gebhart/patrepeval huggingface dataset:
TU‐G‐217A‐02: Voxel‐Based Residual Analysis of High Spectral and Spatial Resolution (HiSS) MRI of Breast Lesions (2012)

Purpose: To extend CADx techniques for High Spectral and Spatial Resolution (HiSS) breast MRI, and to assess the ability of the Lorentzian‐fit‐ subtraction residual maxima of the water resonance spectra to distinguish between benign and malignant breast lesions on a voxel‐by‐voxel basis. Methods: HiSS high resolution spectroscopic MR images were collected under an IRB‐approved protocol. To analyze HiSS data, we fit a Lorentzian curve to a 25 bin (140 Hz) region of the proton‐resonance spectra in each lesion, centered at the water resonance and normalized to the water peak height. After subtracting this fit from each spectrum, the maximum residual value in nine spectral bins from +22.4 to +67.2 Hz to the right of the water peak was recorded with its corresponding frequency bin. We automatically excluded voxels in each lesion with maximum residual lower than 60% of the maximum residual in the entire lesion in order to eliminate voxels with off‐peaks close to or below the noise floor. These residual maxima were evaluated on a voxel‐by‐voxel basis, for each frequency bin based on the known diagnosis (9 malignant; 8 benign cases) and the performance of this single feature was assessed using ROC analysis. Results: In the task of distinguishing between voxels in malignant and benign lesions, analysis across all nine spectral bins yielded an AUC value of 0.96 ± 0.007. AUC values within specific spectral bins ranged from 0.72 at 5.6 Hz from the water peak to 1.0 at 60.6 Hz ‐ noting that the latter could be artificially high due to our limited database. Conclusions: We have presented a technique utilizing a voxel‐based approach to HiSS spectral analysis, with potential for use in the diagnosis of cancerous breast lesions. We are currently extending this method to include lesion‐based classification rather than voxel‐based evaluation. M.L. Giger is a stockholder in R2 Technology/Hologic, has equity in Quantitative Insights, and receives royalties from Hologic, GE Medical Systems, MEDIAN Technologies, Riverain Medical, Mitsubishi and Toshiba. G.S. Karczmar has an institutional research agreement with Philips Healthcare. It is the University of Chicago Conflict of Interest Policy that investigators disclose publicly actual or potential significant financial interest that would reasonably appear to be directly and significantly affected by the research activities.
A Rab-GAP TBC Domain Protein Binds Hepatitis C Virus NS5A and Mediates Viral Replication (2007)

Hepatitis C virus (HCV) is an important cause of liver disease worldwide. Current therapies are inadequate for most patients. Using a two-hybrid screen, we isolated a novel cellular binding partner interacting with the N terminus of HCV nonstructural protein NS5A. This partner contains a TBC Rab-GAP (GTPase-activating protein) homology domain found in all known Rab-activating proteins. As the first described interaction between such a Rab-GAP and a viral protein, this finding suggests a new mechanism whereby viruses may subvert host cell machinery for mediating the endocytosis, trafficking, and sorting of their own proteins. Moreover, depleting the expression of this partner severely impairs HCV RNA replication with no obvious effect on cell viability. These results suggest that pharmacologic disruption of this NS5A-interacting partner can be contemplated as a potential new antiviral strategy against a pathogen affecting nearly 3% of the world's population.
Development of a direct fabrication technique for full-shell x-ray optics (2016)

Future astrophysical missions will require fabrication technology capable of producing high angular resolution x-ray optics. A full-shell direct fabrication approach using modern robotic polishing machines has the potential for producing high resolution, light-weight and affordable x-ray mirrors that can be nested to produce large collecting area. This approach to mirror fabrication, based on the use of the metal substrates coated with nickel phosphorous alloy, is being pursued at MSFC. A model of the wear pattern as a function of numerous physical parameters is developed and verified using a mandrel sample. The results of the polishing experiments are presented.
Fabrication tolerant and wavelength independent arbitrary power splitters on a monolithic silicon photonics platform (2022)

