gebhart/patrepeval huggingface dataset:
Dynamics of Antibody Domains Studied by Solution NMR (2008)

Information on local dynamics of antibodies is important to evaluate stability, to rationally design variants, and to clarify conformational disorders at the epitope binding sites. Such information may also be useful for improved understanding of antigen recognition. NMR can be used for characterization of local protein dynamics at the atomic level through relaxation measurements. Due to the complexity of the NMR spectra, an extensive use of this method is limited to small protein molecules, for example, antibody domains and some scFv. Here, we describe a protocol that was used to study the dynamics of an antibody domain in solution using NMR. We describe protein preparation for NMR studies, NMR sample optimization, signal assignments, and dynamics experiments.
Intermolecular Hydroamination of 1,3-Dienes Catalyzed by Bis(phosphine)carbodicarbene–Rhodium Complexes (2014)

A carbodicarbene (CDC)-based pincer ligand scaffold is reported, along with its application to site-selective Rh(I)-catalyzed intermolecular hydroamination of 1,3-dienes with aryl and alkyl amines. To the best of our knowledge, this is the first example of the use of a well-defined CDC complex as an efficient catalyst. Transformations proceed in the presence of 1.0-5.0 mol % Rh complex at 35-120 °C; allylic amines are obtained in up to 97% yield and with >98:2 site selectivity.
Induction of specific transcription by RNA polymerase III in transformed cells. (1986)

RNA polymerase III (pol III) transcripts of the highly repeated mouse B2 gene family are increased in many oncogenically transformed murine cell lines. In cells transformed by simian virus 40, the small, cytoplasmic B2 RNAs are present at 20-fold-higher levels than in normal cells (M. R. D. Scott, K. Westphal, and P. W. J. Rigby, Cell 34:557-567, 1983; K. Singh, M. Carey, S. Saragosti, and M. Botchan, Nature [London] 314:553-556). We found that transcripts of the highly repeated B1 gene family are also increased 20-fold upon simian virus 40 transformation and showed that these RNAs result from pol III transcription. In contrast, transcripts from less highly repeated pol III templates such as the 5S, 7SL, 7SK, 4.5SI, tRNAMet, and tRNAPro genes are unaffected. The expression of the B2 RNAs in isolated nuclei shows that the augmentation is due mainly to an increased rate of transcription by pol III. There is thus specific transformation-inducible pol III transcription. We developed an in vitro transcription assay which utilizes genomic DNA as a template to study the transcription of all members of a repetitive gene family in their native context. This assay reproduces the low cytoplasmic levels of B1 compared with B2 RNAs suggesting that this ratio is dictated by intrinsic signals in the DNA.
A model of magnetostriction interaction in thin double-layer magnetic films of Ni-Fe alloy (1970)

Under the assumption that in a double-layer film both layers are equally deformed, the following formula for the magnetostriction energy E = K_{c} \sin^{2} \alpha has been derived where K_{c} = (9/40)(2U'U/U'_{0} + U_{0}) is the coupling constant and α is the angle between the magnetization vectors. This formula is valid if we can neglect interaction with the substrate. The sign of the coupling constant is discussed. It turns out that where the composition of the two layers are different, the value of K c can be, in some special cases, negative.
Assessment of Conditions Influencing Porous Si Electroluminescence (1997)

Visible electroluminescence (EL) characteristics of porous Si formed on p, n, p+‐n, and n+‐p junction substrates are studied under pulse current regime. We provide experimental proof that porous Si structures characterized by highest EL intensity have simultaneously highest photoluminescence (PL) intensity and lowest surface roughness. PL and EL can be correlated via surface roughness. Two types of EL instabilities are observed: fast, with time constant in the milliseconds range and slow, with time constant in the hours range. The fast EL instability is affected by the type of ambient and/or sample temperature during electrical excitation and is likely to be associated with the charging of the porous network.
Stability of organic thin-film transistors based on ultrathin films of dinaphtho[2,3-b:2′,3′-f]thieno[3,2-b]thiophene (DNTT) (2020)

