gebhart/patrepeval huggingface dataset:
Fundamental mechanisms of laser-induced damage in optical materials: today’s state of understanding and problems (2014)

Theoretical models of laser-induced damage mechanisms in optical materials are reviewed: inclusioninitiated thermal explosion (extrinsic mechanism) and impact ionization (II) and photoionization (intrinsic mechanisms). Different approaches to II theory based on quantum kinetic equation, Boltzman equations, and rate equations are briefly described. A relative contribution of II and photoionization predicted by these models at different laser pulse durations, including femtosecond-range, are discussed and compared with available experimental data. Basing on an analysis of published theoretical and experimental results, a today's state of understanding fundamental laser damage mechanisms is concluded.
Online Denoising Solutions for Forecasting Applications (2016)

Dealing with noisy time series is a crucial task in many data-driven real-time applications. Due to the inaccuracies in data acquisition, time series suffer from noise and instability which leads to inaccurate forecasting results. Therefore, in order to improve the performance of time series forecasting, an important pre-processing step is the denoising of data before performing any action. In this research, we will propose various approaches to tackle the noisy time series in forecasting applications. For this purpose, we use different machine learning methods and information theoretical approaches to develop online denoising algorithms. In this dissertation, we propose four categories of time series denoising methods that can be used in different situations, depending on the noise and time series properties. In the first category, a seasonal regression technique is proposed for the denoising of time series with seasonal behavior. In the second category, multiple discrete universal denoisers are developed that can be used for the online denoising of discrete value time series. In the third category, we develop a noisy channel reversal model based on the similarities between time series forecasting and data communication and use that model to deploy an out-of-band noise filtering in forecasting applications. The last category of the proposed methods is deep-learning based denoisers. We use information theoretic concepts to analyze a general feed-forward deep neural network and to prove theoretical bounds for deep neural networks behavior. Furthermore, we propose a denoising deep neural network method for the online denoising of time series. Real-world and synthetic time series are used for numerical experiments and performance evaluations. Experimental results show that the proposed methods can efficiently denoise the time series and improve their quality.
New aspects of through-casing resistivity theory (1998)

Abstract A closed-form solution for a basic model of the through-casing resistivity measurement is found. The solution reveals fundamental characteristics of the measurement and the dependence of these characteristics on the parameters of the casing and formation. We start our consideration with an analysis of the current distribution in the vicinity of a single electrode energizing the casing. This analysis shows that the distribution becomes axially symmetrical at a distance of just a few radii from the injection point. As a consequence, the number and the physical location of the electrodes used to inject electric current become unimportant if the measurement electrodes are not placed too close to the sensing electrodes. We also derive a closed-form solution for the distribution of the current flowing in a homogeneous casing embedded in a homogeneous formation. This consideration results in an expression specifying the so-called characteristic length. The electric field potential is analyzed as a function of the vertical and radial distances from the current injection electrode. Explicit closed-form expressions are derived for the electric potential distribution at a distance that is greater or less than the characteristic length. A transition from a cylindrical to spherical pattern of the current flow occurs at a radial distance controlled by the characteristic length. This phenomenon bounds the "current tube" resistance. An analytical result is also found for the casing surrounded with a homogeneous cement sheath. The concept of the characteristic length is related closely to the geometrical factor of the through-casing resistivity measurement. It follows from our solution that the geometrical factor displays a significant dependence on the resistivity of the formation and the parameters of the casing. This dependence should be taken into account in the quantitative interpretation of through-casing resistivity logs.
Virulence Inhibition by Zinc in Shiga-Toxigenic <i>Escherichia coli</i> (2011)

