gebhart/patrepeval huggingface dataset:
Serum and Lymph-node Collagenase in Sarcoidosis: Comparison with Angiotensin-converting Enzyme (1978)

Serum collagenase was significantly elevated in stage II, but not stage I sarcoidosis, in contrast to elevation of serum angiotensin-converting enzyme in stages I and II. Neither serum collagenase nor angiotensin-converting enzyme was elevated in active tuberculosis. Elevated serum collagenase and angiotensin-converting enzyme levels were decreased with steroid therapy. Serum collagenase and angiotensin-converting enzyme were significantly correlated but did not vary identically. Collagenase was not elevated in lymph nodes in sarcoidosis, in contrast to marked elevation of angiotensin-converting enzyme. The results suggest that serum angiotensin-converting enzyme is a more sensitive index of sarcoidosis activity than serum collagenase, which may have an ancillary role in assessment of the disease.
Production of vapor grown carbon fiber using high sulfur coal as a feedstock (1994)

Vapor grown carbon fiber (VGCF) is a highly graphitic fiber production in a CVD process from the pyrolysis of hydrocarbons in the gas phase. The high degree of graphitic perfection and high aspect ratio indicate that this type of fiber may be a superior reinforcement for several composite applications. The elimination of multiple processing steps used for conventional carbon fiber production and the use of inexpensive hydrocarbon feedstocks combine to promise a significant reduction of cost in the production of carbon fiber reinforcements. Such a development would enable widespread use of carbon fiber reinforced composites in automotive, electronics, aerospace, and sports applications. It has been shown in earlier work that adding equimolar quantities of sulfur such as hydrogen sulfide to the catalytic iron particles significantly increases the nucleation rate of carbon filaments; however, hydrogen sulfide is very toxic, corrosive, and flammable. The authors have shown that coal from the Ohio Upper Freeport Seam, containing 2.5% sulfur, can be used as a convenient and inexpensive source of both hydrocarbon and sulfur in the process for the production of vapor grown carbon fiber. Furthermore, there is evidence that the sulfur becomes entrapped in the carbon fiber catalyst, and does not exit themore » reactor in the form of sulfur oxides.« less
Automatic masking for robust 3D-2D image registration in image-guided spine surgery (2016)

During spinal neurosurgery, patient-specific information, planning, and annotation such as vertebral labels can be mapped from preoperative 3D CT to intraoperative 2D radiographs via image-based 3D-2D registration. Such registration has been shown to provide a potentially valuable means of decision support in target localization as well as quality assurance of the surgical product. However, robust registration can be challenged by mismatch in image content between the preoperative CT and intraoperative radiographs, arising, for example, from anatomical deformation or the presence of surgical tools within the radiograph. In this work, we develop and evaluate methods for automatically mitigating the effect of content mismatch by leveraging the surgical planning data to assign greater weight to anatomical regions known to be reliable for registration and vital to the surgical task while removing problematic regions that are highly deformable or often occluded by surgical tools. We investigated two approaches to assigning variable weight (i.e., "masking") to image content and/or the similarity metric: (1) masking the preoperative 3D CT ("volumetric masking"); and (2) masking within the 2D similarity metric calculation ("projection masking"). The accuracy of registration was evaluated in terms of projection distance error (PDE) in 61 cases selected from an IRB-approved clinical study. The best performing of the masking techniques was found to reduce the rate of gross failure (PDE > 20 mm) from 11.48% to 5.57% in this challenging retrospective data set. These approaches provided robustness to content mismatch and eliminated distinct failure modes of registration. Such improvement was gained without additional workflow and has motivated incorporation of the masking methods within a system under development for prospective clinical studies.
High-throughput computational screening of metal–organic frameworks (2014)

There is an almost unlimited number of metal-organic frameworks (MOFs). This creates exciting opportunities but also poses a problem: how do we quickly find the best MOFs for a given application? Molecular simulations have advanced sufficiently that many MOF properties - especially structural and gas adsorption properties - can be predicted computationally, and molecular modeling techniques are now used increasingly to guide the synthesis of new MOFs. With increasing computational power and improved simulation algorithms, it has become possible to conduct high-throughput computational screening to identify promising MOF structures and uncover structure-property relations. We review these efforts and discuss future directions in this new field.
Distributed Network Center and Size Estimation (2018)

