a dry powder. The dry powder was blended with excipients and encapsulated in a hard gelatin capsule. The resulting capsule was enteric coated using Eudragit L30-D55 polymer coat, which provided sufficient resistance to gastric conditions (> 1 h in 0.01 M HCl, pH 2 with pepsin) and rapid release under duodenal conditions (15-30 min release in pH 6.0 in the presence of trypsin and chymotrypsin). In conjunction with pancreatic enzymes, MX PEP breaks down whole gluten into a product mixture that is virtually indistinguishable from that generated by the Flavobacterium meningosepticum (FM) PEP as judged by chromatographic assays. Competitive studies involving selected immunogenic peptides mixed with whole gluten reveal that both PEPs have a wide range of substrate specificity. Our results support further in vitro and in vivo evaluation of the MX PEP capsule as an oral therapeutic agent for Celiac Sprue patients.
Detecting Early‐Stage Liver Fibrosis Using Macromolecular Proton Fraction Mapping Based on Spin‐Lock MRI: Preliminary Observations (2023)

Macromolecular proton fraction (MPF) and T1rho maps for two representative patients with F0 and F2 stage fibrosis as confirmed by liver histology. (A) MPF maps from a patient with F0 stage fibrosis, (B) MPF maps from a patient with F2 stage fibrosis, (C) T1rho maps from the same patient with F0 stage fibrosis, and (D) T1rho maps from the same patient with F2 stage fibrosis. by Jian Hou et al. (485–492). image
Sequentially addressable dielectrophoretic array for high-throughput sorting of large-volume biological compartments (2020)

Droplet microfluidics has become a powerful tool in precision medicine, green biotechnology, and cell therapy for single-cell analysis and selection by virtue of its ability to effectively confine cells. However, there remains a fundamental trade-off between droplet volume and sorting throughput, limiting the advantages of droplet microfluidics to small droplets (<10 pl) that are incompatible with long-term maintenance and growth of most cells. We present a sequentially addressable dielectrophoretic array (SADA) sorter to overcome this problem. The SADA sorter uses an on-chip array of electrodes activated and deactivated in a sequence synchronized to the speed and position of a passing target droplet to deliver an accumulated dielectrophoretic force and gently pull it in the direction of sorting in a high-speed flow. We use it to demonstrate large-droplet sorting with ~20-fold higher throughputs than conventional techniques and apply it to long-term single-cell analysis of <i>Saccharomyces cerevisiae</i> based on their growth rate.
On Throughput Optimality With Delayed Network-State Information (2011)

The problem of routing/scheduling in a wireless network with partial/delayed network (channel and queue) state information (NSI) is studied in this paper. Two cases are considered: (i) centralized routing/scheduling, where a central controller obtains heterogeneously delayed information from each of the nodes (thus, the controller has NSI with different delays from different nodes), and makes routing/scheduling decisions; (ii) decentralized routing/scheduling, where each node makes a decision based on its current channel and queue states along with homogeneous delayed NSI from other nodes. For each of the cases (with additional flow restrictions for the decentralized routing/scheduling case), the optimal network throughput regions are characterized under the above described NSI models and it is shown that the throughput regions shrinks with the increase of delay. Further, channel and queue length based routing/scheduling algorithms that achieve the above throughput regions are proposed in this paper.
High frequency characteristics of Fe<inf>65</inf>Co<inf>35</inf> alloy cluster-assembled films prepared by energetic cluster deposition (2010)

Size-monodispersed Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">65</sub> Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">35</sub> alloy clusters whose average sizes ranged between 7 and 12 nm were obtained using a plasma-gas-condensation (PGC)-type cluster deposition apparatus. Positively charged clusters in a cluster beam were accelerated electrically and deposited onto a negatively biased substrate together with neutral clusters from the same cluster source, leading to formation of a high-density Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">65</sub> Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">35</sub> alloy cluster-assembled films with soft magnetic properties. High frequency magnetic characteristics were studied for these films prepared at room temperature by an energetic cluster deposition with and without O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> gas addition into a cluster deposition chamber.
Response Surface Methodology As a New Approach for Finding Optimal MALDI Matrix Spraying Parameters for Mass Spectrometry Imaging (2020)