Previously, our laboratories reported that zinc inhibited expression of several important virulence factors in enteropathogenic Escherichia coli (EPEC) and reduced EPEC-induced intestinal damage in vivo. Since EPEC is genetically related to Shiga-toxigenic E. coli (STEC), we wondered whether the beneficial effects of zinc extended to STEC as well. Treatment options for STEC infection are very limited, since antibiotics tend to exacerbate disease via enhanced toxin production, so a safe intervention for this infection would be welcome. In this study, we report that in STEC strains zinc inhibits adherence to cultured cells as well as expression of EHEC secreted protein A (EspA). In addition, zinc inhibits the expression of Shiga toxin (Stx) at both the protein and the RNA level. Zinc inhibits basal and antibiotic-induced Stx production and inhibits both Stx1 and Stx2 by ≥90% at a concentration of 0.4 mM zinc. Rabbit EPEC strains were selected for acquisition of Stx-encoding bacteriophages, and these rabbit STEC strains (designated RDEC-H19A and E22-stx2) were used to test the effects of zinc in vivo in ligated rabbit intestinal loops. In vivo, zinc reduced fluid secretion into loops, inhibited mucosal adherence, reduced the amount of toxin in the loops, and reduced STEC-induced histological damage (villus blunting). Zinc has beneficial inhibitory effects against STEC strains that parallel those observed in EPEC. In addition, zinc strongly inhibits Stx expression; since Stx is responsible for the extraintestinal effects of STEC infection, such as hemolytic-uremic syndrome (HUS), zinc might be capable of preventing severe sequelae of STEC infection.
Experimental and Modeling Investigations of Biomass Particle Combustion (2006)

GRADUATE COMMITTEE APPROVAL of a dissertation submitted by Hong Lu This dissertation has been read by each member of the following graduate committee and by majority vote has been found to be satisfactory.
TSV technology for 2.5D IC solution (2012)

TSV (Through Silicon Via) is the key enabling technology for 2.5D & 3D IC packaging solution. As the 2.5D interposer design pushing towards smaller & shorter via due to I/O density and electrical performance, the warpage of thinner interposer is therefore much more challenging in thin wafer handling and assembly process. In this presentation, a TSV structure is introduced with fabricated interposer prototype, and could be assembled together with single-die/multi-chip on a substrate. The demonstrated interposer assembled in FCBGA (Flip Chip Ball Grid Array) has covered features such as low temperature fabrication process, low warpage, and low leakage with minimized TSV parasitic parameters. Electrical and stress characterizations, current density characterization up to 1100mA and Shadow Moiré are performed and compared with simulation models for correlation study. Known-Good TSV and Si interposer are also reviewed and discussed in this presentation. Full validated reliability test, both die and package level, in conjunction with board level drop test, are presented to verify interposer fabrication, assembly process optimization, and interconnection stability.
Corn Distillers Grains versus a Blend of Protein Supplements with or without Ruminally Protected Amino Acids for Lactating Cows (2000)

In a replicated 4 x 4 Latin square design with 4-wk periods, we used 12 multiparous Holstein cows averaging 83 d postpartum to compare corn distillers grains (CDG) versus a blend (BLEND) of other protein sources with CDG (fish meal and soybean meal), and to determine the effectiveness of ruminally protected lysine and methionine (RPLM) in improving the utilization of CDG as a protein supplement for lactating cows. The 2 x 2 factorial arrangement of treatments was as follows: CDG diet, CDG diet plus RPLM, BLEND diet, and BLEND diet plus RPLM. All diets contained 30% corn silage, 20% alfalfa hay, and 50% the respective corn-based concentrate mixture. The array of amino acids available for absorption when cows were fed the BLEND diet was more desirable than for the CDG diet according to Milk Protein Score and Cornell Net Carbohydrate and Protein System. Dry matter intakes were similar among all diets. Milk yields (32.6, 31.7, 32.8, and 32.8 kg/d, respectively) were similar for cows fed all diets. Milk fat yields and percentages (3.72, 3.76, 3.67, and 3.63%) were unaffected by diet, but milk protein percentages (3.23, 3.26, 3.25, and 3.26%) tended to be higher when fed RPLM. Concentrations of most protein fractions in milk were similar for all diets, although beta-lactoglobulin was increased slightly when cows were fed BLEND diets. Lysine, Met, and Phe were indicated as the most limiting amino acids for all diets according to extraction efficiency and transfer efficiency of amino acid from blood by the mammary gland. Methionine status was apparently improved by RPLM supplementation; Lys status was improved by the BLEND diets. Milk yield and composition when cows were fed CDG were not further improved by feeding blends of protein sources or RPLM; however, such dietary changes improved Lys and Met status of the cows.
Ternary TiAlGe ohmic contacts for <i>p</i>-type 4H-SiC (2004)

