gebhart/patrepeval huggingface dataset:
Progressive coding of stereo images using wavelets and overlapping blocks (2003)

In this paper, we introduce a stereo image coder, which is based on the discrete wavelet transform. To estimate the disparity, overlapping bilinear windows are used. This combination proves to be a very efficient. Our coder outperforms the best stereo image coders known so far. In addition, it supports the progressive mode.
A Method for Measuring Changes in Tracheal Mucus Gel Layer Thickness as an Indication of an Immediate Hypersensitivity Response (1984)

A visual method for measuring increase in tracheal mucus gel layer thickness as an indication of an immediate hypersensitivity response, using a Zeiss slitlamp and pachymeter is described. Mucus gel layer thickening is antigen dose dependent. Antigen challenge of nonsensitized rats does not cause significant increases in gel thickness dispelling the notion that changes in the gel layer result from nonspecific irritation. Cromolyn sodium, cimetidine, and FPL-55712 inhibit increases in gel layer thickness following antigen challenge of actively sensitized rats, while atropine, pyrilamine, and methysergide do not.
Identification of marker genes distinguishing human periodontal ligament cells from human mesenchymal stem cells and human gingival fibroblasts (2006)

Human periodontal ligament cells may be distinguished from human bone marrow mesenchymal stem cells and human gingival fibroblasts by the genes for apolipoprotein D, major histocompatibility complex-DR-alpha, and major histocompatibility complex-DR-beta.
Enclosed Volume Determination of Concentrated Dioctadecyldimethylammonium Chloride (DODAC) Vesicular Dispersions by Low-Resolution Proton NMR Diffusometry and <i>T</i><sub>2</sub> Relaxometry (2011)

The enclosed volume of concentrated dioctadecyldimethylammonium chloride (DODAC) dispersions has been determined by means of low-resolution NMR pfg-diffusometry and T(2) relaxometry. The pfg-NMR diffusometry method is based on the different diffusion behaviors of water in the external and internal phases and as such does not require the addition of a tracer. On the other hand, T(2) relaxometry is based on the different relaxation behaviors of water fractions upon addition of manganese chloride as external (paramagnetic) probe. It was noticed that reliable results are found only for temperatures below the phase transition temperature of DODAC, when the exchange between the two water compartments can be neglected. At 5 °C, these two independent methods resulted in similar enclosed volume values, meaning that the results are reliable and reflect the real enclosed volume. In addition, the T(2) relaxometry method has been proven to be useful in the investigation of the DODAC membrane permeability.
Prevention of urinary catheter-associated infections by coating antimicrobial peptides from crowberry endophytes (2019)

Urinary catheters are extensively used in hospitals, being responsible for about 75% of hospital-acquired infections. In this work, a de novo designed antimicrobial peptide (AMP) Chain201D was studied in the context of urinary catheter-associated infections. Chain201D showed excellent antimicrobial activity against relevant ATCC strains and clinical isolates of bacteria and yeast and demonstrated high stability in a wide range of temperatures, pH and salt concentrations. Moreover, the bactericidal activity of Chain201D immobilized on a model surface was studied against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus), some of the most prevalent strains found in urinary catheter-associated infections. Chain201D was successfully tethered to ((1-mercapto-11-undecyl)-(tetra(ethylene glycol) (EG4)) terminated self-assembled monolayers (SAMs), (EG4-SAMs), activated by 1,1'-Carbonyldiimidazole (CDI) at different concentrations. Chain201D surfaces can bind and kill by contact a high percentage of adherent bacteria. These achievements are obtained without any peptide modification (for chemoselective conjugation) and without the use of a spacer. Moreover, increased amounts of immobilized AMP lead to higher numbers of adhered/dead bacteria, revealing a concentration-dependent behaviour and demonstrating that Chain201D has excellent potential for developing antimicrobial urinary catheters.
Graded-index mid-infrared planar optical waveguides made from silver halides (2001)

Since the index of refraction of AgCl(x)Br(1-x) (x<1) is higher than that of AgCl, by diffusing Br(-) ions into AgCl it was possible to control the index and thus obtain planar waveguides made from silver chlorobromide (AgClBr) on a AgCl substrate. Silver halides are transparent in the mid IR, and it was therefore possible to characterize the waveguides by transmission of 10.6-mum CO(2)-laser radiation through them. In a typical case, the thickness was optically measured and was found to be 65mum , and the propagation loss was 16 dB/cm. The output-beam profile distribution was determined experimentally and found to be well correlated with a numerical analysis simulation based on a ray-tracing model of the eikonal equation. Planar waveguides that are transparent in the mid IR will likely be useful in numerous applications.
Assimilation of Crustal Material by Basaltic Magma: Strontium Isotopic and Trace Element Data from the Edgecumbe Volcanic Field, SE Alaska (1984)