A fully distributed algorithm for estimating the center and the radius of the smallest sphere that contains a wireless sensor network is proposed. The center finding problem is formulated as a convex optimization problem in summation form by using a soft-max approximation to the maximum function. Diffusion adaptation method is used where states of nodes converge to the estimated center distributively. Then, distributed max consensus is used to compute the radius. The proposed algorithm is fully distributed in the sense that each node in the network only needs to know its own location and nodes do not need to be pre-labeled. The algorithm works for any connected graph structure. The performance of the proposed algorithm is analyzed and it is shown that there is a tradeoff: a larger design parameter results in a more accurate center estimation but also makes the convergence speed of the distributed algorithm slower. It is also shown that the proposed algorithm can also be used to estimate the center and radius of the (not necessarily location-based) data at sensor nodes in a distributed way, thereby providing information and insights about the global data at each sensor. Simulation results corroborating the theory are also provided.
Design of a femtosecond laser assisted tomographic atom probe (2006)

A tomographic atom probe (TAP) in which the atoms are field evaporated by means of femtosecond laser pulses has been designed. It is shown that the field evaporation is assisted by the laser field enhanced by the subwavelength dimensions of the specimen without any significant heating of the specimen. In addition, as compared with the conventional TAP, due to the very short duration of laser pulses, no spread in the energy of emitted ions is observed, leading to a very high mass resolution in a straight TAP in a wide angle configuration. At last, laser pulses can be used to bring the intense electric field required for the field evaporation on poor conductive materials such as intrinsic Si at low temperature. In this article, the performance of the laser TAP is described and illustrated through the investigation of metals, oxides, and silicon materials.
ParaBox (2017)

Service Function Chains (SFCs) comprise a sequence of Network Functions (NFs) that are typically traversed in-order by data flows. Consequently, SFC delay grows linearly with the length of the SFC. Yet, for highly latency sensitive applications, this delay may be unacceptable---particularly when the constituent NFs are virtualized, running on commodity servers. In this paper, we investigate how SFC latency may be reduced by exploiting opportunities for parallel packet processing across NFs. We propose ParaBox, a novel hybrid packet processing architecture that, when possible, dynamically distributes packets to VNFs in parallel and merges their outputs intelligently to ensure the preservation of correct sequential processing semantics. To demonstrate the feasibility of our approach, we implement a ParaBox prototype on top of the DPDK-enabled Berkeley Extensible Software Switch. Our preliminary experiment results show that ParaBox can not only significantly reduce the service chaining latency, but also improve throughput.
A link between the fibroblast growth factor axis and the miR‐16 family reveals potential new treatment combinations in mesothelioma (2017)

Malignant pleural mesothelioma (MPM) is an aggressive malignancy with very limited therapeutic options. Fibroblast growth factor (FGF) signals play important roles in mesothelioma cell growth. Several FGFs and FGF receptors (FGFRs) are predicted targets of the miR-15/16 family, which is downregulated in MPM. The aim of this study was to explore the link between the miR-15/16 family and the FGF axis in MPM. Expression analyses via RT-qPCR showed downregulation of the FGF axis after transfection with miR-15/16 mimics. Direct interaction was confirmed by luciferase reporter assays. Restoration of miR-15/16 led to dose-dependent growth inhibition in MPM cell lines, which significantly correlated with their sensitivity to FGFR inhibition. Treatment with recombinant FGF2 prevented growth inhibition and further reduced the levels of FGF/R-targeting microRNAs, indicating a vicious cycle between miR-15/16 down- and FGF/FGFR signaling upregulation. Combined inhibition of two independent miR-15/16 targets, the FGF axis and Bcl-2, resulted in additive or synergistic activity. Our data indicate that post-transcriptional repression of FGF-mediated signals contributes to the tumor suppressor function of the microRNA-15/16 family. Inhibiting hyperactivated FGF signals and Bcl-2 might serve as a novel therapeutic combination strategy in MPM.
Novel nonlinear optical polymer optoelectronic devices (1998)

Presented is a novel design for opto-electronic integrated optic devices utilizing a nonlinear optical polymer core and conductive polymer claddings that will potentially have an order of magnitude shorter interaction length than conventional NLO polymer OE devices operating at TTL voltage levels and allows for in-situ poling.
Synthesis of periodic mesoporous phosphorus–nitrogen frameworks by nanocasting from mesoporous silica using melt-infiltration (2009)