Automated spraying devices have become ubiquitous in laboratories employing matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI), in part because they permit control of a number of matrix application parameters that can easily be reproduced for intra- and interlaboratory studies. Determining the optimal parameters for MALDI matrix application, such as temperature, flow rate, spraying velocity, number of spraying cycles, and solvent composition for matrix application, is critical for obtaining high-quality MALDI-MSI data. However, there are no established approaches for optimizing these multiple parameters simultaneously. Instead optimization is performed iteratively (i.e., one parameter at a time), which is time-consuming and can lead to overall nonoptimal settings. In this report, we demonstrate the use a novel experimental design and the response surface methodology to optimize five parameters of MALDI matrix application using a robotic sprayer. Thirty-two combinations of MALDI matrix spraying conditions were tested, which allowed us to elucidate relationships between each of the application parameters as determined by MALDI-MS (specifically, using a 15 T Fourier transform ion cyclotron resonance mass spectrometer). As such, we were able to determine the optimal automated spraying parameters that minimized signal delocalization and enabled high MALDI sensitivity. We envision this optimization strategy can be utilized for other matrix application approaches and MALDI-MSI analyses of other molecular classes and tissue types.
Childhood trauma history is linked to abnormal brain connectivity in major depression (2019)

Patients with major depressive disorder (MDD) present with heterogeneous symptom profiles, while neurobiological mechanisms are still largely unknown. Brain network studies consistently report disruptions of resting-state networks (RSNs) in patients with MDD, including hypoconnectivity in the frontoparietal network (FPN), hyperconnectivity in the default mode network (DMN), and increased connection between the DMN and FPN. Using a large, multisite fMRI dataset (<i>n</i> = 189 patients with MDD, <i>n</i> = 39 controls), we investigated network connectivity differences within and between RSNs in patients with MDD and healthy controls. We found that MDD could be characterized by a network model with the following abnormalities relative to controls: (<i>i</i>) lower within-network connectivity in three task-positive RSNs [FPN, dorsal attention network (DAN), and cingulo-opercular network (CON)], (<i>ii</i>) higher within-network connectivity in two intrinsic networks [DMN and salience network (SAN)], and (<i>iii</i>) higher within-network connectivity in two sensory networks [sensorimotor network (SMN) and visual network (VIS)]. Furthermore, we found significant alterations in connectivity between a number of these networks. Among patients with MDD, a history of childhood trauma and current symptoms quantified by clinical assessments were associated with a multivariate pattern of seven different within- and between-network connectivities involving the DAN, FPN, CON, subcortical regions, ventral attention network (VAN), auditory network (AUD), VIS, and SMN. Overall, our study showed that traumatic childhood experiences and dimensional symptoms are linked to abnormal network architecture in MDD. Our results suggest that RSN connectivity may explain underlying neurobiological mechanisms of MDD symptoms and has the potential to serve as an effective diagnostic biomarker.
Plerixafor (Mozobil®) Alone to Mobilize Hematopoietic Stem Cells from Multiple Myeloma Patients for Autologous Transplantation (2010)

Rapid and durable recovery of hematopoietic function after hematopoietic stem cell transplantation (HSCT) requires the infusion of a sufficient number of hematopoietic stem cells (HSC). Granulocyte colony-stimulating factor (G-CSF), either alone or with chemotherapy, has been the traditional backbone of regimens used to mobilize HSC. Plerixafor (previously known as AMD3100), a selective antagonist of CXCR4, has recently been approved for autologous HSC mobilization in combination with G-CSF. The current study assessed the safety and efficacy of plerixafor as a single agent when given subcutaneously and followed by apheresis 6 hours later for the mobilization of HSC for transplantation in 9 patients with multiple myeloma (MM). All patients mobilized enough cells for at least 1 transplant, and demonstrated prompt recovery of hematopoietic function. Median time to engraftment was 10.5 days for neutrophils and 21 days for platelets. Significant adverse events were not observed. Recovery of peripheral blood cell counts was durable in all surviving patients. Despite these successes, mobilization with plerixafor alone was modest. However, in clinical circumstances where G-CSF or chemotherapy based-mobilization should not be used, mobilization with plerixafor alone may be required and effective. Further research into single agent use should focus on alternate route of administration as well as adjustment of the timing of the apheresis to improve cell HSC yield.
Application of rigorous electromagnetic simulation to SLM-based maskless lithography for 65-nm node (2003)

