gebhart/patrepeval huggingface dataset:
Growth and Characterization of a GaAs Quantum Well Buried in GaAsP/GaAs Vertical Heterostructure Nanowires by Selective-Area Metal Organic Vapor Phase Epitaxy (2011)

We developed a growth method for forming a GaAs quantum well (QW) buried in GaAsP/GaAs heterostructure nanowires (NWs) by selective-area metal organic vapor phase epitaxy (SA-MOVPE). To determine the optimum growth conditions of GaAsP NWs, we varied the [(C 4 H 9 )PH 2 + AsH 3 ]/[(CH 3 ) 3 Ga] ratio between 20 and 185. As a result, we could obtain NWs with good height uniformity when the ratio was 20. To form such NWs with a GaAs QW, we fabricated GaAs NWs of about 60 nm in diameter before the GaAsP growth. The NW uniformity was considerably improved by introducing GaAs growth. Photoluminescence (PL) measurements at 4.2 K indicated that the QW had a spectral peak about 150 meV higher than the acceptor-related recombination emission peak of GaAs, which is near 1.5 eV. The QW thickness estimated from the spectral peak energy of PL was 5.2 nm, which is in fair agreement with the value calculated from the GaAs growth rate.
Mutation of Arginine 228 to Lysine Enhances the Glucosyltransferase Activity of Bovine β-1,4-Galactosyltransferase I<sup>,</sup><sup>,</sup> (2005)

Beta-1,4-galactosyltransferase I (beta4Gal-T1) normally transfers Gal from UDP-Gal to GlcNAc in the presence of Mn(2+) ion (Gal-T activity) and also transfers Glc from UDP-Glc to GlcNAc (Glc-T activity), albeit at only 0.3% efficiency. In addition, alpha-lactalbumin (LA) enhances this Glc-T activity more than 25 times. Comparison of the crystal structures of UDP-Gal- and UDP-Glc-bound beta4Gal-T1 reveals that the O4 hydroxyl group in both Gal and Glc moieties forms a hydrogen bond with the side chain carboxylate group of Glu317. The orientation of the O4 hydroxyl of glucose causes a steric hindrance to the side chain carboxylate group of Glu317, accounting for the enzyme's low Glc-T activity. In this study, we show that mutation of Arg228, a residue in the vicinity of Glu317, to lysine (R228K-Gal-T1) results in a 15-fold higher Glc-T activity, which is further enhanced by LA to nearly 25% of the Gal-T activity of the wild type. The kinetic parameters indicate that the main effect of the mutation of Arg228 to lysine is on the k(cat) of Glc-T, which increases 3-4-fold, both in the absence and in the presence of LA; simultaneously, the k(cat) for the Gal-T reaction is reduced 30-fold. The crystal structure of R228K-Gal-T1 complexed with LA, UDP-Gal, and Mn(2+) determined at 1.9 A resolution shows that the Asp318 side chain exhibits a minor alternate conformation, compared to that in the wild type. This alternate conformation now causes a steric hindrance to the O4 hydroxyl group of the Gal moiety of UDP-Gal, probably causing the dissociation of UDP-Gal and the reduced k(cat) of the Gal-T reaction.
A Sequential Greedy Search Algorithm With Bayesian Updating for Testing in High-Speed Milling Operations (2010)

This paper describes a probabilistic greedy search optimization algorithm for stability testing in high-speed milling. The test parameters (i.e., the experiment setup decisions) consist of the axial depth of cut and the spindle speed. These parameters are selected to maximize the expected value of profit using a greedy search approach (an approach that maximizes the expected value of each stage one step at a time). After a test is performed, Bayesian updating is applied to determine the posterior distribution of stability. The algorithm is then repeated to identify a new test point. The motivation for this work is that, while deterministic models for milling stability prediction are available, uncertainty in the inputs always exists. In this study, it is assumed that the tool point frequency response function, which is required for stability lobe diagram development, is unknown. Therefore, the probability of stability over the selected axial depth-spindle speed domain must be determined experimentally. The greedy search algorithm identifies the maximum expected value of profit within the selected domain, where profit is determined from the product of the profit function and the stability cumulative distribution function, referred to as the probability of stability. This optimal point is then tested to evaluate stability. Whether stable or unstable, the results are used to update the probability of stability. A stable test updates all axial depths smaller than test depth to be stable at the selected spindle speed, while an unstable test specifies that all axial depths above the test depth are unstable. After updating, a new test point is selected by the greedy search algorithm and the process is repeated. This select/test/update sequence is repeated until a preselected stopping criterion is reached. This paper presents both numerical results and experimental validation that the optimization/updating approach quickly converges to the well-known stability lobe behavior described in the literature. However, in this probabilistic technique the issue of uncertainty is also addressed and results can be obtained even if no information about the dynamic system is available.
Wiley Series on Bioinformatics: Computational Techniques and Engineering (2007)

