gebhart/patrepeval huggingface dataset:
Comparative systems pharmacology of HIF stabilization in the prevention of retinopathy of prematurity (2016)

Retinopathy of prematurity (ROP) causes 100,000 new cases of childhood blindness each year. ROP is initiated by oxygen supplementation necessary to prevent neonatal death. We used organ systems pharmacology to define the transcriptomes of mice that were cured of oxygen-induced retinopathy (OIR, ROP model) by hypoxia-inducible factor (HIF) stabilization via HIF prolyl hydroxylase inhibition using the isoquinolone Roxadustat or the 2-oxoglutarate analog dimethyloxalylglycine (DMOG). Although both molecules conferred a protective phenotype, gene expression analysis by RNA sequencing found that Roxadustat can prevent OIR by two pathways: direct retinal HIF stabilization and induction of aerobic glycolysis or indirect hepatic HIF-1 stabilization and increased serum angiokines. As predicted by pathway analysis, Roxadustat rescued the hepatic HIF-1 knockout mouse from retinal oxygen toxicity, whereas DMOG could not. The simplicity of systemic treatment that targets both the liver and the eye provides a rationale for protecting the severely premature infant from oxygen toxicity.
Nonlinear and Quantum Optics with Whispering Gallery Resonators (2015)

Whispering Gallery Mode resonators made from optically nonlinear crystals have small mode volume and extremely high quality factor which makes them ideal for various nonlinear conversion process at low power, ultimately at single photon level.
Strength of High Performance Glass Reinforcement Fiber (2012)

The practical strength of glass is highly dependent on the amount and type of damage that a glass article has experienced in its lifetime and can be 50% less than its theoretical strength. Glass reinforcement fibers in the pristine state exhibit some of the highest failure strengths of any glass form. Strength degradation is a sequential process the further from the point of formation a glass travels. Individual filament strength is important in the manufacturing process as the fiber interacts with water, HVAC , sizing applicators, contact shoes, and guide eyes and ultimately this combination impacts productivity. A discussion of glass fiber strength — pristine versus usable, and the effects of temperature, humidity, and composition on glass strength follows in this manuscript. New data collected in Owens Corning's Glass Properties Laboratory on the effect of temperature and relative humidity on strength and modulus for Advantex ® glass, Owens Corning's S‐glass (XStrand ® S, FliteStrand ® S, and ShieldStrand ® S) and H‐glass (WindStrand ® H) are presented. Owens Corning's understanding of the effect of composition on strength and modulus, and particularly how individual oxides contribute to these properties are shared.
Photon Logic Gates Using Ultraslow Light (2009)

Photon logic gates are observed using ultraslow light. The building block of the photon logic gate is photon routing phenomenon, where the routing is based on atomic coherence enhanced by ultraslow light.
MUTZ-3, a human cell line model for the cytokine-induced differentiation of dendritic cells from CD34+precursors (2002)

Many human myeloid leukemia-derived cell lines possess the ability to acquire a dendritic cell (DC) phenotype. However, cytokine responsiveness is generally poor, requiring direct manipulation of intracellular signaling mechanisms for differentiation. In contrast, the CD34+ human acute myeloid leukemia cell line MUTZ-3 responds to granulocyte macrophage- colony-stimulating factor (GM-CSF), interleukin 4 (IL-4), and tumor necrosis factor alpha (TNFalpha), cytokines known to be pivotal both in vivo and in vitro for DC generation from monocytes and CD34+ stem cells. In all respects, MUTZ-3 cells behave as the immortalized equivalent of CD34+ DC precursors. Upon stimulation with specific cytokine cocktails, they acquire a phenotype consistent with either interstitial- or Langerhans-like DCs and upon maturation (mDC), express CD83. MUTZ-3 DC display the full range of functional antigen processing and presentation pathways. These findings demonstrate the unique suitability of MUTZ-3 cells as an unlimited source of CD34+ DC progenitors for the study of cytokine-induced DC differentiation.
Chemical modification of fortimicins II. Selective protection of fortimicins A and B. (1981)