Ultrathin DNTT films are unstable due to rapid morphological changes. This work investigates the stability of ultrathin DNTT films and the fabrication of ultrathin DNTT organic transistors.
14 Continuous-Flow Syntheses of Active Pharmaceutical Ingredients (2018)

Abstract This chapter describes synthetic strategies and technologies used to perform multistep flow syntheses of active pharmaceutical ingredients (APIs). The APIs or potential drug candidates highlighted are efavirenz, imatinib, (–)-oseltamivir, ibuprofen, rolipram, methylphenidate hydrochloride, and rufinamide.
Implementation of a hands-free car phone with echo cancellation and noise-dependent loss control (2002)

An implementation of a complete hands-free telephone system on a low-cost DSP with 16-bit fixed-point arithmetic is presented. The prototype, consisting of an adaptive echo canceller, was developed for an industrial customer. The main emphasis is laid on the control unit of the system being necessary for a reliable performance in all environments and the attenuation introduced by the loss control unit. Keeping the loss as small as possible, which is most important for a natural communication including full double-talk capabilities, requires exact knowledge of the current system performance and the background noise level. In case of background noise the applied total loss is adjusted to the power of the noise. The measures we used and their application to our system control are discussed.
Editorial: Functional Eye Diseases: Visual Deficits and Rehabilitation (2022)

EDITORIAL article Front. Neurosci., 10 February 2022 | https://doi.org/10.3389/fnins.2022.842767
Effect of Cardiac Stem Cells on Left-Ventricular Remodeling in a Canine Model of Chronic Myocardial Infarction (2012)

Intramyocardial injection of autologous CSCs in a late phase model of chronic infarction resulted in less increase in LV end-systolic volume and preservation of LV ejection fraction.
Exploitation of the Antibody Repertoire of Cancer Patients for the Identification of Human Tumor Antigens (1999)

The screening of tumor-derived expression libraries for antigens which are recognized by high titered IgG antibodies present in autologous sera of the cancer patients by SEREX (serological identification of antigens by recombinant expression cloning) allows for the systematic identification of antigens in human cancers. SEREX has led to the definition of a plentitude of new tumor antigens in many different tumor entities. The majority of the antigens are encoded by hitherto unknown genes and can be grouped into different classes of antigens. The abundance of serologically defined human tumor antigens is not only of relevance for tumor biology and serodiagnosis of cancer, but also facilitates the identification of proteins recognized by tumor specific T lymphocytes, thus providing a molecular basis for polyvalent peptide-based and gene-therapeutic vaccine strategies in a wide variety of human neoplasms.
Extraframework aluminium in steam- and SiCl4-dealuminated Y zeolite. A 27Al and 29Si nuclear magnetic resonance study (1988)

29 Si and 27Al m.a.s.n.m.r. techniques have been used to study the dealumination process of a Y zeolite. Dealumination by steaming or SiCl4 treatment leads to the formation of silica and/or silica–alumina type phases. Extraframework aluminium shows a different type of coordination (tetra-, penta- or octa-hedral) depending on the method of dealumination.
Crystallization and preliminary X-ray analysis of neoagarobiose hydrolase fromSaccharophagus degradans2-40 (2009)

Many agarolytic bacteria degrade agar polysaccharide into the disaccharide unit neoagarobiose [O-3,6-anhydro-alpha-L-galactopyranosyl-(1-->3)-D-galactose] using various beta-agarases. Neoagarobiose hydrolase is an enzyme that acts on the alpha-1,3 linkage in neoagarobiose to yield D-galactose and 3,6-anhydro-L-galactose. This activity is essential in both the metabolism of agar by agarolytic bacteria and the production of fermentable sugars from agar biomass for bioenergy production. Neoagarobiose hydrolase from the marine bacterium Saccharophagus degradans 2-40 was overexpressed in Escherichia coli and crystallized in the monoclinic space group C2, with unit-cell parameters a = 129.83, b = 76.81, c = 90.11 A, beta = 101.86 degrees . The crystals diffracted to 1.98 A resolution and possibly contains two molecules in the asymmetric unit.
Guest Editorial (2011)