Reduction of annealing temperature to prepare low resistance ohmic contact materials for p-type 4H-SiC was achieved by adding Ge to the conventional TiAl contacts. Although the binary TiAl contact is required to anneal at temperature as high as 1000 °C to convert Schottky to ohmic behavior after deposition of the Ti and Al layers on the SiC substrate, the GeTiAl contacts provided the specific contact resistance of about 1×10−4 Ω cm2 by annealing at temperature as low as 600 °C. This low annealing temperature is desirable to reduce the gate leakage current of the SiC devices. The GeTiAl ohmic contacts were thermally stable during isothermal annealing at 400 °C subsequently after preparing the ohmic contacts by annealing at 600 °C, which is also required by the device packaging process.
Mechanism of large-scale flow reversals in turbulent thermal convection (2018)

It is commonly believed that heat flux passing through a closed thermal convection system is balanced so that the convection system can remain at a steady state. Here, we report a new kind of convective instability for turbulent thermal convection, in which the convective flow stays over a long steady "quiet period" having a minute amount of heat accumulation in the convection cell, followed by a short and intermittent "active period" with a massive eruption of thermal plumes to release the accumulated heat. The rare massive eruption of thermal plumes disrupts the existing large-scale circulation across the cell and resets its rotational direction. A careful analysis reveals that the distribution of the plume eruption amplitude follows the generalized extreme value statistics with an upper bound, which changes with the fluid properties of the convecting medium. The experimental findings have important implications to many closed convection systems of geophysical scale, in which massive eruptions and sudden changes in large-scale flow pattern are often observed.
Three-dimensional particle-in-cell simulations of rapid start-up in strapped oven magnetrons due to variation in the insulating magnetic field (2004)

A three-dimensional parallel particle-in-cell code, ICEPIC, is used to simulate the geometry and the magnetic field profiles of the recent low-noise, fast startup magnetron experiments at the University of Michigan. The fast startup, the power levels, and the starting currents that have been observed in these experiments are quantitatively reproduced in the simulations. The tendency for low noise operation has also been reproduced with the use of an azimuthally varying magnetic field.
First-in-human dose-escalation safety and PK trial of a novel intravenous humanized monoclonal CovX body inhibiting angiopoietin 2. (2010)

2524 Background: CVX-060 is a recombinant humanized monoclonal antibody fused to two angiopoietin-2 (Ang2) binding peptides. In preclinical studies, CVX-060 is antiangiogenic and decreases tumor proliferation. Methods: In stage 1, pts with solid tumors received escalating doses of CVX-060 in cohorts of 3-6 pts at the following doses: 0.3, 1, 3, 6, 12, or 15 mg/kg. An additional 13 pts were treated at the 15 mg/kg dose in stage 2. CVX-060 was given once weekly in 4 week cycles as a 90 min IV infusion, decreased to 30 min as tolerated. DLTs were defined as ≥ Gr 3 AEs unrelated to tumor progression in cycle 1. Serum PK was assessed by ELISA. DCE-MRI were conducted pre- dose, Day 4, and Day 28, in pts at 3 mg/kg and higher. Results: Complete data are available on 30 of 34 pts who were enrolled in the study. Among the 30 pts (19F/11M), the median age was 65 years (21-90), ECOG performance status 0-1. Drug exposure in pts ranged from 6-407 days (median 49 days). One pt in the 0.3 mg/kg cohort experienced a DLT (Gr 3 back pain). The most common AE was fatigue (23%).The MTD was not defined. There were 5 (17%) pts with proteinuria (one with Gr 3 and the rest Gr 1-2) and 2 (7%) pts with Gr 1 hemorrhage (vaginal spotting). Cmax and AUC increased linearly with dose, with mean ß t1/2 of 5.5 days. Total serum Ang2 (bound plus free) increased with escalating doses, plateauing at 15 mg/kg. Patients with the highest baseline Ang2 levels had the highest increases in total Ang2 after treatment. There were significant mean decreases in Ktrans by DCE-MRI at Day 4 (p=0.034) and Day 28 (p=0.0025) in 11 pts with data available at all 3 time points. 10/11 patients had decreases in Ktranswith mean decreases of 12.9% (0.94%- 44%) at Day 4 and 25.6% (8-61%) at Day 28. Of the 34 patients enrolled, 24 (71%) remained on study ≥8 weeks and 4 patients continue on treatment (maximum of 17+ months in a patient with refractory cervical cancer). Based on the PK/PD analysis, 15 mg/kg is the recommended phase II dose. Conclusions: CVX-060 is a well-tolerated novel therapy targeting angiogenesis. PK results support once-weekly dosing. There is preliminary evidence of biological activity based on DCE-MRI and prolonged stable disease. A combination trial with sunitinib is underway. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Pfizer Pfizer Data Safety Committee for non-oncology compound Pfizer
Corneal Dystrophy in Dutch Belted Rabbits as a Possible Model of Thiel-Behnke Subtype of Epithelial-Stromal TGFβ-Induced Corneal Dystrophy (2020)