The four amino groups of fortimicin B(4) could be differentiated from each other and 2'-N-benzyloxycarbonyl-, 2',6'-di-N-benzyloxycarbonyl-, 2'-N-tert-butoxycarbonyl-, 6'-N-tert-butoxycarbonyl- and 2',6'-di-N-tert-butoxycarbonyl-fortimicin B (7, 8, 16, 18, 17) were prepared from 4. From these fortimicin B derivatives, selectively protected fortimicin A derivatives 13, 15, 21, 22 and 25 were prepared by combination of procedures of benzyloxycarbonylation or tert-butoxycarbonylation, 4-N-glycylation.
Investigation of Post-Bond Distortion in Direct Wafer Bonding (2020)

Direct wafer bonding process is used in semiconductor manufacturing for heterogeneous integration of devices. When two silicon wafers are directly bonded together, the alignment along the bonded interface is critical to device performance and yield. This paper studies the relative alignment, or post-bond distortion, of a direct wafer bonding process using finite element simulation method. The methodology of constructing a 2D axisymmetric model to calibrate a 3D model is discussed. The simulation results showed that the post-bond distortion was sensitive to upper wafer pre-bond shapes and does not depend on lower wafer shapes. The simulation models enable reduced hardware development costs and time.
Passive millimeter-wave imaging (2003)

This article introduces the concept of passive millimeter-wave (PMMW) imaging, describes the phenomenology that defines its performance, explains the technology advances that have made these systems a reality, and presents some of the missions in which these sensors can be used.
Using frequency‐labeled exchange transfer to separate out conventional magnetization transfer effects from exchange transfer effects when detecting ParaCEST agents (2012)

Paramagnetic chemical exchange saturation transfer agents combine the benefits of a large chemical shift difference and a fast exchange rate for sensitive MRI detection. However, the in vivo detection of these agents is hampered by the need for high B(1) fields to allow sufficiently fast saturation before exchange occurs, thus causing interference of large magnetization transfer effects from semisolid macromolecules. A recently developed approach named frequency-labeled exchange transfer utilizes excitation pulses instead of saturation pulses for detecting the exchanging protons. Using solutions and gel phantoms containing the europium (III) complex of DOTA tetraglycinate (EuDOTA-(gly)(-) (4) ), it is shown that frequency-labeled exchange transfer allows the separation of chemical exchange effects and magnetization transfer (MT) effects in the time domain, therefore allowing the study of the individual resonance of rapidly exchanging water molecules (k(ex) >10(4) s(-1) ) without interference from conventional broad-band MT.
Sortilin mediates vascular calcification via its recruitment into extracellular vesicles (2016)

Vascular calcification is a common feature of major cardiovascular diseases. Extracellular vesicles participate in the formation of microcalcifications that are implicated in atherosclerotic plaque rupture; however, the mechanisms that regulate formation of calcifying extracellular vesicles remain obscure. Here, we have demonstrated that sortilin is a key regulator of smooth muscle cell (SMC) calcification via its recruitment to extracellular vesicles. Sortilin localized to calcifying vessels in human and mouse atheromata and participated in formation of microcalcifications in SMC culture. Sortilin regulated the loading of the calcification protein tissue nonspecific alkaline phosphatase (TNAP) into extracellular vesicles, thereby conferring its calcification potential. Furthermore, SMC calcification required Rab11-dependent trafficking and FAM20C/casein kinase 2-dependent C-terminal phosphorylation of sortilin. In a murine model, Sort1-deficiency reduced arterial calcification but did not affect bone mineralization. Additionally, transfer of sortilin-deficient BM cells to irradiated atherosclerotic mice did not affect vascular calcification, indicating a primary role of SMC-derived sortilin. Together, the results of this study identify sortilin phosphorylation as a potential therapeutic target for ectopic calcification/microcalcification and may clarify the mechanism that underlies the genetic association between the SORT1 gene locus and coronary artery calcification.
Transfer RNA recognition by class I lysyl‐tRNA synthetase from the Lyme disease pathogen <i>Borrelia burgdorferi</i> (2005)

Borrelia burgdorferi and other spirochetes contain a class I lysyl-tRNA synthetase (LysRS), in contrast to most eubacteria that have a canonical class II LysRS. We analyzed tRNA(Lys) recognition by B. burgdorferi LysRS, using two complementary approaches. First, the nucleotides of B. burgdorferi tRNA(Lys) in contact with B. burgdorferi LysRS were determined by enzymatic footprinting experiments. Second, the kinetic parameters for a series of variants of the B. burgdorferi tRNA(Lys) were then determined during aminoacylation by B. burgdorferi LysRS. The identity elements were found to be mostly located in the anticodon and in the acceptor stem. Transplantation of the identified identity elements into the Escherichia coli tRNA(Asp) scaffold endowed lysylation activity on the resulting chimera, indicating that a functional B. burgdorferi lysine tRNA identity set had been determined.
Development of an Individual Device for Exhaled Breath Temperature Measurement (2009)