We experimentally demonstrate wavelength-independent couplers based on an asymmetric Mach-Zehnder interferometer on a monolithic silicon-photonics platform in a state-of-the-art CMOS foundry. The devices are also designed to exhibit fabrication tolerant performance for arbitrary splitting ratios. We have developed a semi-analytical model to optimize the device response and the reliability of the model is benchmarked against 3D-FDTD simulations. Experimental results are consistent with the simulation results obtained by the model and show uniform performance across different wafer sites with a standard deviation for the splitting ratio of only 0.6% at 1310 nm wavelength. The maximum spectral deviation of the splitting ratio (3-dB splitter) is measured to be 1.2% over a wavelength range of at least 80 nm and the insertion loss ranges from 0.08 to 0.38 dB. The wavelength-independent coupler has a compact footprint of 60 × 40 <i>μ</i> <i>m</i> <sup>2</sup>.
Subspace self-collision culling (2010)

We show how to greatly accelerate self-collision detection (SCD) for reduced deformable models. Given a triangle mesh and a set of deformation modes, our method precomputes Subspace Self-Collision Culling (SSCC) certificates which, if satisfied, prove the absence of self-collisions for large parts of the model. At runtime, bounding volume hierarchies augmented with our certificates can aggressively cull overlap tests and reduce hierarchy updates. Our method supports both discrete and continuous SCD, can handle complex geometry, and makes no assumptions about geometric smoothness or normal bounds. It is particularly effective for simulations with modest subspace deformations, where it can often verify the absence of self-collisions in constant time. Our certificates enable low amortized costs, in time and across many objects in multi-body dynamics simulations. Finally, SSCC is effective enough to support self-collision tests at audio rates, which we demonstrate by producing the first sound simulations of clattering objects.
Carbon‐11, Nitrogen‐13, and Oxygen‐15 Chemistry (2014)

This chapter first introduces the field of carbon-11, nitrogen-13, and oxygen-15 chemistry, and then provides an up-to-date account of their chemistry. The carbon-11 isotope is most widely produced by the proton bombardment of nitrogen-14 in a gas phase cyclotron target. 11CO2 is the most widely produced in target C-11 primary precursor. Methylation reactions are commonly used for the production of many of the key 11C-tracers. Palladium-mediated C-11 carbonylation reactions are most widely exploited and used to effectively label imides, ketones, carboxylic acids, esters, amides, and acrylamides. N-13 labelled amines are of interest for improving positron emission tomography (PET) myocardial perfusion imaging and representing their metabolism. Oxygen-15 is generally produced in target via the bombardment of nitrogen gas with deuterons. The majority of O-15 chemistry is therefore based on the production of small molecules either directly within the cyclotron target or via one chemical transformation using high temperature gas phase methods.
Nanostructures Fabrication on Ta Thin Film Using Atomic Force Microscope Lithography (2006)

ABSTRACT Atomic force microscope (AFM) lithography based on localized current injection was carried out for fabricating nanostructures of metal oxide on tantalum (Ta). Fabricated nanopatterns of tantalum oxide (Ta2O5) were selectively etched by magnetically enhanced inductively coupled plasma (MEICP) etching system. Nanopatterns of Ta with feature size in the range of a few tens-hundreds nm were successfully fabricated.
Durability of glycaemic control with dapagliflozin, an SGLT2 inhibitor, compared with saxagliptin, a DPP4 inhibitor, in patients with inadequately controlled type 2 diabetes (2019)

Dapagliflozin is associated with greater reductions in HbA1c and weight than saxagliptin in management of type 2 diabetes mellitus (T2DM). The present post hoc analyses compared the durability of these effects over short- and long-term follow-up in patients with T2DM who were inadequately controlled with metformin (≥1500 mg/day) and who were receiving either dapagliflozin (10 mg/day) or saxagliptin (5 mg/day). Failure of glycaemiccontrol was assessed using the slope of the change in HbA1c from baseline-over-time regression line (coefficient of failure [CoF]). CoF was compared directly (dapagliflozin vs saxagliptin) over the short term (NCT01606007, 24 weeks) and indirectly (placebo-adjusted) over the long term (NCT00528879 and NCT00121667, 102 weeks). A low CoF value indicated greater durability. CoF was lower for dapagliflozin versus saxagliptin over 18-24 weeks (-1.38%/year; 95% CI, -2.41 to -0.35; P = .009) and 20-102 weeks (-0.37%/year; 95% CI, -0.73 to -0.02; P = .04). Fewer dapagliflozin-treated patients versus saxagliptin-treated patients required rescue medication or discontinued the study because of failure to achieve glycaemic control at 24 weeks (3.4% vs 9.4%; P = .0191). In patients with T2DM who were inadequately controlled with metformin, dapagliflozin was associated with greater durability of glycaemic control than saxagliptin over 18-24 and 20-102 weeks.
Antithrombotic Therapy and Prevention of Thrombosis, 9th ed: American College of Chest Physicians Evidence-Based Clinical Practice Guidelines (2014)

