gebhart/patrepeval huggingface dataset:
Thermal crystallization of amorphous calcium phosphate combined with citrate and fluoride doping: a novel route to produce hydroxyapatite bioceramics (2021)

Amorphous calcium phosphate (ACP) is a material of high interest for dentistry, orthopedics, and other biomedical sectors. Being intrinsically metastable, the process of transformation of ACP into a crystalline phase upon heating is of high relevance for the development of innovative bioceramics. Here we have first studied the thermal behavior of a citrate-stabilized ACP (Cit-ACP) also doped with fluoride ions (Cit-FACP) prepared at three different nominal Cit/Ca ratios (i.e. 4, 2, 1) by differential thermal analysis. Next, the physico-chemical features of the crystalline products as well as the in vitro cell response to the materials were investigated. A citrate and fluoride free ACP sample was also tested as the blank. We have found that the activation energy of crystallization of Cit-(F)ACP samples is lower in comparison to the blank ACP and this is influenced by the nominal Cit/Ca molar ratio. Interestingly, we have discovered that the thermal treatment of Cit-(F)ACP at 800 °C yields hydroxyapatite (HA) or fluorapatite (FHA) as the main products differently from blank ACP that, like most of the ACPs reported in the literature, yields β-tricalcium phosphate. This was attributed to the Ca/P ratio of Cit-(F)ACP, which is similar to HA. A study of the crystalline products has revealed that all the (F)HA samples were non-cytotoxic, and retained carbonate ions in the crystal structure despite the heat treatment that should have induced decarbonation. The morphology of the products is influenced by the nominal Cit/Ca ratio and the presence of fluoride, ranging from spherical nanoparticles to micrometric hexagonal rods. Overall, our results prove that the thermal crystallization of Cit-(F)ACP is markedly different from classic ACP based materials and the thermal treatment of Cit-(F)ACP represents an attractive route for producing pure bioactive HA ceramics.
Automated Non-Invasive Measurement of Single Sperm’s Motility and Morphology (2018)

Measuring cell motility and morphology is important for revealing their functional characteristics. This paper presents automation techniques that enable automated, non-invasive measurement of motility and morphology parameters of single sperm. Compared to the status quo of qualitative estimation of single sperm's motility and morphology manually, the automation techniques provide quantitative data for embryologists to select a single sperm for intracytoplasmic sperm injection. An adapted joint probabilistic data association filter was used for multi-sperm tracking and tackled challenges of identifying sperms that intersect or have small spatial distances. Since the standard differential interference contrast (DIC) imaging method has side illumination effect which causes inherent inhomogeneous image intensity and poses difficulties for accurate sperm morphology measurement, we integrated total variation norm into the quadratic cost function method, which together effectively removed inhomogeneous image intensity and retained sperm's subcellular structures after DIC image reconstruction. In order to relocate the same sperm of interest identified under low magnification after switching to high magnification, coordinate transformation was conducted to handle the changes in the field of view caused by magnification switch. The sperm's position after magnification switch was accurately predicted by accounting for the sperm's swimming motion during magnification switch. Experimental results demonstrated an accuracy of 95.6% in sperm motility measurement and an error <10% in morphology measurement.
Revisiting Spectral Printing: A Data Driven Approach (2012)

Spectral printing is a well–established part of imaging that can boast of a rich body of literature. Nonetheless there has been limited commercial uptake of this approach to visual content reproduction, in spite of its clear benefits. The aim of the present paper is therefore to explore what may lie behind this apparent mismatch by looking at how colorimetric (metameric) and spectral reproduction compare on an 11–ink printing system. To aid the above exploration, the paper proposes a new metric for evaluating spectral reproduction in a visually meaningful way and presents an analysis of the spectral properties of colorimetric and spectral reproductions of a variety of original content including spot colors and fine art.
Polymers containing the [2H]‐1,2,4‐triazoline‐3‐thione ring (1987)