Bioinformatics and computational biology involve the comprehensive application of mathematics, statistics, science, and computer science to the understanding of living systems. Research and development in these areas require cooperation among specialists from the fields of biology, computer science, mathematics, statistics, physics, and related sciences. The objective of this book series is to provide timely treatments of the different aspects of bioinformatics spanning theory, new and established techniques, technologies and tools, and application domains. This series emphasizes algorithmic, mathematical, statistical, and computational methods that are central in bioinformatics and computational biology.
Bayesian sequential tests for comparing the number of species in two populations (1996)

We study a problem of scquentially comparing the number of species in two populations. We consider a sequential Bayesian approach which incorporates a sampling cost and a misclassification loss, and examine optimal and sub-optimal stopping rules. The optimal stopping rule is shown to be truncated when the prior distribution of the number of species is bounded. or when the prior is unbounded and satisfies certain conditions.
Facile Gene Delivery Derived from Branched Low Molecular Weight Polyethylenimine by High Efficient Chemistry (2018)

Convenient methods for the preparation of gene delivery platforms based on branched low molecular weight polyethylenimine (PEI) were described. Firstly, PEI lipids, with a low molecular weight PEI headgroup and hexadecyl chain tail group, were prepared through a highly efficient ring-opening reaction of glycidyl hexadecyl ether (EpoxyC16) by amine from PEI. Then, the PEI lipids were used as a component of cationic liposomes and as a surfactant for the preparation of poly(D,L-lactide-co-glycolide) (PLGA) nanoparticle (NP) via solvent extraction/evaporation method. As potential effective gene delivery platforms, their preparation, size, size distribution, toxicities, plasmid DNA loading, in vitro transfection and intracellular trafficking were studied. Both facile platforms showed less toxicity and higher transfection efficacy when compared to high molecular weight PEI in vitro, and may have further versatile applications in the gene delivery field.
Development and design of a multi-column experimental setup for Kr/Xe separation (2014)

As a precursor to FY-15 Kr/Xe separation testing, design modifications to an existing experimental setup are warranted. The modifications would allow for multi-column testing to facilitate a Xe separation followed by a Kr separation using engineered form sorbents prepared using an INL patented process. A new cooling apparatus capable of achieving test temperatures to -40° C and able to house a newly designed Xe column was acquired. Modifications to the existing setup are being installed to allow for multi-column testing and gas constituent analyses using evacuated sample bombs. The new modifications will allow for independent temperature control for each column enabling a plethora of test conditions to be implemented. Sample analyses will be used to evaluate the Xe/Kr selectivity of the AgZ-PAN sorbent and determine the Kr purity of the effluent stream following Kr capture using the HZ-PAN sorbent.
X-ray Structure Determination of Ion-Channel Crystalline Architectures Close to Bilayer Membrane-Confined Conditions (2014)

Experimental evidence presented in this paper shows that long-range crystalline order as observed in the macrocyclic heteroditopic receptors’ single-crystal structures is preserved when embedded in the bilayer membranes. Investigations presented here showed that MCM41-type mesoporous hydrophobic hybrids can be used as biomimetic platforms for ion-channel biomimetic structure elucidation, while showing similar hydrophobic interactions with confined ligands/receptors as in bilayer membranes. This gives access to information concerning the structural pictures of the bilayer’s confined ion-channel structures, as well as of their relatives in the presence of ion effectors.
Spin-labeling Coronary MR Angiography with Steady-State Free Precession and Radial k-Space Sampling: Initial Results in Healthy Volunteers (2005)