Different thermometers have been constructed over the decades to measure the temperature of the body to help detect and monitor morbid states. They yield slightly different estimates of the core body temperature depending on the proximity of the measurement site to the internal milieu of the organism, the principle of temperature assessment, and the specific characteristics of the gauging devices. Evaluation of the exhaled breath temperature (EBT) has been recently suggested as a new method to detect inflammatory processes in the conducting airways due to changes in the blood flow perfusion of their walls and adjacent structures. While the first reported EBT experiments required sealed laboratory environment and sophisticated equipment, we designed a simple handheld instrument for EBT measurement and proven its precision, reproducibility and validity in subjects with asthma. We now describe the construction principles of our instrument, the procedure to test the fitness for purpose of the separate units and the novel features of the newest prototypes outfitted with microprocessor and memory. We also outline the potential clinical applications of an individual device for EBT measurement.
Nondestructive Evaluation of Adhesive Bonds via Ultrasonic Phase Measurements (2016)

The use of advanced composites utilizing adhesively bonded structures offers advantages in weight and cost for both the aerospace and automotive industries. Conventional nondestructive evaluation (NDE) has proved unable to reliably detect weak bonds or bond deterioration during service life conditions. A new nondestructive technique for quantitatively measuring adhesive bond strength is demonstrated. In this paper, an ultrasonic technique employing constant frequency pulsed phased-locked loop (CFPPLL) circuitry to monitor the phase response of a bonded structure from change in thermal stress is discussed. Theoretical research suggests that the thermal response of a bonded interface relates well with the quality of the adhesive bond. In particular, the effective stiffness of the adhesive-adherent interface may be extracted from the thermal phase response of the structure. The sensitivity of the CFPPLL instrument allows detection of bond pathologies that have been previously difficult-to-detect. Theoretical results with this ultrasonic technique on single epoxy lap joint (SLJ) specimens are presented and discussed. This technique has the potential to advance the use of adhesive bonds - and by association, advanced composite structures - by providing a reliable method to measure adhesive bond strength, thus permitting more complex, lightweight, and safe designs.
A PCR Marker for Growth Habit in Common Wheat Based on Allelic Variation at the <i>VRN‐A1</i> Gene (2004)

Growth habit varies among accessions of hexaploid wheat ( Triticum aestivum L.). The winter habit genotype (homozygous recessive for vrn‐A1 , vrn‐B1 , vrn‐D1 ) requires a cold treatment to induce flowering and is generally planted in the fall. Spring habit genotypes flower in the absence of a vernalization treatment. Spring habit is conferred by a dominant allele at any of the three VRN‐1 loci, but varieties carrying the VRN‐A1 locus are the most frequent and usually flower earlier. To facilitate selection in populations segregating at the VRN‐A1 locus and to assist in genotyping wheat accessions of unknown VRN‐1 composition, a PCR‐based marker for growth habit would be useful. The VRN‐A1 gene was recently cloned allowing for the development of markers for growth habit. In this report, we designed primer sets specific for the VRN‐A1 locus, and used them to amplify an 810‐bp segment of the VRN‐A1 gene between intron 4 and exon 8 from 40 spring wheat lines and 37 winter wheat lines. Three diagnostic nucleotide changes were identified that differentiated the dominant Vrn‐A1 and recessive vrn‐A1 alleles in 75 out of the 77 genotypes analyzed in this study. One of these differences resulted in the presence of an additional Aci I restriction site in the allele for spring growth habit. This difference was exploited to develop a cleavage amplification polymorphic sequence (CAPS) that can be used to determine the allelic state at VRN‐A1 in germplasm collections, and as a marker in backcross breeding projects. An additional pair of dominant markers was developed from a different polymorphism.
Jones phase microscopy of transparent and anisotropic samples (2008)