This article describes the pharmacology of approved parenteral anticoagulants. These include the indirect anticoagulants, unfractionated heparin (UFH), low-molecular-weight heparins (LMWHs), fondaparinux, and danaparoid, as well as the direct thrombin inhibitors hirudin, biva- lirudin, and argatroban. UFH is a heterogeneous mixture of glycosaminoglycans that bind to antithrombin via a unique pentasaccharide sequence and catalyze the inactivation of thrombin, factor Xa, and other clotting enzymes. Heparin also binds to cells and plasma proteins other than antithrombin causing unpredictable pharmacokinetic and pharmacodynamic properties and trig- gering nonhemorrhagic side effects, such as heparin-induced thrombocytopenia (HIT) and osteo- porosis. LMWHs have greater inhibitory activity against factor Xa than thrombin and exhibit less binding to cells and plasma proteins than heparin. Consequently, LMWH preparations have more predictable pharmacokinetic and pharmacodynamic properties, have a longer half-life than heparin, and are associated with a lower risk of nonhemorrhagic side effects. LMWHs can be administered once daily or bid by subcutaneous injection, without coagulation monitoring. Based on their greater convenience, LMWHs have replaced UFH for many clinical indications. Fonda- parinux, a synthetic pentasaccharide, catalyzes the inhibition of factor Xa, but not thrombin, in an antithrombin-dependent fashion. Fondaparinux binds only to antithrombin. Therefore, fonda- parinux-associated HIT or osteoporosis is unlikely to occur. Fondaparinux exhibits complete bio- availability when administered subcutaneously, has a longer half-life than LMWHs, and is given once daily by subcutaneous injection in fidoses, without coagulation monitoring. Three addi- tional parenteral direct thrombin inhibitors and danaparoid are approved as alternatives to hep- arin in patients with HIT.
Opportunities and Barriers of Telemedicine in Rheumatology: A Participatory, Mixed-Methods Study (2021)

Despite all its promises, telemedicine is still not widely implemented in the care of rheumatic and musculoskeletal diseases (RMDs). The aim of this study is to investigate opportunities, barriers, acceptance, and preferences concerning telemedicine among RMD patients and professional stakeholders. From November 2017 to December 2019, a participatory, mixed-methods study was conducted, consisting of (1) expert interviews (<i>n</i> = 27) with RMD patients and professional stakeholders, (2) a national paper-based patient survey (<i>n</i> = 766), and (3) focus groups (<i>n</i> = 2) with patient representatives and rheumatologists. The qualitative findings indicate that patients equate personal contact with physical face-to-face contact, which could be reduced by implementing telemedicine, thus negatively influencing the patient-doctor relationship. Correspondingly "no personal contact with the doctor" is the main reason (64%) why 38% of the surveyed patients refuse to try telemedicine. Professional stakeholders expect telemedicine to contribute to the effective allocation of scarce resources in rheumatology care. The main barriers reported by stakeholders were the scarcity of time resources in RMD care, the absence of physical examinations, and organizational challenges associated with the implementation of telemedicine in RMD care. While the exact integration of telemedicine into routine care has yet to be found, the consequences on the patient-physician relationship must be permanently considered.
Atomic resolution electron microscopy in a magnetic field free environment (2019)

Atomic-resolution electron microscopes utilize high-power magnetic lenses to produce magnified images of the atomic details of matter. Doing so involves placing samples inside the magnetic objective lens, where magnetic fields of up to a few tesla are always exerted. This can largely alter, or even destroy, the magnetic and physical structures of interest. Here, we describe a newly developed magnetic objective lens system that realizes a magnetic field free environment at the sample position. Combined with a higher-order aberration corrector, we achieve direct, atom-resolved imaging with sub-Å spatial resolution with a residual magnetic field of less than 0.2 mT at the sample position. This capability enables direct atom-resolved imaging of magnetic materials such as silicon steels. Removing the need to subject samples to high magnetic field environments enables a new stage in atomic resolution electron microscopy that realizes direct, atomic-level observation of samples without unwanted high magnetic field effects.
PEGylated Viral Nanoparticles for Biomedicine: The Impact of PEG Chain Length on VNP Cell Interactions In Vitro and Ex Vivo (2009)