The 20 papers in this second part of this special section are classified by energy sources (wind, photovoltaic, hydro, etc.), grid-related issues (islanding, synchronization, microgrid, and smart grid), and converters for renewable energy sources.
Towards 11nm half-pitch resolution for a negative-tone chemically amplified molecular resist platform for extreme-ultraviolet lithography (2015)

We have synthesized a new resist molecule and investigated its high-resolution capability. The material showed resolved line-spaces with 14 nm half-pitch (hp) and the potential to pattern 11 nm hp features. Line edge roughness values as low as 3.15 nm were seen in optimized formulations. The dose-to-size is estimated at around 20-30 mJ/cm<sup>2</sup>. The role of the molecule in the patterning process was studied by comparing it with structurally similar compounds. Furthermore we present first results from exposures of our materials at the Berkeley Micro Exposure Tool. Finally it is also demonstrated that the material works as a resist in 100 kV electron beam lithography as well.
Characterization of high electron mobility transistor fabricated on hydride vapor phase epitaxy‐grown GaN templates containing various Fe concentrations (2017)

An AlGaN/GaN high electron mobility transistor (HEMT) structure was grown on a semi‐insulating (SI) GaN layer or substrate to suppress a leakage current and achieve a high breakdown voltage. Fe can be used as doping material to obtain SI‐GaN. However, the relationship between the Fe concentration in the GaN layers and its influence on HEMT characteristics has not yet been investigated. In this study, we therefore investigated the influence of Fe concentration in the GaN layers on HEMT characteristics. The GaN layers containing several Fe concentrations were grown by hydride vapor phase epitaxy (HVPE). The Fe concentration was varied from 3 × 10 17 to 3 × 10 20 atoms cm −3 . It was determined that the source‐drain current ( I DS ) decreased as the Fe concentration increased. In the case of a low Fe concentration of 3 × 10 17 atoms cm −3 , I DS was almost the same as that of HEMT on the non‐Fe‐doped GaN template. Thus, HEMT characteristics deteriorated as the Fe concentration increased. The channel layer played a role in blocking the adverse effects of Fe doping on the two‐dimensional electron gas concentration in AlGaN/GaN. Moreover, it was shown that the GaN channel layer must become thicker as the Fe concentration of the GaN layers increases.
Generating Continual Human Motion in Diverse 3D Scenes (2023)

We introduce a method to synthesize animator guided human motion across 3D scenes. Given a set of sparse (3 or 4) joint locations (such as the location of a person's hand and two feet) and a seed motion sequence in a 3D scene, our method generates a plausible motion sequence starting from the seed motion while satisfying the constraints imposed by the provided keypoints. We decompose the continual motion synthesis problem into walking along paths and transitioning in and out of the actions specified by the keypoints, which enables long generation of motions that satisfy scene constraints without explicitly incorporating scene information. Our method is trained only using scene agnostic mocap data. As a result, our approach is deployable across 3D scenes with various geometries. For achieving plausible continual motion synthesis without drift, our key contribution is to generate motion in a goal-centric canonical coordinate frame where the next immediate target is situated at the origin. Our model can generate long sequences of diverse actions such as grabbing, sitting and leaning chained together in arbitrary order, demonstrated on scenes of varying geometry: HPS, Replica, Matterport, ScanNet and scenes represented using NeRFs. Several experiments demonstrate that our method outperforms existing methods that navigate paths in 3D scenes. For more results we urge the reader to watch our supplementary video available at: https://www.youtube.com/watch?v=0wZgsdyCT4A&amp;t=1s
Resection of Recurrent Pulmonary Metastases in Patients With Soft-Tissue Sarcomas (1986)

Survival benefit and prognostic factors useful for patient selection have not been previously analyzed for patients with recurrent pulmonary metastases from soft-tissue sarcomas. Twenty-nine patients in our study had two or more resections of pulmonary metastases from 1976 to 1983. There were no operative deaths and three complications for 40 operations (7.5%). Factors predictive of increased survival following the second resection of pulmonary metastases were resectability and a disease-free interval of greater than six months from the first thoracotomy to the second recurrence in the lung. The tumor doubling time of the first recurrence and the presence of three or fewer nodules on full-lung tomography before the first thoracotomy, which were predictors of survival following initial resection, also predicted survival following subsequent resections. Overall median survival following the second resection was 14.5 months (22% overall three-year survival). The postresection actuarial survival curves for patients undergoing 1, 2, or 3 or more resections were not significantly different. Our findings demonstrate that patients undergoing repeated resections of pulmonary metastases from soft-tissue sarcomas can achieve prolonged survival.
Supplementary Table 4 from Aristolochic Acid in the Etiology of Renal Cell Carcinoma (2023)