The International Committee for Classification of Corneal Dystrophies (IC3D) categorized corneal dystrophies in humans using anatomic, genotypic, and clinicopathologic phenotypic features. Relative to the IC3D classification, a review of the veterinary literature confirmed that corneal dystrophy is imprecisely applied to any corneal opacity and to multiple poorly characterized histologic abnormalities of the cornea in animals. True corneal dystrophy occurs in mice with targeted mutations and spontaneously in pet dogs and cats and in Dutch belted (DB) rabbits, but these instances lack complete phenotyping or genotyping. Corneal dystrophy in DB rabbits can be an important confounding finding in ocular toxicology studies but has only been described once. Therefore, the ophthalmology and pathology of corneal dystrophy in 13 DB rabbits were characterized to determine whether the findings were consistent with or a possible model of any corneal dystrophy subtypes in humans. Slit lamp and optical coherence tomography (OCT) imaging were used to characterize corneal dystrophy over 4 months in young DB rabbits. The hyperechoic OCT changes correlated with light microscopic findings in the anterior stroma, consisting of highly disordered collagen fibers and enlarged keratocytes. Histochemical stains did not reveal abnormal deposits. Small clusters of 8 to 16 nm diameter curly fibers identified by transmission electron microscopy were consistent with Thiel-Behnke (TBCD) subtype of epithelial-stromal transforming growth factor β-induced dystrophies. Sporadic corneal dystrophy in DB rabbits appears to be a potential animal model of TBCD, but genotypic characterization will be required to confirm this categorization.
A Class III Semaphorin (Sema3e) Inhibits Mouse Osteoblast Migration and Decreases Osteoclast Formation In Vitro (2012)

Originally identified as axonal guidance cues, semaphorins are expressed throughout many different tissues and regulate numerous non-neuronal processes. We demonstrate that most class III semaphorins are expressed in mouse osteoblasts and are differentially regulated by cell growth and differentiation: Sema3d expression is increased and Sema3e expression decreased during proliferation in culture, while expression of Sema3a is unaffected by cell density but increases in cultures of mineralizing osteoblasts. Expression of Sema3a, -3e, and -3d is also differentially regulated by osteogenic stimuli; inhibition of GSK3β decreased expression of Sema3a and -3e, while 1,25-(OH)(2)D(3) increased expression of Sema3e. Parathyroid hormone had no effect on expression of Sema3a, -3b, or -3d. Osteoblasts, macrophages, and osteoclasts express the Sema3e receptor PlexinD1, suggesting an autocrine and paracrine role for Sema3e. No effects of recombinant Sema3e on osteoblast proliferation, differentiation, or mineralization were observed; but Sema3e did inhibit the migration of osteoblasts in a wound-healing assay. The formation of multinucleated, tartrate-resistant acid phosphatase-positive osteoclasts was decreased by 81% in cultures of mouse bone marrow macrophages incubated with 200 ng/mL Sema3e. Correspondingly, decreased expression of osteoclast markers (Itgb3, Acp5, Cd51, Nfatc1, CalcR, and Ctsk) was observed by qPCR in macrophage cultures differentiated in the presence of Sema3e. Our results demonstrate that class III semaphorins are expressed by osteoblasts and differentially regulated by differentiation, mineralization, and osteogenic stimuli. Sema3e is a novel inhibitor of osteoclast formation in vitro and may play a role in maintaining local bone homeostasis, potentially acting as a coupling factor between osteoclasts and osteoblasts.
Determining the Cutting Time for Maximum Yield and Quality of Alfalfa Swards (1983)