Abstract High‐molecular‐weight polymers containing [2H]‐1,2,4‐triazoline‐3‐thione rings are prepared by the condensations of diisothiocyanates with bis(acid hydrazides) to give intermediate polymeric acylthiosemicarbazides that are ring‐closed by refluxing in 1 M aqueous sodium carbonate. Thermal cyclization of the polymeric acylthiosemicarbazides leads to cross‐linked insoluble products. The acylation of bis(thiosemicarbazides) with bis(acid chlorides) produces polymers of a similar structure but lower molecular weight.
Non-line-of-sight 3D imaging (Conference Presentation) (2018)

In an optical Line-of-Sight (LOS) scenario, such as one involving a LIDAR system, the goal is to recover an image of a target in the direct path of the transmitter and receiver. In Non-Line-of-Sight (NLOS) scenarios the target is hidden from both the transmitter and the receiver by an occluder, i.e. a wall. Recent advancements in technology, computer vision and inverse light transport theory have shown that it is possible to recover an image of a hidden target by exploiting the temporal information encoded in multiple-scattered photons. The core idea is to acquire data using an optical system, composed of an ultra-fast laser that emits short pulses (in the order of femtoseconds) and a camera capable of recovering the photons time-of-flight information (a typical resolution is in the order of picoseconds). We reconstruct 3D images from this data based on the backprojection algorithm, a method typically found in the computational tomography field, which is parallelizable and memory efficient, although it only provides an approximate solution. Here we present improved backprojection algorithms for applications to large scale scenes with with a large number of scatterers and meters to hundreds of meters diameter. We apply these methods to the NLOS imaging of rooms and lunar caves.
Zombie memory: Extending memory lifetime by reviving dead blocks (2013)

Zombie is an endurance management framework that enables a variety of error correction mechanisms to extend the lifetimes of memories that suffer from bit failures caused by wearout, such as phase-change memory (PCM). Zombie supports both single-level cell (SLC) and multi-level cell (MLC) variants. It extends the lifetime of blocks in working memory pages (primary blocks) by pairing them with spare blocks, i.e., working blocks in pages that have been disabled due to exhaustion of a single block's error correction resources, which would be 'dead' otherwise. Spare blocks adaptively provide error correction resources to primary blocks as failures accumulate over time. This reduces the waste caused by early block failures, making working blocks in discarded pages a useful resource. Even though we use PCM as the target technology, Zombie applies to any memory technology that suffers stuck-at cell failures.
Bifunctional Organometallic Catalysts Involving Proton Transfer or Hydrogen Bonding (2005)

Inspired by the cooperativity displayed by metalloenzymes, bifunctional organometallic complexes featuring pendant basic functional groups are designed and evaluated as catalysts in reactions for which enzymes are not suited. Anti-Markovnikov hydration of terminal alkynes is the focus, as are hydrogen bonding and proton transfer facilitated by the pendant groups.
Generalized occurrence of the broadly antiviral substance UTI beta in mammalian sera. (1993)

This study compares the characteristics of naturally occurring antiviral activities in nonhuman mammalian sera to UTI beta (University of Texas virus inhibitor beta), an innate, non-specific viral inhibitor found in human serum. The antiviral agent in sera from four different species appears to possess properties similar to those of UTI beta, e.g. molecular weight of 60 +/- 10 kDa, broad spectrum antiviral activity, glycoprotein structure with antiviral oligosaccharide moiety(s) attached to a carrier protein, and inhibition of most viruses by preventing their attachment to target cells. These findings suggest that UTI beta or UTI beta-like virus inhibitors are a normal component of the non-specific immune defenses of mammals.
A gene-edited mouse model of limb-girdle muscular dystrophy 2C for testing exon skipping (2019)