&lt;p&gt;Summary of exome sequence analysis of ten Taiwanese ccRCC patients&lt;/p&gt;
Clinical Images: Imaging Manifestations of Orbital Neurofibromatosis Type 1. (2016)

Neurofibromatosis type 1 (NF1) or von Recklinghausen disease is an inherited autosomal dominant disorder and the most common of the phakomatoses (neurocutaneous syndromes), affecting 1 in 3,000 individuals.[1][1] Pathogenesis involves mutations in the NF1 gene that encodes the protein neurofibromin
On the feasibility of die-to-wafer inorganic dielectric bonding (2016)

A feasibility study of die-to-wafer (D2W) bonding of inorganic dielectric layers is conducted on common industrial tools in a typical cleanroom environment. With the help of an additional cleaning step after dicing of the top wafers or using stealth dicing process, 100% bonding success rate from wafers with chemical mechanical polished (CMP-ed) SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> has been achieved. Plasma treatment of the top dies has no clear impact on the bonding success rate. However, die shear test shows a significant bonding strength improvement from 10.7±2.6 MPa of samples without pre-bonding plasma treatment to 24.8±9.1 MPa with the treatment. The failure mechanism in the shear test is identified to be fractures in bulk Si, confirming the high bonding strength. The study highlights particle control as the major challenge and current bottleneck in D2W inorganic dielectric bonding. Even in the best experimental split which yields 100% bonding success rate, scanning acoustic microscopy (SAM) and infrared (IR) microscopy show voids in every stack, which are clearly caused by entrapped particles. Cross-sectioning and inspection of the bonding interface by focused ion beam (FIB) show well bonded interfaces between SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> layers in the no-void (dark) areas as revealed under SAM, and a narrow gap in the order of tens of nm in the voiding (bright) areas.
Synthesis of an Effective Flame-Retardant Hydrogel for Skin Protection Using Xanthan Gum and Resorcinol Bis(diphenyl phosphate)-Coated Starch (2021)

We report on the production of a flame-resistant xanthan gum (XG)-based hydrogel formulation, which could be directly applied onto the skin for protection against burning projectiles. The hydrogel cream represents an efficient use of XG and starch, both of which are biodegradable, reusable natural materials and are also GRAS-certified. The flame-retardant agent resorcinol bis(diphenyl phosphate) (RDP) was shown to be nontoxic to cells in vitro when adsorbed directly onto the starch delivery vehicle. Three hydrogel formulations were studied, the pure XG hydrogel, commercial FireIce hydrogel, and RDP-XG/RDP-starch hydrogel. After application of a direct flame for 150 s, the RDP-XG/RDP-starch hydrogel produced a thick char layer, which was easily removed, showing undamaged chicken skin and tissue underneath. In contrast, complete burning of skin and tissue was observed on untreated control samples and those covered with FireIce and pure XG hydrogels. The thermal protective performance test was also performed, where the heat transfer was measured as a function of time for all three hydrogels. The RDP-XG/RDP-starch hydrogel was able to prolong the protection time before obtaining a second-degree burn for 103 s, which is double that for FireIce and triple that for the pure XG hydrogel. The model proposed involves endothermic reactions, producing char and burning "cold", as opposed to simply relying on the adsorbed water in the hydrogel for burn protection.
A multimodal contrast agent for simultaneous magnetic resonance and optical imaging of small animal (2010)