Journal Article Assimilation of Crustal Material by Basaltic Magma: Strontium Isotopic and Trace Element Data from the Edgecumbe Volcanic Field, SE Alaska Get access JAMES D. MYERS, JAMES D. MYERS 1Department of Geology and Geophysics, University of WyomingLaramie, Wyoming 82071 Search for other works by this author on: Oxford Academic Google Scholar A. KRISHNA SINHA, A. KRISHNA SINHA 2Department of Geological Sciences, Virginia Polytechnic Institute and State UniversityBlacksburg, Virginia 24061 Search for other works by this author on: Oxford Academic Google Scholar BRUCE D. MARSH BRUCE D. MARSH 3Department of Earth and Planetary Sciences, The Johns Hopkins UniversityBaltimore, Maryland 21218 Search for other works by this author on: Oxford Academic Google Scholar Journal of Petrology, Volume 25, Issue 1, February 1984, Pages 1–26, https://doi.org/10.1093/petrology/25.1.1 Published: 01 February 1984 Article history Received: 18 February 1982 Revision received: 05 July 1983 Published: 01 February 1984
BRCA2mutation carriers, reproductive factors and breast cancer risk (2003)

The association between breast cancer and the number of pregnancies and between breast cancer and the duration of breast feeding was not the same for carriers and noncarriers of a detrimental BRCA2 mutation. In the context of other epidemiological and laboratory studies, this may indicate that the product of the BRCA2 gene has a function relating to the differentiation of epithelial tissue in the breast.
Microbial system for biosynthesis of natural and engineered products coupled to in situ extraction in supercritical CO&lt;sub&gt;2&lt;/sub&gt; (2023)

Provided herein are methods of producing a bioproduct by culturing a cell in a multiphase reactor that comprises supercritical CO&lt;sub&gt;2&lt;/sub&gt;, near critical CO&lt;sub&gt;2&lt;/sub&gt;, or liquid CO&lt;sub&gt;2&lt;/sub&gt;.
Abstract 11254: Double Product Privilege in Predicting All-cause and Cardiovascular Disease Mortality Compare to Heart Rate and Blood Pressure Separately, the Nippon-data 80 Study (2019)

Background: To clarify whether the double product (DP) (systolic blood pressure (SBP) * resting heart rate (HR)/100) measurement has prognostic value for mortality. Method: We followed up 8,307 par...
Detailed Electrochemical Studies of the Tetraruthenium Polyoxometalate Water Oxidation Catalyst in Acidic Media: Identification of an Extended Oxidation Series using Fourier Transformed Alternating Current Voltammetry (2012)

The electrochemistry of the water oxidation catalyst, Rb(8)K(2)[{Ru(4)O(4)(OH)(2)(H(2)O)(4)}(γ-SiW(10)O(36))(2)] (Rb(8)K(2)-1(0)) has been studied in the presence and absence of potassium cations in both hydrochloric and sulfuric acid solutions by transient direct current (dc) cyclic voltammetry, a steady state dc method in the rotating disk configuration and the kinetically sensitive technique of Fourier transformed large-amplitude alternating current (ac) voltammetry. In acidic media, the presence of potassium ions affects the kinetics (apparent rate of electron transfer) and thermodynamics (reversible potentials) of the eight processes (A'/A to H/H') that are readily detected under dc voltammetric conditions. The six most positive processes (A'/A to F/F'), each involve a one electron ruthenium based charge transfer step (A'/A, B'/B are Ru(IV/V) oxidation and C/C' to F/F' are Ru(IV/III) reduction). The apparent rate of electron transfer of the ruthenium centers in sulfuric acid is higher than in hydrochloric acid. The addition of potassium cations increases the apparent rates and gives rise to a small shift of reversible potential. Simulations of the Fourier transformed ac voltammetry method show that the B'/B, E/E', and F/F' processes are quasi-reversible, while the others are close to reversible. A third Ru(IV/V) oxidation process is observed just prior to the positive potential limit via dc methods. Importantly, the ability of the higher harmonic components of the ac method to discriminate against the irreversible background solvent process allows this (process I) as well as an additional fourth reversible ruthenium based process (J) to be readily identified. The steady-state rotating disk electrode (RDE) method confirmed that all four Ru-centers in Rb(8)K(2)-1(0) are in oxidation state IV. The dc and ac data indicate that reversible potentials of the four ruthenium centers are evenly spaced, which may be relevant to understanding of the water oxidation electrocatalysis. A profound effect of the potassium cation is observed for the one-electron transfer process (G/G') assigned to Ru(III/II) reduction and the multiple electron transfer reduction process (H/H') that arise from the tungstate polyoxometalate framework. A significant shift of E°' to a more positive potential value for process H/H' was observed on removal of K(+) (~100 mV in H(2)SO(4) and ~50 mV in HCl).
Surgical outcomes in lung cancer presenting as ground-glass opacities of 3 cm or less: A review of 5 years' experience (2013)