The cutting schedule for the maximum yield of DM and quality was applied to alfalfa swards. Harvesting at the cutting time for the maximum total yield to (Chang 1971) was selected as the criterion which provided the highest DM yield in accordance with high consistent levels of CP and IVD as well as persistance of the species in the pure stands. On the same theoretical basis, ceiling LAI and 25% bloom stages proved most satisfactory for harvesting pure stands of alfalfa.
Biotechnological production of the European corn borer sex pheromone in the yeast <i>Yarrowia lipolytica</i> (2021)

The European corn borer (ECB) Ostrinia nubilalis is a widespread pest of cereals, particularly maize. Mating disruption with the sex pheromone is a potentially attractive method for managing this pest; however, chemical synthesis of pheromones requires expensive starting materials and catalysts and generates hazardous waste. The goal of this study was to develop a biotechnological method for the production of ECB sex pheromone. Our approach was to engineer the oleaginous yeast Yarrowia lipolytica to produce (Z)-11-tetradecenol (Z11-14:OH), which can then be chemically acetylated to (Z)-11-tetradecenyl acetate (Z11-14:OAc), the main pheromone component of the Z-race of O. nubilalis. First, a C14 platform strain with increased biosynthesis of myristoyl-CoA was obtained by introducing a point mutation into the α-subunit of fatty acid synthase, replacing isoleucine 1220 with phenylalanine (Fas2p<sup>I1220F</sup> ). The intracellular accumulation of myristic acid increased 8.4-fold. Next, fatty acyl-CoA desaturases (FAD) and fatty acyl-CoA reductases (FAR) from nine different species of Lepidoptera were screened in the C14 platform strain, individually and in combinations. A titer of 29.2 ± 1.6 mg L<sup>-1</sup> Z11-14:OH was reached in small-scale cultivation with an optimal combination of a FAD (Lbo_PPTQ) from Lobesia botrana and FAR (HarFAR) from Helicoverpa armigera. When the second copies of FAD and FAR genes were introduced, the titer improved 2.1-fold. The native FAS1 gene's overexpression led to a further 1.5-fold titer increase, reaching 93.9 ± 11.7 mg L<sup>-1</sup> in small-scale cultivation. When the same engineered strain was cultivated in controlled 1 L bioreactors in fed-batch mode, 188.1 ± 13.4 mg L<sup>-1</sup> of Z11-14:OH was obtained. Fatty alcohols were extracted from the biomass and chemically acetylated to obtain Z11-14:OAc. Electroantennogram experiments showed that males of the Z-race of O. nubilalis were responsive to biologically-derived pheromone blend. Behavioral bioassays in a wind tunnel revealed attraction of male O. nubilalis, although full precopulatory behavior was observed less often than for the chemically synthesized pheromone blend. The study paves the way for the production of ECB pheromone by fermentation.
Hypothyroidism as a risk factor for open angle glaucoma: A systematic review and meta-analysis (2017)

The findings of this meta-analysis indicate that individuals with hypothyroidism have an increased risk of developing POAG.
Expression of Recombinant Proteins From lac Promoters (2003)

The Gram-negative bacterium Escherichia coli enjoys widespread use in modern biology as both a model organism and a microbiological tool. One of the keys to its popularity lies in the functionality of the lac operon. This regulated E. coli operon has been manipulated and utilized in diverse and creative ways since it was first studied by Jacob and Monod in 1961 (1). Excellent in-depth reviews of the lac operon and its uses in classical genetics are provided in refs. 2 and 3. Its enduring use can be attributed to the development of a wide range of engineered mutants and plasmid constructs designed to take advantage of specific features of the operon, particularly its inducibility by β-galactosides. This chapter will focus on the use of the lac operon in E. coli protein expression, although it has also been utilized for protein expression in mammalian systems (4). The application of lacZ as a reporter gene is discussed in Chapter 30 .