Our goal is to assess the feasibility of a bi-functional contrast agent that is intravenously injected to an R3230 induced small animal breast tumor model. The MR/optical contrast agent was produced by GE Global Research, NY, and it was available in one size, Dp20. We used a combined frequency domain diffuse optical tomography (DOT) and a 4T magnetic resonance (MR) scanner to simultaneously measure the kinetics of the contrast agent in vivo. Both systems detected the signal change in the tumor and the non-tumor region. MR measurements served as a gold standard to validate the optical kinetics. We present both MR and DOT dynamic curves as well as the reconstructed optical absorption map.
Behavior of 157 nm excimer-laser-induced refractive index changes in silica (2006)

This study describes the observation of large induced refractive index changes produced by 157nm excimer laser exposure in high-purity synthetic silica glasses. With 157nm exposure, large induced changes are observed within a few hundred thousand pulses of exposure. Similar to 193 nm exposures, exposure with polarized 157 nm light yields polarization-induced birefringence (PIB). However, the 157 nm exposure also exhibits a behavior not observed with 193 nm exposures; namely, the initial response of the glass is a decrease in refractive index, followed by an increase with continued exposure. An explanation of the behaviors for both wavelength results is proposed where the induced refractive index is considered to arise from two different concurrent phenomena. One produces a decreased refractive index and also accounts for the PIB. The other, which accounts for the increased refractive index, is associated with an isotropic laser-induced volume change.
A new parameter estimation algorithm for an electrical analogue battery model (2012)

This paper describes a new parameter estimation algorithm for a well-recognized electrical analogue battery model. The limited bandwidth characteristic of the electrical analogue battery model is introduced and discussed, on which the new parameter estimation algorithm is built. While a real battery system is non-linear and time variant, a truncated representation of the system is provided by a commonly studied non-physical "electrical analogue" battery model. However, the limited bandwidth characteristic of the electrical analogue battery model is often overlooked. The proposed algorithm starts by assessing a desired battery application, followed by modeling the battery according to the application bandwidth, and then estimating the model parameters using the sequential quadratic programming method. This approach recognizes and makes use of the limited bandwidth of the battery model by reconciling the approximation with the limited bandwidth required by the simulation. This approach has been experimentally verified on a 6.8 Ah Ultralife UBBL10 Lithium-ion battery module. Since this electrical analogue battery model is independent of the battery chemistry it is applicable to Lithium-ion, Nickel-Metal-Hydride (NiMH), and Lead-acid batteries, among others.
An OFDM Design for Underwater Acoustic Channels with Doppler Spread (2009)

In this paper, we study the performance of orthogonal frequency division multiplexing (OFDM) over underwater acoustic multipath channels with different Doppler scales on different paths. We first derive an exact inter-carrier-interference (ICI) expression after incorporating the compensation of nonuniform Doppler shifts across OFDM sub-carriers. Based on the assumption that the residual ICI is dominantly from immediate neighbors, we suggest a practical design that divides subcarriers into groups, where each group of eight subcarriers consists of three contiguous data subcarriers, one pilot subcarrier, and five carefully spaced null subcarriers. We use the orthogonal matching pursuit (OMP) algorithm for sparse channel estimation that identifies distinct physical paths with different Doppler scales. System performance is evaluated using data recorded from the GLINT08 and SPACE08 experiments. Relative to the receiver that ignores the residual ICI, we observe that explicitly suppressing the residual ICI induced by Doppler spread leads to improved performance for the SPACE08 data, while not for the GLINT08 data.
<p>Synthesis and characterization of a long-acting emtricitabine prodrug nanoformulation</p> (2019)

NMFTC shows improved antiretroviral activities over native FTC. This is coordinate with its extended apparent half-life. The work represents an incremental advance in the development of a long-acting FTC formulation.
5.2: New Technique of Measuring of the Jones Matrix for a Polarization Medium at Oblique Light Incidence (2005)

Abstract We propose a new technique of measuring the Jones matrix for a polarization medium (ex. optical compensation film) based on ellipsometry experimental methodology at oblique light incidence. Unlike uniaxial, biaxial, and N‐stacked birefringent layer models, this technique describes the medium's polarization properties directly without any assumptions about the internal microscopic physical parameters. The obtained Jones matrix gives an accurate prediction of viewing angle properties of the liquid crystal displays.