The percentage of malignancy is high in pulmonary GGOs. Surgery results in an excellent prognosis in these patients.
Using HfC(210) and HfC(110) as high brightness electron sources (2016)

We report on high-brightness, thermal-field emission cathodes using (210) and (110) oriented hafnium carbide. HfC(210) cathodes are shown to deliver very high angular intensities to >50 mA/sr and remain stable. Modeling and experimental data are shown which highlights the utility of these sources for SEM and other high-brightness uses.
Characterization of Statin Dose Response in Electronic Medical Records (2013)

Efforts to define the genetic architecture underlying variable statin response have met with limited success, possibly because previous studies were limited to effect based on a single dose. We leveraged electronic medical records (EMRs) to extract potency (ED50) and efficacy (Emax) of statin dose-response curves and tested them for association with 144 preselected variants. Two large biobanks were used to construct dose-response curves for 2,026 and 2,252 subjects on simvastatin and atorvastatin, respectively. Atorvastatin was more efficacious, was more potent, and demonstrated less interindividual variability than simvastatin. A pharmacodynamic variant emerging from randomized trials (PRDM16) was associated with Emax for both. For atorvastatin, Emax was 51.7 mg/dl in subjects homozygous for the minor allele vs. 75.0 mg/dl for those homozygous for the major allele. We also identified several loci associated with ED50. The extraction of rigorously defined traits from EMRs for pharmacogenetic studies represents a promising approach to further understand the genetic factors contributing to drug response.
A self-supervised learning strategy for postoperative brain cavity segmentation simulating resections (2021)

We present a self-supervised learning strategy for 3D CNNs using simulated RCs to accurately segment real RCs on postoperative MRI. Our method generalizes well to data from different institutions, pathologies and modalities. Source code, segmentation models and the EPISURG dataset are available at https://github.com/fepegar/resseg-ijcars .
Problems and emerging approaches in HIV/AIDS vaccine development (2007)

According to recent estimates, 39.5 million people have been infected with HIV and 2.9 million have already died. The effect of HIV infection on individuals and communities is socially and economically devastating. Although antiretroviral drugs have had a dramatically beneficial impact on HIV-infected individuals who have access to treatment, it has had a negligible impact on the global epidemic. Therefore, the need for an efficacious HIV/AIDS vaccine remains the highest priority of the world HIV/AIDS agenda. The generation of a vaccine against HIV/AIDS has turned out to be extremely challenging, as indicated by > 20 years of unsuccessful attempts. This review discusses the major challenges in the field and key experimental evidence providing a rationale for the use of non-structural HIV proteins, such as Rev, Tat and Nef, either in the native form or expressed by viral vectors such as a replicating adeno-vector. These non-structural proteins alone or in combination with modified structural HIV-1 Env proteins represent a novel strategy for both preventative and therapeutic HIV/AIDS vaccine development.
CHAPTER 11: Detection of <i>Pseudomonas syringae</i> pv. <i>phaseolicola</i> in Bean Seeds (2017)

Halo blight of beans, caused by Pseudomonas syringae pv. phaseolicola (syns. P. savastanoi pv. phaseolicola, P. phaseolicola), is the most destructive disease of garden beans worldwide. Pathogen-contaminated seed is the primary source of inoculum, and planting pathogen-free seed and using host resistance are the most effective strategies for disease management. The pathogen survives in infected plant residue and can spread to healthy plants through splashing rain or irrigation water droplets. Disease symptoms, management methods, and protocols for pathogen detection are included in this chapter.
GATA elements are necessary for the activity and tissue specificity of the T-cell receptor beta-chain transcriptional enhancer. (1994)