Limb-girdle muscular dystrophy type 2C is caused by autosomal recessive mutations in the γ-sarcoglycan (<i>SGCG</i>) gene. The most common <i>SGCG</i> mutation is a single nucleotide deletion from a stretch of five thymine residues in <i>SGCG</i> exon 6 (521ΔT). This founder mutation disrupts the transcript reading frame, abolishing protein expression. An antisense oligonucleotide exon-skipping method to reframe the human 521ΔT transcript requires skipping four exons to generate a functional, internally truncated protein. <i>In vivo</i> evaluation of this multi-exon skipping, antisense-mediated therapy requires a genetically appropriate mouse model. The human and mouse γ-sarcoglycan genes are highly homologous in sequence and gene structure, including the exon 6 region harboring the founder mutation. Herein, we describe a new mouse model of this form of limb-girdle muscular dystrophy generated using CRISPR/Cas9-mediated gene editing to introduce a single thymine deletion in murine exon 6, recreating the 521ΔT point mutation in <i>Sgcg</i> These mice express the 521ΔT transcript, lack γ-sarcoglycan protein and exhibit a severe dystrophic phenotype. Phenotypic characterization demonstrated reduced muscle mass, increased sarcolemmal leak and fragility, and decreased muscle function, consistent with the human pathological findings. Furthermore, we showed that intramuscular administration of a murine-specific multiple exon-directed antisense oligonucleotide cocktail effectively corrected the 521ΔT reading frame. These data demonstrate a molecularly and pathologically suitable model for <i>in vivo</i> testing of a multi-exon skipping strategy to advance preclinical development of this genetic correction approach.
Design and Optimization of 20-O-Linked Camptothecin Glycoconjugates as Anticancer Agents (2001)

To improve the biological profile of 20(S)-camptothecin, a novel class of 20-O-linked camptothecin glycoconjugates has been designed for preferential cellular uptake into tumor cells by an active transport mechanism. Such conjugates have been optimized for enhanced solubility, stabilization of the camptothecin lactone ring, sufficient hydrolytic and proteolytic stability, and for an overall improvement in tumor selectivity. The constitution of the peptide spacer has a major impact on stability and biological activity of the conjugates both in vitro and in vivo. Glycoconjugates 17-22 with valine residues at the linkage position to camptothecin are sufficiently stable and show good antitumor activity in vitro against HT29 and other tumor cell lines. Fluorescence microscopy and flow cytometry experiments indicate that glycoconjugates such as 19 are taken up into lysosomal compartments of the tumor cell line HT29 by an active transport mechanism. The steric configuration of the particular amino acid residues linked to the camptothecin moiety has a major impact on the in vivo activity of the corresponding glycoconjugates in the breast cancer xenograft MX-1 model. Inhibiting tumor growth by >96%, the glycoconjugates 19 and 21 show the best activity in this particular model and have been investigated more extensively. The glycoconjugate 19 compares favorably to topotecan 4 and glycoconjugate 21 with respect to toxicity against hematopoietic stem cells and hepatocytes. Based on its profile, 19 has been selected for clinical trials.
Fused vertical directional couplers (2002)

Integrated waveguide couplers and switches are important devices for optical communication systems. In order to fabricate large size switches, it is essential to have compact, high extinction ratio directional couplers. In this paper we analyze the use of wafer fusion to give an extra degree of freedom in the fabrication of coupled waveguide structures. The technique of wafer fusion has been used to combine materials of very different lattice constant which could not be grown by heteroepitaxy.
Self-Learning Classifier for Internet traffic (2013)

Network visibility is a critical part of traffic engineering, network management, and security. Recently, unsupervised algorithms have been envisioned as a viable alternative to automatically identify classes of traffic. However, the accuracy achieved so far does not allow to use them for traffic classification in practical scenario. In this paper, we propose SeLeCT, a Self-Learning Classifier for Internet traffic. It uses unsupervised algorithms along with an adaptive learning approach to automatically let classes of traffic emerge, being identified and (easily) labeled. SeLeCT automatically groups flows into pure (or homogeneous) clusters using alternating simple clustering and filtering phases to remove outliers. SeLeCT uses an adaptive learning approach to boost its ability to spot new protocols and applications. Finally, SeLeCT also simplifies label assignment (which is still based on some manual intervention) so that proper class labels can be easily discovered. We evaluate the performance of SeLeCT using traffic traces collected in different years from various ISPs located in 3 different continents. Our experiments show that SeLeCT achieves overall accuracy close to 98%. Unlike state-of-art classifiers, the biggest advantage of SeLeCT is its ability to help discovering new protocols and applications in an almost automated fashion.
Programmed loading and rapid purification of engineered bacterial microcompartment shells (2018)