We developed an interferometric microscopy technique, referred to as Jones phase microscopy, capable of extracting the spatially resolved Jones polarization matrix associated with transparent and anisotropic samples. This is a generalization of quantitative phase imaging, which is recovered from one diagonal element of the measured matrix. The principle of the technique is demonstrated with measurements of a liquid crystal spatial light modulator and the potential for live cell imaging with experiments on live neurons in culture.
Characterization of <i>TMPRSS2</i> -ETS Gene Aberrations in Androgen-Independent Metastatic Prostate Cancer (2008)

Recurrent gene fusions between the androgen-regulated gene TMPRSS2 and the ETS transcription factor family members ERG, ETV1, and ETV4 have been identified as a critical event in prostate cancer development. In this study, we characterized the prevalence and diversity of these rearrangements in hormone-refractory metastatic prostate cancer. We used a fluorescence in situ hybridization (FISH) split probe strategy to comprehensively evaluate TMPRSS2-ETS aberrations across 97 nonosseous metastatic sites of prostate cancer from 30 rapid autopsies of men who died of androgen-independent disease. Tissue microarrays were constructed representing multiple metastatic sites from each patient, and split signal FISH probes for TMPRSS2, ERG, ETV1, and ETV4 were used to assess for TMPRSS2-ETS rearrangements. In patients exhibiting these aberrations, multiple sites from an individual case harbored the same gene fusion molecular subtype suggesting clonal expansion of disease. The most common prostate cancer gene fusion, TMPRSS2-ERG, can be generated by the mechanism of interstitial deletion (Edel) about 39% to 60% of the time in clinically localized disease. Interestingly, we observed that all of the androgen-independent metastatic prostate cancer sites harboring TMPRSS2-ERG were associated with Edel. These findings suggest that TMPRSS2-ERG with Edel is an aggressive and, in this study, uniformly lethal molecular subtype of prostate cancer associated with androgen-independent disease.
Ammonia‐based intermittent aeration control optimized for efficient nitrogen removal (2015)

This work describes the development of an intermittently aerated pilot-scale process (V = 0.45 m(3) ) operated for optimized efficient nitrogen removal in terms of volume, supplemental carbon and alkalinity requirements. The intermittent aeration pattern was controlled using a strategy based on effluent ammonia concentration set-points. The unique feature of the ammonia-based aeration control was that a fixed dissolved oxygen (DO) set-point was used and the length of the aerobic and anoxic time (anoxic time ≥25% of total cycle time) were changed based on the effluent ammonia concentration. Unlike continuously aerated ammonia-based aeration control strategies, this approach offered control over the aerobic solids retention time (SRT) to deal with fluctuating ammonia loading without solely relying on changes to the total SRT. This approach allowed the system to be operated at a total SRT with a small safety factor. The benefits of operating at an aggressive SRT were reduced hydraulic retention time (HRT) for nitrogen removal. As a result of such an operation, nitrite oxidizing bacteria (NOB) out-selection was also obtained (ammonia oxidizing bacteria [AOB] maximum activity: 400 ± 79 mgN/L/d, NOB maximum activity: 257 ± 133 mgN/L/d, P < 0.001) expanding opportunities for short-cut nitrogen removal. The pilot demonstrated a total inorganic nitrogen (TIN) removal rate of 95 ± 30 mgN/L/d at an influent chemical oxygen demand: ammonia (COD/NH4 (+) -N) ratio of 10.2 ± 2.2 at 25°C within the hydraulic retention time (HRT) of 4 h and within a total SRT of 5-10 days. The TIN removal efficiency up to 91% was observed during the study, while effluent TIN was 9.6 ± 4.4 mgN/L. Therefore, this pilot-scale study demonstrates that application of the proposed on-line aeration control is capable of relatively high nitrogen removal without supplemental carbon and alkalinity addition at a low HRT.
Multispectral image enhancement for H&E stained pathological tissue specimens (2008)