Three high-affinity binding sites for the GATA family of transcriptional regulators have been identified within the T-cell receptor beta-chain (TCR beta) transcriptional enhancer, and their functional significance has been determined in an effort to understand the T-cell specificity of the enhancer more fully. One site, TE4, is important for activity of the enhancer in T cells. Neither site TE1 nor site TE2 can functionally replace a mutated TE4 site in T cells; however, the same protein, probably GATA-3, binds all three sites, as judged by electrophoretic mobility shift, oligonucleotide competition, and proteolytic clipping assays. These data suggest that additional proteins are critical for the ability of GATA-3 to activate the TCR beta enhancer. In fibroblasts, the GATA sequence at site TE1 appears to bind a negative regulator. Since this is not true in B cells, B cells and fibroblasts appear to have different mechanisms for negative regulation of the TCR beta enhancer.
A Modified Drift Tube Ion Mobility-Mass Spectrometer for Charge-Multiplexed Collision-Induced Unfolding (2019)

Collision-induced unfolding (CIU) of protein ions and their noncovalent complexes offers relatively rapid access to a rich portfolio of biophysical information, without the need to tag or purify proteins prior to analysis. Such assays have been characterized extensively for a range of therapeutic proteins, proving exquisitely sensitive to alterations in protein sequence, structure, and post-translational modification state. Despite advantages over traditional probes of protein stability, improving the throughput and information content of gas-phase protein unfolding assays remains a challenge for current instrument platforms. In this report, we describe modifications to an Agilent 6560 drift tube ion mobility-mass spectrometer in order to perform robust, simultaneous CIU across all precursor ions detected. This approach dramatically increases the speed associated with typical CIU assays, which typically involve mass selection of narrow m/ z regions prior to collisional activation, and thus their development requires a comprehensive assessment of charge-stripping reactions that can unintentionally pollute CIU data with chemical noise when more than one precursor ion is allowed to undergo simultaneous activation. By studying the unfolding and dissociation of intact antibody ions, a key analyte class associated with biotherapeutics, we reveal a predictive relationship between the precursor charge state, the amount of buffer components bound to the ions of interest, and the amount of charge stripping detected. We then utilize our knowledge of antibody charge stripping to rapidly capture CIU data for a range of antibody subclasses and subtypes across all charge states simultaneously, demonstrating a strong charge state dependence on the information content of CIU. Finally, we demonstrate that CIU data collection times can be further reduced by scanning fewer voltage steps, enabling us to optimize the throughput of our improved CIU methods and confidently differentiate antibody variant ions using ∼20% of the data typically collected during CIU. Taken together, our results characterize a new instrument platform for biotherapeutic stability measurements with dramatically improved throughput and information content.
Angiotensin II receptor I auto-antibodies following SARS-CoV-2 infection (2021)

These findings support an association between COVID-19 and AT1R-Ab, emphasizing that vascular pathology may be present in individuals with mild COVID-19 as well as those with severe disease.
A way to fast response and high power density - synthesis of soft-switching dual-quasi-square-wave (DQSW) DC-DC converters (2004)

A synthesis approach for dual-quasi-square-wave (DQSW) transformer-isolated DC-DC converters is proposed. The converters possess low stresses and can achieve soft switching. The required volume of passive components is smaller than that of the conventional transformer-isolated DC-DC converters with the same power rating. These features make them more attractive for the fast-response and high-power-density applications. Analyses of three new converters are performed as examples of the DQSW converter family. Simulations and experiments verified the theoretical principle.
Development of a high-current laser ion source for induction accelerators (2000)

We have developed a high-current laser ion source that can provide low-charge-state ions for induction accelerators. A frequency-doubled Nd:YAG laser (λ=532 nm) irradiated a copper target with relatively low intensities of 108–109 W/cm2. The laser-produced plasma supplied a large number of Cu+ and Cu2+ ions over 1014 ions/cm2 at a distance of 10 cm from the target. We have successfully extracted high-current copper beams over 0.1 A/cm2 using an inductive acceleration module. The beam emittance measured by a pepper-pot method was about 40 πmm mrad. © 2000 American Institute of Physics.
Data from Compartmental Analysis of T-cell Clonal Dynamics as a Function of Pathologic Response to Neoadjuvant PD-1 Blockade in Resectable Non–Small Cell Lung Cancer (2023)