The purpose of this study was to prospectively compare free-breathing navigator-gated cardiac-triggered three-dimensional steady-state free precession (SSFP) spin-labeling coronary magnetic resonance (MR) angiography performed by using Cartesian k-space sampling with that performed by using radial k-space sampling. A new dedicated placement of the two-dimensional selective labeling pulse and an individually adjusted labeling delay time approved by the institutional review board were used. In 14 volunteers (eight men, six women; mean age, 28.8 years) who gave informed consent, signal-to-noise ratio (SNR), contrast-to-noise ratio (CNR), vessel sharpness, vessel length, and subjective image quality were investigated. Differences between groups were analyzed with nonparametric tests (Wilcoxon, Pearson chi2). Radial imaging, as compared with Cartesian imaging, resulted in a significant reduction in the severity of motion artifacts, as well as an increase in SNR (26.9 vs 12.0, P < .05) in the coronary arteries and CNR (23.1 vs 8.8, P < .05) between the coronary arteries and the myocardium. A tendency toward improved vessel sharpness and vessel length was also found with radial imaging. Radial SSFP imaging is a promising technique for spin-labeling coronary MR angiography.
Isolation of Human CD49f+ Astrocytes and In Vitro iPSC-Based Neurotoxicity Assays (2020)

Given the critical roles of astrocytes in neuroinflammation and neurological diseases, models for studying human astrocyte biology are in increasing demand. Here, we present a protocol to isolate human astrocytes from induced pluripotent stem cell (iPSC)-based cultures, neural organoids, and primary tissue, using the surface marker CD49f. Moreover, we provide protocols for <i>in vitro</i> co-cultures of human iPSC-derived neurons and astrocytes, as well as for neurotoxicity assays that expose neurons to conditioned media from reactive astrocytes. For complete details on the use and execution of this protocol, please refer to Barbar et al. (2020).
Supplementary Table from Randomized, Double-Blind, Placebo-Controlled Phase III Study of Paclitaxel ± Napabucasin in Pretreated Advanced Gastric or Gastroesophageal Junction Adenocarcinoma (2023)

Supplementary Table from Randomized, Double-Blind, Placebo-Controlled Phase III Study of Paclitaxel ± Napabucasin in Pretreated Advanced Gastric or Gastroesophageal Junction Adenocarcinoma
Embedded GaN nanostripes on <i>c</i>‐sapphire for DFB lasers with semipolar quantum wells (2015)

Abstract GaN based laser diodes with semipolar quantum wells are typically grown on free‐standing pseudo‐substrates of small size. We present an approach to create a distributed‐feedback (DFB) laser with semipolar quantum wells (QWs) on c ‐oriented templates. The templates are based on 2‐inch sapphire wafers, the method could easily be adapted to larger diameters which are available commercially. GaN nanostripes with triangular cross‐section are grown by selective area epitaxy (SAE) and QWs are grown on their semipolar side facets. The nanostripes are completely embedded and can be sandwiched inside a waveguide. For optical pumping, open waveguide structures with only a bottom cladding are used. Using nanoimprint lithography, stripe masks with 250 nm periodicity were fabricated over the whole wafer area. The periodicity corresponds to a 3rd order DFB structure for a laser emitting in the blue wavelength regime. These samples were analyzed structurally by high‐resolution transmission electron microscopy (HRTEM), and spatio‐spectrally by cathodoluminescence (CL) inside a scanning transmission electron microscope (STEM). Samples with an undoped cap are pumped optically for stimulated emission. To prove the feasibility of realizing a 2nd order DFB structure with this approach, stripes with a 170 nm periodicity are fabricated by electron beam lithography and SAE.
Genome Scan for Parent-of-Origin QTL Effects on Bovine Growth and Carcass Traits (2011)