The presence of a liver disease such as cirrhosis can be determined by examining the proliferation of collagen fiber from a tissue slide stained with special stain such as the Masson's trichrome(MT) stain. Collagen fiber and smooth muscle, which are both stained the same in an H&E stained slide, are stained blue and pink respectively in an MT-stained slide. In this paper we show that with multispectral imaging the difference between collagen fiber and smooth muscle can be visualized even from an H&E stained image. In the method <i>M</i> KL bases are derived using the spectral data of those H&E stained tissue components which can be easily differentiated from each other, i.e. nucleus, cytoplasm, red blood cells, etc. and based on the spectral residual error of fiber weighting factors are determined to enhance spectral features at certain wavelengths. Results of our experiment demonstrate the capability of multispectral imaging and its advantage compared to the conventional RGB imaging systems to delineate tissue structures with subtle colorimetric difference.
Differences in Renal Tubule Primary Cilia Length in a Mouse Model of Bardet-Biedl Syndrome (2007)

Lacking Bbs4 does not lead to aberrant cilia or basal body structure. However, the dynamics of cilia assembly is altered in Bbs4(-/-) cells, suggesting a role for Bbs4 in the regulation of ciliary assembly.
Divergent Oriented Synthesis For the Design of Reagents for Protein Conjugation (2009)

Instead of using diversity oriented syntheses (DOS) to obtain compounds with biological activities, we employed the DOS method to efficiently obtain multifunctional single attachment point (MSAP) reagents for the conjugation to proteins. Acid insensitive functional groups (chelators, fluorochromes) were attached to Lys-Cys-NH(2) or Lys-Lys-betaAla-Cys-NH(2) peptide scaffolds. After cleavage from solid supports, the modified peptide intermediates were split and further modified by two solution phase, chemoselective reactions employing the single amine and single thiol presented on the intermediates. MSAP-based fluorochrome-chelates were obtained, some possessing a third functional group like a polyethylene glycol (PEG) polymer or "click chemistry" reactive alkynes and azides. The DOS of MSAP reagents permitted the efficient generation of panels of MSAP reagents that can be used to obtain multifunctional proteins with a single modified amino acid (a single attachment point).
High-Emittance and Low-Brightness Electron Gun for Reducing-Image Projection System: Computer Simulation (1997)

The required electron gun characteristics for a reducing-image projection system so that the emittance is much larger than 187 µ m· mrad and the brightness is variable around 7.3×10 4 A/cm 2 sr are estimated. For an electron gun with flat cathode, Wehnelt, control-anode and anode electrodes, an emittance of more than 1000 µ m· mrad is obtained by optimization of the cathode to control anode distance, the control-anode radius and the Wehnelt electrode shape. The brightness is variable from 3.9×10 4 to 9×10 4 A/cm 2 sr by control of the control-anode voltage. The optimum control-anode radius increases and the brightness tends to decrease with increasing cathode to control-anode distance. The angle between the beam edge and Wehnelt electrode is optimum at about 62°, which is smaller than the well-known 67.5° in a Pierce-type electron gun.
Molecular evolutionary engineering of xylose isomerase to improve its catalytic activity and performance of micro-aerobic glucose/xylose co-fermentation in Saccharomyces cerevisiae (2019)

This study demonstrated that <i>Lp</i>XI has the highest d-xylose consumption rate among the XIs expressed in IR-2 under micro-aerobic co-fermentation conditions. A combination of novel mutations (T63I and V162A) significantly improved the enzymatic activity of <i>Lp</i>XI, indicating that <i>Lp</i>XI-<i>T63I/V162A</i> would be a potential construct for highly efficient production of cellulosic ethanol.
Automatic sleep apnoea detection using measures of amplitude and heart rate variability from the electrocardiogram (2003)

A method for the automatic processing of the electrocardiogram (ECG) for the detection of disordered breathing associated with obstructive sleep apnoea is presented. The method provides a minute-by-minute analysis of night-time single lead ECG recordings. An independently validated database of 35 ECG recordings acquired from normal subjects and subjects with obstructive and mixed sleep apnoea, each of approximately eight hours in duration, was used throughout the study. A wide variety of features based on heart beat intervals and an electrocardiogram derived respiratory signal were considered. Classifiers based on linear and quadratic discriminants were used. Results show that a 90% success rate in correctly identifying one-minute segments containing disordered breathing is achievable.
Extremely Broad-gain Quantum-Cascade Lasers based on Dual-upper-state design (2011)

Broad-gain quantum cascade lasers based on dual-upper-state design are reported. The devices exhibit a wide (~570 cm-1) electroluminescence spectra, a low cw threshold-current-density of 1.5 kA/cm2 and a high cw output-power of ~200 mW at 300 K.