PEGylation is an effective strategy for reducing biospecific interactions for pharmaceuticals. The plant virus Cowpea mosaic virus (CPMV) has been studied for potential nanobiomedical applications by virtue of its natural interactions with mammalian endothelial cells. To investigate the degree of PEGylation required to retarget CPMV-based formulations to other destinations, two CPMV-PEG formulations, CPMV-PEG1000 (P1) and CPMV-PEG2000 (P2) were tested. Modeling suggested that the PEG chains were displayed as flattened mushrooms on the particle with an estimated surface grafting area of 0.53% for P1 and 0.83% for P2. Only the P2 formulation effectively shielded the particles from interacting with cells or tissues, suggesting that either key interacting regions on the particle surface were blocked or that a sufficient hydration shell had been generated to inhibit cellular interactions. The large CPMV surface area available after PEGylation allows further attachment of imaging and therapeutic molecules to the particle to generate multifunctionality.
CHEWING PATTERNS OF VARIOUS TEXTURE FOODS STUDIED BY ELECTROMYOGRAPHY IN YOUNG AND ELDERLY POPULATIONS (2002)

ABSTRACT The effects of food texture on the chewing patterns of elderly and young people, masticatory recordings using electromyography (EMG) were carried out. Fourteen French adults (mean 29.4 years) and 23 elderly (mean 67.7 years) participated. Six food products (rice, beef, cheese, crispy bread, apple and peanuts) were tested. The chewing pattern of elderly subjects was characterized by a significant increase of number of chews and chewing duration for all foods except rice. Whatever the food type, muscle activity per chew (mean amplitude × burst duration) was lower for elderly than for young subjects. Single chews appeared less effective for food reduction in elderly than in young subjects. This can be partly compensated for by increasing the chewing duration and number of chews. No significant difference was found between both groups of subject for the total amount of EMG activity required prior to swallow whatever the food chewed.
Linkage of Infection to Adverse Systemic Complications: Periodontal Disease, Toll-Like Receptors, and Other Pattern Recognition Systems (2018)

Toll-like receptors (TLRs) are a group of pattern recognition receptors (PRRs) that provide innate immune sensing of conserved pathogen-associated molecular patterns (PAMPs) to engage early immune recognition of bacteria, viruses, and protozoa. Furthermore, TLRs provide a conduit for initiation of non-infectious inflammation following the sensing of danger-associated molecular patterns (DAMPs) generated as a consequence of cellular injury. Due to their essential role as DAMP and PAMP sensors, TLR signaling also contributes importantly to several systemic diseases including cardiovascular disease, diabetes, and others. The overlapping participation of TLRs in the control of infection, and pathogenesis of systemic diseases, has served as a starting point for research delving into the poorly defined area of infection leading to increased risk of various systemic diseases. Although conflicting studies exist, cardiovascular disease, diabetes, cancer, rheumatoid arthritis, and obesity/metabolic dysfunction have been associated with differing degrees of strength to infectious diseases. Here we will discuss elements of these connections focusing on the contributions of TLR signaling as a consequence of bacterial exposure in the context of the oral infections leading to periodontal disease, and associations with metabolic diseases including atherosclerosis and type 2 diabetes.
A Declarative Query Interface for Large Semantic Networks (2002)

The OQAFMA Query Agent for the Foundational Model of Anatomy (OQFMA) was designed to enhance the capabilities of an earlier server and to provide more rapid access to a large knowledge base than the ProtÃ©gÃ© knowledge acquisition tool. The system architecture was optimized using indexes for the most common classes of queries. Additional performance benefits were gained by pre-computing the transitive closure of appropriate relationships. Flexible, random access of the data is provided via a declarative query language, derived from StruQL, a language for querying semi-structured data. The poster provides several examples of queries supported by OQAFMA.
Multiple acoustic source localization based on multiple hypotheses testing using particle approach (2010)