Parent-of-origin effects (POE) such as genomic imprinting influence growth and body composition in livestock, rodents, and humans. Here, we report the results of a genome scan to detect quantitative trait loci (QTL) with POE on growth and carcass traits in Angus × Brahman cattle crossbreds. We identified 24 POE-QTL on 15 Bos taurus autosomes (BTAs) of which six were significant at 5% genome-wide (GW) level and 18 at the 5% chromosome-wide (CW) significance level. Six QTL were paternally expressed while 15 were maternally expressed. Three QTL influencing post-weaning growth map to the proximal end of BTA2 (linkage region of 0-9 cM; genomic region of 5.0-10.8 Mb), for which only one imprinted ortholog is known so far in the human and mouse genomes, and therefore may potentially represent a novel imprinted region. The detected QTL individually explained 1.4 ∼ 5.1% of each trait's phenotypic variance. Comparative in silico analysis of bovine genomic locations show that 32 out of 1,442 known mammalian imprinted genes from human and mouse homologs map to the identified QTL regions. Although several of the 32 genes have been associated with quantitative traits in cattle, only two (GNAS and PEG3) have experimental proof of being imprinted in cattle. These results lend additional support to recent reports that POE on quantitative traits in mammals may be more common than previously thought, and strengthen the need to identify and experimentally validate cattle orthologs of imprinted genes so as to investigate their effects on quantitative traits.
Efficient Subgroup C Avian Sarcoma and Leukosis Virus Receptor Activity Requires the IgV Domain of the Tvc Receptor and Proper Display on the Cell Membrane (2008)

We recently identified and cloned the receptor for subgroup C avian sarcoma and leukosis viruses [ASLV(C)], i.e., Tvc, a protein most closely related to mammalian butyrophilins, which are members of the immunoglobulin protein family. The extracellular domain of Tvc contains two immunoglobulin-like domains, IgV and IgC, which presumably each contain a disulfide bond important for native function of the protein. In this study, we have begun to identify the functional determinants of Tvc responsible for ASLV(C) receptor activity. We found that the IgV domain of the Tvc receptor is responsible for interacting with the glycoprotein of ASLV(C). Additional experiments demonstrated that a domain was necessary as a spacer between the IgV domain and the membrane-spanning domain for efficient Tvc receptor activity, most likely to orient the IgV domain a proper distance from the cell membrane. The effects on ASLV(C) glycoprotein binding and infection efficiency were also studied by site-directed mutagenesis of the cysteine residues of Tvc as well as conserved amino acid residues of the IgV Tvc domain compared to other IgV domains. In this initial analysis of Tvc determinants important for interacting with ASLV(C) glycoproteins, at least two aromatic amino acid residues in the IgV domain of Tvc, Trp-48 and Tyr-105, were identified as critical for efficient ASLV(C) infection. Interestingly, one or more aromatic amino acid residues have been identified as critical determinants in the other ASLV(A-E) receptors for a proper interaction with ASLV glycoproteins. This suggests that the ASLV glycoproteins may share a common mechanism of receptor interaction with an aromatic residue(s) on the receptor critical for triggering conformational changes in SU that initiate the fusion process required for efficient virus infection.
&lt;title&gt;Multipurpose interface for still/moving image retrieval&lt;/title&gt; (1994)

Recently, calculation speed of computers has become faster and capacity of archival media has become larger. These situations enable image databases which efficiently archive, retrieve and utilize large amounts of image data. In order to retrieve required images efficiently from large amounts of image data, it is necessary to extract effective keywords from original images automatically. Many methods have been proposed for this purpose. However, satisfactory methods have not been found yet. In this paper, a new image data management method using vector expression of hue distribution of color images is proposed. A kind of normalized histogram of hue of a color image is regarded as a vector which represents image features. This unit vector of hue is utilized as a basis of the keywords of the image. The proposed image data management method enables flexible interface for various requests on retrieval. For example, `navigation in image data space based on similarity,' `retrieval of partial images or similarity retrieval using partial images,' `retrieval by semantic description,' such as `mountain view with clear sky and green forest' can be realized using the proposed method. The results of simulation experiments reveal the effectiveness of the proposed method.
Neurocritical Care Management of Hepatic Encephalopathy and Coma in Liver Failure (2018)