Periodic mesoporous phosphorus–nitrogen (P–N) frameworks with p6mm hexagonal and Imm body centered cubic symmetries were synthesized by a solvent-free nanocasting route using periodic mesoporous silicas (SBA-15 and SBA-16) as hard templates and (PNCl2)3 as precursor. The (PNCl2)3 was molten at 120 °C in nitrogen atmosphere and infiltrated into the pores of mesoporous silicas. The nitridization of (PNCl2)3 in an ammonia atmosphere at 700 °C followed by the SiO2 template removal by etching with a HF/acetone mixture resulted in the formation of the desired periodic mesoporous P–N frameworks with high surface areas of 240 to 380 m2·g−1 and pore volumes in the range of 0.29 to 0.53 cm3·g−1. The excellent mesopore uniformity and periodicity of the obtained specimens were studied by electron microscopy, small angle X-ray diffraction, N2 sorption, FT-IR, EDS, and elemental analysis. The materials are thermally stable up to 550 and 700 °C in an inert atmosphere depending on the pore systems and exhibit photoluminescence between 280 and 450 nm.
Tamper detection and localization for categorical data using fragile watermarks (2004)

Today, database relations are widely used and distributed over the Internet. Since these data can be easily tampered with, it is critical to ensure the integrity of these data. In this paper, we propose to make use of fragile watermarks to detect and localize malicious alterations made to a database relation with categorical attributes. Unlike other watermarking schemes which inevitably introduce distortions to the cover data, the proposed scheme is distortion free. In our algorithm, all tuples in a database relation are first securely divided into groups according to some secure parameters. Watermarks are embedded and verified in each group independently. Thus, any modifications can be localized to some specific groups. Theoretical analysis shows that the probability of missing detection is very low.
Bone Marrow–Derived Kruppel-Like Factor 10 Controls Reendothelialization in Response to Arterial Injury (2013)

Collectively, these observations demonstrate a protective role for BM-derived KLF10 in paracrine and homing responses important for arterial endothelial injury and highlight KLF10 as a possible therapeutic target to promote endothelial repair in vascular disease states.
Conditional Superagonist CTL Ligands for the Promotion of Tumor-Specific CTL Responses (2010)

Although it has been demonstrated that CTLs can be raised against tumor-associated self-antigens, achieving consistent and effective clinical responses has proven challenging. Superagonist altered peptide ligands (APLs) can often elicit potent antitumor CTL responses where the native tumor-associated epitope fails. Current methods have identified a limited number of superagonist APLs, including the prototypic 27L mutant of MART-1. However, more comprehensive screening strategies would be desirable. In this study, we use a novel genetic screen, involving recombinant technology and class I Ag cross-presentation, to search for supraoptimal superagonists of the 27L MART-1 mutant by surveying the effectiveness of virtually every single amino acid substitution mutant of 27L to activate human Ag-specific CTL clones recognizing the wild-type MART-1(26-35) epitope. We identify three novel mutant epitopes with superagonist properties that are functionally superior to 27L; however, the ability of a given analogue to act as superagonist varies among patients and suggests that a given superagonist APL may be ideally suited to different patients. These findings endorse the use of comprehensive methods to establish panels of potential superagonist APLs to individualize tumor peptide vaccines among patients.
Synthesis of new antineoplastic alkylidenecyclopentenones. (1985)

Novel conjugated cyclopentenones, 5-alkylidene-4-hydroxy-2-cyclopentenones (3) and 5-alkylidene-2-chloro-4-hydroxy-2-cyclopentenones (4) were synthesized from 4-tert-butyldimethylsilyloxy-2-cyclopentenone (5) by two different pathways. These new compounds and their synthetic intermediates strongly inhibited L1210 tumor cell growth in vitro.
Nanoparticle doped organic-inorganic hybrid photorefractives (2008)

The gain characteristics of liquid crystal photorefractive cells doped with ferroelectric nanoparticles has been measured. The liquid crystal two beam coupling gain is found to reverse in sign and increase in magnitude through the addition of ferroelectric BaTiO(3) nanoparticles, yielding gain coefficients up to 1100 cm(-3) in the Bragg regime. We attribute the novel effects of gain reversal and magnitude increase to interactions between the ferroelectric particles' spontaneous polarization and the local liquid crystal flexopolarization.
Genomic hallmarks of homologous recombination deficiency in invasive breast carcinomas (2015)