Localization of multiple acoustic sources in a non-ideal environment has a number of difficulties, among which are accurate acoustic feature estimation for multiple sources and association uncertainty between measurements and their corresponding sources. This paper focuses more on the latter and proposes an algorithm based on a multiple-hypothesis framework for both a measurement model and a measurement association model to localize multiple sources. A conditional data likelihood model based on a measurement hypothesis is proposed and implemented using particles. Simulation results demonstrate that the proposed algorithm is capable of localizing the positions of multiple sources with a small number of microphones without any prior knowledge when the amount of reverberation is moderate.
Multicore erbium doped fiber amplifier with 5 THz bandwidth, high-gain and low NF (2013)

Core-pumped 7-core EDFA with two stage amplification is realized. Combination of its higher gain and GFF enables wide bandwidth operation. NF of Less than 5.5 dB is achieved with improved fan-in device.
Effects of interface charges on imprint of epitaxial Bi4Ti3O12 thin films (1997)

Using La0.5Sr0.5CoO3 (LSCO) or Pt film as a bottom electrode layer, epitaxial Bi4Ti3O12 (BTO) thin films were grown on MgO(001) substrates by pulsed laser deposition. A symmetric Pt/BTO/Pt capacitor structure shows a surprisingly large asymmetric polarization switching behavior, but a Pt/BTO/LSCO structure has a nearly symmetric P–V hysteresis. The strong asymmetric behavior in the Pt/BTO/Pt was attributed to positive charges resulting from interdiffusion at the bottom BTO/Pt interface. P–V hysteresis studies using numerous top electrode materials and Auger electron spectroscopy depth profile measurement also support formation of interfacial charges. Imprint pulse test shows that such an imprint failure cannot be recovered by applying a dc bias field.
Method for rapid, controllable growth and thickness, of epitaxial silicon films (2023)

A method of producing epitaxial silicon films on a c-Si wafer substrate using hot wire chemical vapor deposition by controlling the rate of silicon deposition in a temperature range that spans the transition from a monohydride to a hydrogen free silicon surface in a vacuum, to obtain phase-pure epitaxial silicon film of increased thickness is disclosed. The method includes placing a c-Si substrate in a HWCVD reactor chamber. The method also includes supplying a gas containing silicon at a sufficient rate into the reaction chamber to interact with the substrate to deposit a layer containing silicon thereon at a predefined growth rate to obtain phase-pure epitaxial silicon film of increased thickness.
In-Plane Coupling into Circular-Grating Resonators for All-Optical Switching (2006)

This paper addresses the issue of in-plane coupling into and out of circular-grating resonators with optical waveguides for all-optical switching applications. Two different designs are proposed: the first design consists in directly accessing the cavity with the waveguides. The second design is based on optimization with an evolutionary algorithm that randomly reshapes the gratings along the waveguides. Passive linear simulations for both approaches are performed with the finite-elements method, and the results will be presented
A new <i>Schizosaccharomyces pombe</i> base excision repair mutant, <i>nth1</i>, reveals overlapping pathways for repair of DNA base damage (2003)

Endonuclease III (Nth) enzyme from Escherichia coli is involved in base excision repair of oxidised pyrimidine residues in DNA. The Schizosaccharomyces pombe Nth1 protein is a sequence and functional homologue of E. coli Nth, possessing both DNA glycosylase and apurinic/apyrimidinic (AP) lyase activity. Here, we report the construction and characterization of the S. pombe nth1 mutant. The nth1 mutant exhibited no enhanced sensitivity to oxidising agents, UV or gamma-irradiation, but was hypersensitive to the alkylating agent methyl methanesulphonate (MMS). Analysis of base excision from DNA exposed to [3H]methyl-N-nitrosourea showed that the purified Nth1 enzyme did not remove alkylated bases such as 3-methyladenine and 7-methylguanine whereas methyl-formamidopyrimidine was excised efficiently. The repair of AP sites in S. pombe has previously been shown to be independent of Apn1-like AP endonuclease activity, and the main reason for the MMS sensitivity of nth1 cells appears to be their lack of AP lyase activity. The nth1 mutant also exhibited elevated frequencies of spontaneous mitotic intrachromosomal recombination, which is a phenotype shared by the MMS-hypersensitive DNA repair mutants rad2, rhp55 and NER repair mutants rad16, rhp14, rad13 and swi10. Epistasis analyses of nth1 and these DNA repair mutants suggest that several DNA damage repair/tolerance pathways participate in the processing of alkylation and spontaneous DNA damage in S. pombe.