Maskless lithography imaging based on SLM tilt mirror architecture requires illumination of light on a non-planar reflective topography. While the actual mirror dimensions can be much larger than the wavelength of light, the spacing between mirrors and the tilt range of interest are on the order of the wavelength. Thus, rigorous electromagnetic solution is required to capture light scattering effects due to the non-planar topography. We combine high NA imaging simulation with rigorous simulation of light scattering from the mirrors to study its effects on 65nm maskless lithography imaging. We vary mirror size, mirror tilt arrangemetn, feature type and illumination settings and compare the rigorous light scattering imagign resutls wtih standard imaging simulations using Kirchoff approximation. While electromagnetic scattering effects are present in the form of lateral standing waves and edge streamers in reflected light near-field intensity, they have negligible effects on SLM imaging for mirror sizes more than 1&mu;m<sup>2</sup>. The effects of mirror tilt arrangement on diffraction orders aer used to study the through-focus behavior of alternating rows arrangement used in the SIGMA maskwriters as well as alternative arrangements. The good imaging properties of the alternating rows arrangement used in the SIGMA maskwriters as well as alternative arrangements. The good imaging properties of the alternating rows arrangement are confirmed and a multipass overlay scheme giving further image fidelity improvements is suggested.
POS-375 AVACOPAN IN ANCA-ASSOCIATED VASCULITIS: EVIDENCE FOR ELIMINATION OF DAILY PREDNISONE THERAPY AND REDUCTION IN GLUCOCORTICOID-RELATED TOXICITY FROM THE PHASE 3 ADVOCATE TRIAL (2021)

Anti-neutrophil cytoplasmic antibody (ANCA)-associated vasculitis is a life- or organ-threatening condition with systemic anti-neutrophil autoantibodies and small vessel inflammation. Therapy with high-dose glucocorticoids (GCs) improves the symptoms of acute vasculitis, but significant therapy-induced toxicities and comorbidities remain.
Application of the National Cancer Institute international criteria for determination of microsatellite instability in ovarian cancer. (2001)

Recently, the National Cancer Institute (NCI) established criteria for determination of microsatellite instability (MSI) in colorectal tumors. Although the best panel of markers for ovarian tumors is not known, we evaluated epithelial ovarian cancers for MSI based on the NCI recommendations. One hundred and nine ovarian tumors were analyzed for MSI by gel analysis of paired germ-line and tumor DNA. PCR amplification was performed using the panel of five microsatellite markers recommended by the NCI (BAT25, BAT26, D5S346, D2S123, and D17S250) and nine additional markers picked based on their genomic location (NME1, D10S197, D11S904, D13S175, DXS981, DXS6800, DXS6807, AR, and D3S1611). Tumors were characterized on the basis of: high-frequency MSI (MSI-H) if two or more of the five NCI markers showed instability or there was instability at 30% or more of all markers tested; or low-frequency MSI (MSI-L) if only one of the five NCI markers showed instability or <30% of all of the markers. All of the other tumors were considered microsatellite stable. On the basis of the NCI markers, 12 (11%) tumors demonstrated MSI-H, and 8 (7%) additional tumors had MSI-L. When all of the 14 markers were considered together, 13 (12%) tumors demonstrated MSI-H (based on 30% or more unstable loci), and 26 (24%) tumors had MSI-L. A single tumor identified to have MSI-H based upon all of the markers tested would have been classified as MSI-L based upon the NCI markers alone. Inclusion of an additional dinucleotide marker (NME1) to the NCI panel allowed detection of all of the tumors with MSI-H using only six markers. MSI-H occurs in approximately 12% of invasive ovarian tumors. For optimal detection of microsatellite instability in ovarian cancer, an additional marker (NME1) may be required, along with the five recommended by the NCI.
Disruptive influence (2013)

Cachexia, a condition that kills about one-fifth of cancer patients, may be linked to Rb-a protein that is already linked to various cancers-moving from the cell nucleus to the cytoplasm.
Optimizing parameters of a mobile ad hoc network protocol with a genetic algorithm (2005)

Mobile ad hoc networks are typically designed and evaluated in generic simulation environments. However the real conditions in which these networks are deployed can be quite different in terms of RF attentution, topology, and traffic load. Furthermore, specific situations often have a need for a network that is optimized along certain characteristics such as delay, energy or overhead. In response to the variety of conditions and requirements, ad hoc networking protocols are often designed with many modifiable parameters. However, there is currently no methodical way for choosing values for the parameters other than intuition and broad experience. In this paper we investigate the use of genetic algorithms for automated selection of parameters in an ad hoc networking system. We provide experimental results demonstrating that the genetic algorithm can optimize for different classes of operating conditions. We also compare our genetic algorithm optimization against hand-tuning in a complex, realistic scenario and show how the genetic algorithm provides better performance.
Supplementary Materials and Methods, Table 1 from Local and Systemic Protumorigenic Effects of Cancer-Associated Fibroblast-Derived GDF15 (2023)

&lt;p&gt;PDF file - 166KB, Supplementary Table 1. Human and murine primer.&lt;/p&gt;
Identification of strong promoter elements ofMycobacterium smegmatisand their utility for foreign gene expression in mycobacteria (2003)