Therapeutic strategies targeting Homologous Recombination Deficiency (HRD) in breast cancer requires patient stratification. The LST (Large-scale State Transitions) genomic signature previously validated for triple-negative breast carcinomas (TNBC) was evaluated as biomarker of HRD in luminal (hormone receptor positive) and HER2-overexpressing (HER2+) tumors. The LST genomic signature related to the number of large-scale chromosomal breakpoints in SNP-array tumor profile was applied to identify HRD in in-house and TCGA sets of breast tumors, in which the status of BRCA1/2 and other genes was also investigated. In the in-house dataset, HRD was predicted in 5% (20/385) of sporadic tumors luminal or HER2+ by the LST genomic signature and the inactivation of BRCA1, BRCA2 or RAD51C confirmed this prediction in 75% (12/16) of the tested cases. In 14% (6/43) of tumors occurring in BRCA1/2 mutant carriers, the corresponding wild-type allele was retained emphasizing the importance of determining the tumor status. In the TCGA luminal and HER2+ subtypes HRD incidence was estimated at 5% (18/329, 95%CI: 5-8%) and 2% (1/59, 95%CI: 2-9%), respectively. In TNBC cisplatin-based neo-adjuvant clinical trials, HRD is shown to be a necessary condition for cisplatin sensitivity. This analysis demonstrates the high performance of the LST genomic signature for HRD detection in breast cancers, which suggests its potential as a biomarker for genetic testing and patient stratification for clinical trials evaluating platinum salts and PARP inhibitors.
Highly Regio- and Enantioselective Reduction of 3,5-Dioxocarboxylates (2000)

Alkoholdehydrogenase aus Lactobacillus brevis (LBADH) katalysiert hochselektiv die Reduktion von 3,5-Dioxocarboxylaten in Position C-5 (siehe Schema). In Anlehnung an die natürlichen Transformationen des Polyketidstoffwechsels wurde ein chemoenzymatischer Zugang zu nahezu enantiomerenreinen 3,5-Dihydroxycarboxylaten entwickelt. Der entscheidende enzymatische Schritt kann in einem präparativ attraktiven Maßstab durchgeführt werden.
Structure and function of the human platelet thrombin receptor. Studies using monoclonal antibodies directed against a defined domain within the receptor N terminus. (1992)

Based upon its recently cloned nucleotide sequence, the human platelet thrombin receptor is thought to be formed by a single polypeptide chain with seven transmembrane domains and an extracellular N terminus that can be cleaved by thrombin. As yet, however, little is known from studies of the receptor protein itself. To obtain such information, we have prepared monoclonal antibodies against a peptide corresponding to receptor residues Ser42 through Phe55, the domain immediately distal to the site of cleavage by thrombin. By flow cytometry, all of the antibodies reacted with the thrombin-responsive megakaryoblastic CHRF-288 and HEL cell lines, but not with the T-lymphoid Sup-T1 cell line. Functionally, the antibodies inhibited platelet responses to alpha-thrombin, gamma-thrombin, and trypsin, but had no effect on platelet activation by ADP, epinephrine, or the thromboxane analog U46619. Radioiodinated antibody bound to approximately 1,800 sites/platelet, a value similar to the reported number of moderate affinity thrombin binding sites per platelet. On Western blots, the antibodies recognized a 66-kDa protein in platelet, HEL, and CHRF-288 membranes. The discrepancy between this apparent size and the predicted mass of the receptor suggests that, as with other G protein-coupled receptors, one or more of the potential sites for N-linked glycosylation have been utilized. Therefore, these results suggest that: 1) the cloned thrombin receptor is involved in a broad range of platelet responses to thrombin, as well as gamma-thrombin and trypsin; 2) as predicted, the N terminus of the receptor is accessible on the platelet surface; 3) the moderate affinity thrombin binding site noted in earlier studies may be the receptor; 4) potentially as much as one third of the mass of the receptor is carbohydrate.
Size Fractionation of Cell-Free DNA in Maternal Plasma Improves the Detection of a Paternally Inherited β-Thalassemia Point Mutation by MALDI-TOF Mass Spectrometry (2009)