Bacterial microcompartments (BMCs) are selectively permeable proteinaceous organelles which encapsulate segments of metabolic pathways across bacterial phyla. They consist of an enzymatic core surrounded by a protein shell composed of multiple distinct proteins. Despite great potential in varied biotechnological applications, engineering efforts have been stymied by difficulties in their isolation and characterization and a dearth of robust methods for programming cores and shell permeability. We address these challenges by functionalizing shell proteins with affinity handles, enabling facile complementation-based affinity purification (CAP) and specific cargo docking sites for efficient encapsulation via covalent-linkage (EnCo). These shell functionalizations extend our knowledge of BMC architectural principles and enable the development of minimal shell systems of precisely defined structure and composition. The generalizability of CAP and EnCo will enable their application to functionally diverse microcompartment systems to facilitate both characterization of natural functions and the development of bespoke shells for selectively compartmentalizing proteins.
Alkylamine-Substituted Perthiocarbamates: Dual Precursors to Hydropersulfide and Carbonyl Sulfide with Cardioprotective Actions (2020)

The recent discovery of hydropersulfides (RSSH) in mammalian systems suggests their potential roles in cell signaling. However, the exploration of RSSH biological significance is challenging due to their instability under physiological conditions. Herein, we report the preparation, RSSH-releasing properties, and cytoprotective nature of alkylamine-substituted perthiocarbamates. Triggered by a base-sensitive, self-immolative moiety, these precursors show efficient RSSH release and also demonstrate the ability to generate carbonyl sulfide (COS) in the presence of thiols. Using this dually reactive alkylamine-substituted perthiocarbamate platform, the generation of both RSSH and COS is tunable with respect to half-life, pH, and availability of thiols. Importantly, these precursors exhibit cytoprotective effects against hydrogen peroxide-mediated toxicity in H9c2 cells and cardioprotective effects against myocardial ischemic/reperfusion injury, indicating their potential application as new RSSH- and/or COS-releasing therapeutics.
On relaxing the strict hierarchical constraints in layered coding of audio signals (2014)

Scalable coders generate hierarchically layered bitstreams to serve content at different quality levels, wherein the base layer provides a coarse quality reconstruction and successive layers incrementally refine the quality. However, it is widely recognized that there is an inherent performance penalty due to the scalable coding structure, when compared to independently encoded copies. To mitigate this loss we propose a layered compression framework, having roots in information theoretic concepts, which relaxes the strict hierarchical constraints, wherein only a “subset” of the information of a lower quality level is shared with higher quality levels. In other words, there is flexibility to also have “private” information at each quality level, beside information that is common to multiple levels. We employ this framework within the MPEG Scalable AAC and propose an optimization scheme to jointly select parameters of all the layers. Experimental evaluation results demonstrate the utility of the flexibility provided by the proposed framework.
Associations of marker panel scores with feed intake and efficiency traits in beef cattle using preselected single nucleotide polymorphisms1 (2011)