&lt;div&gt;AbstractPurpose:&lt;p&gt;Neoadjuvant PD-1 blockade is a promising treatment for resectable non–small cell lung cancer (NSCLC), yet immunologic mechanisms contributing to tumor regression and biomarkers of response are unknown. Using paired tumor/blood samples from a phase II clinical trial (NCT02259621), we explored whether the peripheral T-cell clonotypic dynamics can serve as a biomarker for response to neoadjuvant PD-1 blockade.&lt;/p&gt;Experimental Design:&lt;p&gt;T-cell receptor (TCR) sequencing was performed on serial peripheral blood, tumor, and normal lung samples from resectable NSCLC patients treated with neoadjuvant PD-1 blockade. We explored the temporal dynamics of the T-cell repertoire in the peripheral and tumoral compartments in response to neoadjuvant PD-1 blockade by using the TCR as a molecular barcode.&lt;/p&gt;Results:&lt;p&gt;Higher intratumoral TCR clonality was associated with reduced percent residual tumor at the time of surgery, and the TCR repertoire of tumors with major pathologic response (MPR; &lt;10% residual tumor after neoadjuvant therapy) had a higher clonality and greater sharing of tumor-infiltrating clonotypes with the peripheral blood relative to tumors without MPR. Additionally, the posttreatment tumor bed of patients with MPR was enriched with T-cell clones that had peripherally expanded between weeks 2 and 4 after anti–PD-1 initiation and the intratumoral space occupied by these clonotypes was inversely correlated with percent residual tumor.&lt;/p&gt;Conclusions:&lt;p&gt;Our study suggests that exchange of T-cell clones between tumor and blood represents a key correlate of pathologic response to neoadjuvant immunotherapy and shows that the periphery may be a previously underappreciated originating compartment for effective antitumor immunity.&lt;/p&gt;&lt;p&gt;&lt;i&gt;See related commentary by Henick, p. 1205&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Large‐Area Gold/Parylene Plasmonic Nanostructures Fabricated by Direct Nanocutting (2013)

High-resolution multilayer plasmonic nanostructures are made in a single fabrication step by nanocutting a gold and parylene C bilayer.. A silicon stamp is used to cut the gold film and vertically displace the nanocut shapes into the polymer. Periodic Au nanopatterns in single and double-layer configurations are fabricated down to the sub-100 nm range, supporting plasmon resonances in the visible range.
Molecular Analysis of Factor IX Gene in an Iranian Female with Severe Hemophilia B (2008)

Hemophilia B, a recessive X-linked coagulopathy, is rare in females, and only a few cases have been reported so far. In this report, we describe a 9-year-old female, offspring of a consanguineous marriage, with a clinically severe course of hemophilia B and a normal 46,XX karyotype. Polymerase chain reaction and conformation sensitive gel electrophoresis techniques have been applied to the important regions of the factor IX gene,and an abnormal conformation sensitive gel electrophoresis profile was identified in exon 5 of the gene. After sequencing, the mutation was found to be C17761T (R116X) in homozygous form. Then, polymerase chain reaction-restriction fragment length polymorphism using the EcoRV restriction enzyme was applied for confirmation of the homozygous mutation in the proband and for carrier testing in the relatives. In addition, haplotype analysis was informative at the HhaI polymorphic site for the female patient.
Differentiated Service Class Recommendations for LLN Traffic (2015)

Differentiated services architecture is widely deployed in traditional
networks. There exist well defined recommendations for the use of
appropriate differentiated service classes for different types of
traffic (eg. audio, video) in these networks. Per-Hop Behaviors are
typically defined based on this recommendations. With emerging Low-
power and Lossy Networks (LLNs), it is important to have similar
defined differentiated services recommendations for LLN traffic.
Defined recommendations are for LLN class of traffic exiting out of
LLNs towards high-speed backbones, converged campus network and for
the traffic in the reverse direction.
THE INTAKE OF OLIVE OIL PHENOLIC COMPOUNDS PROMOTES MACROPHAGE-SPECIFIC REVERSE CHOLESTEROL TRANSPORT IN VIVO (2019)

Trabajo presentado en el 87th European Atherosclerosis Society (EAS) Congress, celebrado en Maastricht (Holanda), del 26 al 29 de mayo de 2019