The isolation of elements driving high-level expression of foreign genes in mycobacteria would significantly aid characterization of mycobacterial antigens and recombinant vaccine development. Mycobacterium smegmatis is a widely employed host for recombinant mycobacterial gene expression. This report describes the identification of strong promoter elements of M. smegmatis. Fluorescence-activated cell sorting was employed to isolate DNA fragments permitting high-level expression of the Aequorea victoria green fluorescent protein within recombinant M. smegmatis. Ten postulated M. smegmatis promoters were identified which showed activity two to six times that of the strong beta-lactamase promoter of Mycobacterium fortuitum. The utility of one of these promoters for the over-expression of foreign genes in mycobacteria was demonstrated by the efficient purification of the Mycobacterium leprae 35-kDa antigen from recombinant M. smegmatis.
Ink-jet 3D printing as a strategy for developing bespoke non-eluting biofilm resistant medical devices (2021)

Chronic infection as a result of bacterial biofilm formation on implanted medical devices is a major global healthcare problem requiring new biocompatible, biofilm-resistant materials. Here we demonstrate how bespoke devices can be manufactured through ink-jet-based 3D printing using bacterial biofilm inhibiting formulations without the need for eluting antibiotics or coatings. Candidate monomers were formulated and their processability and reliability demonstrated. Formulations for in vivo evaluation of the 3D printed structures were selected on the basis of their in vitro bacterial biofilm inhibitory properties and lack of mammalian cell cytotoxicity. In vivo in a mouse implant infection model, Pseudomonas aeruginosa biofilm formation on poly-TCDMDA was reduced by ∼99% when compared with medical grade silicone. Whole mouse bioluminescence imaging and tissue immunohistochemistry revealed the ability of the printed device to modulate host immune responses as well as preventing biofilm formation on the device and infection of the surrounding tissues. Since 3D printing can be used to manufacture devices for both prototyping and clinical use, the versatility of ink-jet based 3D-printing to create personalised functional medical devices is demonstrated by the biofilm resistance of both a finger joint prosthetic and a prostatic stent printed in poly-TCDMDA towards P. aeruginosa and Staphylococcus aureus.
Syphilis reinfection is associated with an attenuated immune profile in the same individual: a prospective observational cohort study (2018)

In this small study of 11 individuals, repeat syphilis was found to present with an attenuated immune response. The relevance of these findings to the design of optimal syphilis screening programs is discussed.
Multigenetic lesions in infant acute leukaemias: correlations with ALL‐1 gene status (1997)

In this study we investigated the presence of structural lesions in the ALL-1, p53 and p16 (cyclin-dependent kinase 4 inhibitor) genes in leukaemic cells obtained from 22 patients with infant acute leukaemia (aged < 18 months). Of these, 18 cases were classified as acute lymphoblastic leukaemia (ALL) and four as acute myeloid leukaemia (AML). Tumour DNAs were analysed by a combination of Southern blot. polymerase chain reaction (PCR), single-strand conformation polymorphism (SSCP), and direct sequence analyses. The results showed ALL-1 gene rearrangements in 15/22 (68%) cases, p53 gene mutations in 5/22 (26%), and a homozygous deletion of p16 in a single T-ALL case. p53 and p16 alterations were all found in the group of patients with ALL-1 gene rearrangements. p53 mutations were more often associated with a myeloid phenotype (3/5). In summary, multiple molecular alterations were found in 6/15 (40%) infant acute leukaemias with ALL-1 rearrangements. As to the clinical course, patients with additional lesions had similar clinical outcome with respect to patients with ALL-1 gene rearrangement as the sole genetic aberration. This may support the hypothesis that ALL-1 alterations are genetic events per se sufficient to confer a fully malignant phenotype to the leukaemic clone.
Development of High-Voltage Vertical GaN PN Diodes (invited). (2020)

Abstract not provided.
Joint metal artifact reduction and material discrimination in X-ray CT using a learning-based graph-cut method (2014)

X-ray Computed Tomography (CT) is an effective nondestructive technology used for security applications. In CT, three-dimensional images of the interior of an object are generated based on its X-ray attenuation. Multi-energy CT can be used to enhance material discrimination. Currently, reliable identification and segmentation of objects from CT data is challenging due to the large range of materials which may appear in baggage and the presence of metal and high clutter. Conventionally reconstructed CT images suffer from metal induced streaks and artifacts which can lead to breaking of objects and inaccurate object labeling. We propose a novel learning-based framework for joint metal artifact reduction and direct object labeling from CT derived data. A material label image is directly estimated from measured effective attenuation images. We include data weighting to mitigate metal artifacts and incorporate an object boundary-field to reduce object splitting. The overall problem is posed as a graph optimization problem and solved using an efficient graphcut algorithm. We test the method on real data and show that it can produce accurate material labels in the presence of metal and clutter.