Because of the moderate heritability and the expense associated with collecting feed intake data, effective selection for residual feed intake would be enhanced if marker-assisted evaluation were used for accurate estimation of genetic merit. In this study, a suite of genetic markers predictive of residual feed intake, DMI, and ADG were preselected using single-marker regression analysis, and the top 100 SNP were analyzed further to provide prediction equations for the traits. The data used consisted of 728 spring-born beef steers, offspring of a cross between a composite dam line and Angus, Charolais, or University of Alberta hybrid bulls. Feed intake data were collected over a 5-yr period, with 2 groups (fall-winter and winter-spring) tested every year. Training and validation data sets were obtained by splitting the data into 2 distinct sets, by randomly splitting the data into training and testing sets based on sire family (split 1) in 5 replicates or by retaining all animals with no known pedigree relationships as the validation set (split 2). A total of 37,959 SNP were analyzed by single-marker regression, of which only the top 100 that corresponded to a P-value <0.002 were retained. The 100 SNP were then analyzed using random regression BLUP, and only SNP that were jointly significant (P < 0.05) were included in the final marker panels. The marker effects from the selected panels were used to derive the molecular breeding values, which were calculated as a weighted sum of the number of copies of the more frequent allele at each SNP locus, with the weights being the allele substitution effects. The correlation between molecular breeding value and phenotype represented the accuracy of prediction. For all traits evaluated, accuracy across breeds was low, ranging between 0.007 and 0.414. Accuracy was least in data split 2, where the validation individuals had no pedigree relationship with animals in the training data. Given the low predictive ability observed, a large number of individuals may be needed for prediction when using such an admixed population. Further, these results suggest that breed composition of the target population in which the marker panels are likely to be used should be an important consideration when developing prediction equations across breeds, especially where an admixed population is used as the training data set.
Modelling and characterisation of a micropole undulator with a 726μm period (1987)

Micropole undulators (i.e. undulators with submillimetre periods) have the potential for fundamentally transforming the current state of synchrotron radiation technology. For example, brightness and photon energy resolution exceeding those of conventional insertion devices will become available on storage rings of much lower energy than those in present use. The authors report on the measurement and modelling of a recently built prototype device consisting of thirty-five 726 mu m periods. This device was constructed on the basis of a novel approach that, coupled with the particular configuration of its permanent magnet and soft steel elements, constitutes a design scheme that will eventually enable much shorter periods to be reached.
ChemInform Abstract: HIGHLY SELECTIVE INHIBITORS OF THROMBOXANE SYNTHETASE. 1. IMIDAZOLE DERIVATIVES (1982)

Abstract Der Halbester (I) wird zum Imidazol (II) cyclisiert, aus dem man die Carbonsäure (III) erhält.
Permanent Magnet Generator with Mechanical Controller (2005)

The power generating efficiency of conventional automotive generators is about 50%. To install vehicles with larger high-power generators that are able to satisfy electrical demand would be difficult. This research project created a generator that uses a permanent magnet (PM) for the rotor and incorporates a new mechanical controller that obtains a generating efficiency of 90% and is capable of maintaining a constant voltage. An air-gap controller between the rotor and the stator was adapted to control the magnetic force in order to adjust the voltage to changes in speed and load.
Artificial Human Corneas (2002)

Novel tissue-engineered corneas that comprise composites of natural and synthetic biopolymers together with corneal cell lines or stem cells will, in the future, replace portions of the cornea that are damaged. Our results provide a basis for the development of both implantable temporary and permanent corneal replacements.
Identification and characterization of specific sequences encoding pathogenicity associated proteins in the genome of commensal<i>Neisseria</i>species (1995)

The distribution of distinct sequences in pathogenic and commensal Neisseria species was investigated systematically by dot blot analysis. Probes representing the genes of Rmp, pilin and IgA1 protease were found to hybridize exclusively to the chromosomal DNA of the pathogenic species, Neisseria gonorrhoeae and/or Neisseria meningitidis. In contrast, specific sequences for the genes of the porin protein Por and the opacity protein (Opa) were also detected in a panel of commensal Neisseria species such as N. lactamica, N. subflava, N. flava, N. mucosa and N. sicca. Using opa-specific oligonucleotides as probes in chromosomal blots, the genomes of the commensal Neisseria species show a totally reduced repertoire of cross-hybridizing loci compared to the complex opa gene family of N. gonorrhoeae. DNA sequence analysis of one opa-related gene derived from N. flava and N. sicca, respectively, revealed a large degree of homology with previously described gonococcal and meningococcal genes, e.g., a typical repetitive sequence in the leader peptide and the distribution of the hypervariable and conserved regions. This observation, together with the finding, that the gene is constitutively transcribed, leads to the assumption that some of the commensal Neisseria species may have the potential for the expression of a protein harboring similar functions as the Opa proteins in pathogenic Neisseriae.