Size fractionation of cell-free DNA may lead to the improved non-invasive detection of fetal point mutations for beta-thalassemia by MALDI-TOF mass spectrometry.
The E358S mutant of <i>Agrobacterium</i> sp. β‐glucosidase is a greatly improved glycosynthase (2000)

Glycosynthases are nucleophile mutants of retaining glycosidases that catalyze the glycosylation of sugar acceptors using glycosyl fluoride donors, thereby synthesizing oligosaccharides. The 'original' glycosynthase, derived from Agrobacterium sp. beta-glucosidase (Abg) by mutating the nucleophile glutamate to alanine (E358A), synthesizes oligosaccharides in yields exceeding 90% [Mackenzie, L.F., Wang, Q., Warren, R.A.J. and Withers, S.G. (1998) J. Am. Chem. Soc. 120, 5583-5584]. This mutant has now been re-cloned with a His(6)-tag into a pET-29b(+) vector, allowing gram scale production and single step chromatographic purification. A dramatic, 24-fold, improvement in synthetic rates has also been achieved by substituting the nucleophile with serine, resulting in improved product yields, reduced reaction times and an enhanced synthetic repertoire. Thus poor acceptors for Abg E358A, such as PNP-GlcNAc, are successfully glycosylated by E358S, allowing the synthesis of PNP-beta-LacNAc. The increased glycosylation activity of Abg E358S likely originates from a stabilizing interaction between the Ser hydroxyl group and the departing anomeric fluorine of the alpha-glycosyl fluoride.
Cherenkov imaging in the potential roles of radiotherapy QA and delivery (2017)

Cherenkov emission has a direct proportionality to the deposited dose at the local level, and capture of these emitted light signals allows visualization of real time maps of dose in vivo. Mapping the Cherenkov signals through water tanks illustrates how 3D Cherenkov can be achieved, either as 2D plus time, or 3D in static imaging. Imaging Cherenkov from patients shows how signals can be acquired which map out radiation dose in real time. The signals are affected by several factors, each of which will take some calibration to resolve, yet intrinsically the signal is shown to be a linear reporter of dose delivered. Development of calibration methodologies is ongoing in both research and development work.
Design Concept of Magneto-Optical Disk (1989)

We have developed a 4-layer magneto-optical disk (SiN/TbFeCo/SiN/Al) with erase/write tolerance for laser power (energy window) at temperatures from 10°C to 60°C. We found that the thickness of the third SiN layer and of the second magneto-optical layer has a critical influence on optical and thermal properties. The optimized thickness is about 500 Å for the third SiN layer and 200 Å for the magneto-optical layer. The energy window is 80% of the write power in writing but only 20% of the erase power in erasing. Since laser power can fluctuate by 30% of the nominal power in practical use and disk sensitivity can vary by 10%, we think temperature compensation is needed, which would make it possible to have an energy window of 50%, even in erasing.
A novel platform to generate peptoid-based mimetic vaccines (P4504) (2013)

Abstract The aim of this research is to generate vaccine candidates for any virus for which a neutralizing monoclonal antibody exists without prior knowledge of the protective epitope. We have developed a platform to generate such vaccine candidates and are working on a device to automate their identification. The platform consists of libraries of B cell epitopes prepared by displaying peptoid sequences on beads, screening with neutralizing monoclonal antibodies to select peptoids bound by the antigen binding site of the monoclonal antibody, and retaining the antibody-bound peptoids with protein G dynabeads and a magnet. Peptoids are similar to peptides but with the R group attached to the nitrogen instead of the carbon. They are haptens that can be attached to protein carriers to elicit anti-peptoid antibody responses. We have conducted platform optimization and proof-of-principle testing using FLAG peptide and anti-FLAG monoclonal antibody. We then applied the optimized platform to screen peptoid libraries with monoclonal anti-FLAG and identified two potential mimetics. Mice immunized with the peptoids have made FLAG peptide-reactive antibodies, thereby demonstrating proof of concept. Implementation of this platform with neutralizing monoclonal antibodies we have in hand against HIV, West Nile virus and hepatitis C virus can identify potential mimetic vaccine candidates without prior knowledge of important epitopes, and could represent an entirely new way to generate safe vaccines.