Hepatic encephalopathy (HE) is a severe complication of liver disease, describing a spectrum of neurological and psychiatric abnormalities ranging from subclinical alterations to coma. HE is the leading cause for hospital readmission, intensive care treatment, and mortality in patients with chronic liver disease. The complex and multifaceted pathogenesis is not yet fully understood, but hypotheses focus on ammonia and systemic inflammation, which are the main targets for currently available therapies in clinical practice. Nevertheless, the remaining high clinical relevance and healthcare burden of this syndrome underlines the emergence for further unraveling the full spectrum of pathomechanisms, as this provides the basis for the development of novel, highly targeted therapies. In this review, the most recent literature about current and future therapies for HE, relevant for intensive care management, will be discussed.
Non-crossing partitions of type (e,e,r) (2004)

We investigate a new lattice of generalised non-crossing partitions, constructed using the geometry of the complex reflection group $G(e,e,r)$. For the particular case $e=2$ (resp. $r=2$), our lattice coincides with the lattice of simple elements for the type $D_n$ (resp. $I_2(e)$) dual braid monoid. Using this lattice, we construct a Garside structure for the braid group $B(e,e,r)$. As a corollary, one may solve the word and conjugacy problems in this group.
III-V Quantum Dot Lasers Monolithically Grown on Silicon (2019)

We review the direct growth of III-V quantum dot laser on Si substrates. A low threading dislocation density, on the order of 105 cm−2, for III-V epilayer on Si has been achieved.
Comparison of Chicken Cecal Microbiota after Metaphylactic Treatment or Following Administration of Feed Additives in a Broiler Farm with Enterococcal Spondylitis History (2021)

Minimizing the clinical signs of <i>Enterococcus cecorum</i> infections causing enterococcal spondylitis in broiler herds is successful when initiated as metaphylaxis in the first week of life. Mechanistically, either the <i>Enterococcus</i> species present at that time are reduced by antibiotic treatment or antibiotic treatment might induce changes in intestinal microbiota composition with an indirect and subsequent influence. The aim of the present study was to examine the cecal microbiota of chickens after administering lincospectin or different additives to evaluate whether these additives have lincospectin-like effects on microbiota. Therefore, 157,400 broiler chickens were reared in four chicken houses (~40,000 birds each) on a broiler farm with history of enterococcal spondylitis. Each flock was treated either with lincospectin or water soluble esterified butyrins, <i>Bacillus</i> (<i>B</i>.) <i>licheniformis</i> or palm oil was added via drinking water during the first days of life. Ten birds per house were dissected at days 11, 20 and 33 of life and cecal microbiota were analyzed (16S rRNA gene sequencing). Lincospectin treatment elicited significant changes in the cecal microbiota composition until slaughter age. Among the tested additives, effects of <i>B. licheniformis</i> on cecal microbiota composition were most similar to those seen after the treatment with lincospectin at day 11.
Results of Surgical Treatment for the Children with Persistent Pupillary Membrane (2002)

Purpose: To evaluate the long-term results of surgical treatment for the children with persistent pupillary membrane. Method: A retrospective study comprised of 12 eyes of 11 Korean patients who underwent surgical removal of persistent pupillary membrane who could be followed up beyond 4 years of age, excluding eyes with any other vision-affecting ocular anomalies. The preoperative and final visual acuity, age at surgery, final refractive status, surgical complication and combined ocular abnormality were reviewed. Mean visual acuity was calculated using logarithm of minimum angle of resolution (logMAR). Results: Mean final BCVA was 20/257 (logMAR 1.110.68) in the unilateral 5 eyes and 20/33 (logMAR 0.220.25) in the bilateral 7 eyes, and there was significant difference (p=0.03).Of the 12 eyes, five eyes were under 0.3 at the last follow-up. Four eyes were unilateral (deprivation amblyopia) and one eye was bilateral (anisometropic amblyopia). Significant anisometropia was found in 7 of the 11 patients. One mild capsular opacity occurred as a postoperative complication. Conclusions: The visual prognoses for eyes with surgically removed persistent pupillary membranes were relatively good if they were bilateral. However, they showed poor visual outcome if they were unilateral in this study, so the early surgical intervention and aggressive management will be helpful if the persistent pupillary membrane is unilateral. Close follow-up with evaluation of visual acuity and refractive status is mandatory because this condition can lead to deprivation amblyopia and anisometropic amblyopia.