gebhart/patrepeval huggingface dataset:
Gingipains from Porphyromonas gingivalis W83 Synergistically Disrupt Endothelial Cell Adhesion and Can Induce Caspase-Independent Apoptosis (2006)

We have shown previously that gingipains from Porphyromonas gingivalis W83 can induce cell detachment, cell adhesion molecule (CAM) cleavage, and apoptosis in endothelial cells; however, the specific roles of the individual gingipains are unclear. Using purified gingipains, we determined that each of the gingipains can cleave CAMs to varying degrees with differing kinetics. Kgp and HRgpA work together to quickly detach endothelial cells. Interestingly, in the absence of active caspases, both gingipain-active W83 extracts and purified HRgpA and RgpB induce apoptotic morphology, suggesting that the gingipains can induce both caspase-dependent and caspase-independent apoptosis. Using z-VAD-FMK to inhibit Kgp activity and leupeptin to inhibit Rgp activity in gingipain-active W83 extracts, we investigated the relative significance of the synergistic role of the gingipains. z-VAD-FMK or leupeptin delayed, but did not inhibit, cell detachment induced by gingipain-active W83 extracts or purified gingipains. There was partial cleavage of N-cadherin and cleavage of VE-cadherin was not inhibited. Degradation of integrin beta1 was inhibited only in the presence of z-VAD-FMK. These results further clarify the role P. gingivalis plays in tissue destruction occurring in the periodontal pocket.
Improved energy efficiency for wireless SC MIMO through data-dependent superimposed training (2012)

In this paper, we compare the energy efficiency of a single carrier multiple-input multiple-output communications in terms of the energy per data bit required to achieve desired performance level or throughput. The comparison on energy efficiency is done between traditional time-domain multiplexed training and a more recently introduced data-dependent superimposed training. We extend our earlier single-input multiple-output system to the multiple-input multiple-output case and show how the data-dependent superimposed training based system can achieve better energy efficiency in small and diversity enabled multiple-input multiple-output links. In addition, we present analytical mean squared error results for DDST based MIMO channel estimation and propose methods to improve their accuracy when using short channel estimators.
Ring resonator induced data timing skew in on-chip WDM optical interconnects (2008)

Device induced data timing skew in optical interconnects is investigated. Up to 28 ps timing skew is induced by ring-resonator cavity Q variation in 10 Gb/s NRZ on-chip scenario, which may lead to 6 dB signal eye opening penalty.
Iron(II)‐Catalyzed Trifluoromethylation of Potassium Vinyltrifluoroborates (2012)

Austausch von BF3 durch CF3: Die Titelreaktion verläuft unter äußerst milden Reaktionsbedingungen und liefert 2-Arylvinyl- und 2-Heteroarylvinyl-substituierte Produkte mit E/Z-Selektivitäten von mehr als 95:5. Experimentelle Befunde sprechen dafür, dass die Reaktion nicht über eine Transmetallierung der RBF3K-Spezies zum Eisenkatalysator verläuft.
Potentiometric Cholesterol Biosensor Based on ZnO Nanowalls and Stabilized Polymerized Lipid Film (2012)

Abstract A novel potentiometric cholesterol biosensor was fabricated by immobilization of cholesterol oxidase into stabilized lipid films using zinc oxide (ZnO) nanowalls as measuring electrode. Cholesterol oxidase was incorporated into the lipid film prior polymerization on the surface of ZnO nanowalls resulting in a sensitive, selective, stable and reproducible cholesterol biosensor. The potentiometric response was 57 mV/ decade concentration. The sensor response had no interferences by normal concentrations of ascorbic acid, glucose, and urea, proteins and lipids. The present biosensor could be implanted in the human body because of the biocompatibility of the lipid film.
The tongue and ear interface (2014)

We address the problem of performing silent speech recognition where vocalized audio is not available (e.g. due to a user's medical condition) or is highly noisy (e.g. during firefighting or combat). We describe our wearable system to capture tongue and jaw movements during silent speech. The system has two components: the Tongue Magnet Interface (TMI), which utilizes the 3-axis magnetometer aboard Google Glass to measure the movement of a small magnet glued to the user's tongue, and the Outer Ear Interface (OEI), which measures the deformation in the ear canal caused by jaw movements using proximity sensors embedded in a set of earmolds. We collected a data set of 1901 utterances of 11 distinct phrases silently mouthed by six able-bodied participants. Recognition relies on using hidden Markov model-based techniques to select one of the 11 phrases. We present encouraging results for user dependent recognition.
Stimulation of T Cells Through the CD3/T-Cell Receptor Complex: Role of Cytoplasmic Calcium, Protein Kinase C Translocation, and Phosphorylation of pp60c-src in the Activation Pathway (1987)

Stimulation of T cells or the Jurkat T-cell line with soluble antibodies to the CD3/T-cell receptor complex causes mobilization of cytoplasmic Ca2+, which is blocked by pertussis toxin but not by ethylene glycol-bis(beta-aminoethyl ether)-N,N,N',N'-tetraacetic acid, and translocation of protein kinase C activity from the cytoplasm to the membrane. Such stimulation also causes phosphorylation of pp60c-src at an amino-terminal serine residue. These activities are consistent with induction of phosphatidylinositol metabolism after antibody binding. Anti-CD3 stimulation with antibody in solution, however, does not cause Jurkat cells to release interleukin 2 and blocks rather than induces proliferation of T cells. Induction of interleukin 2 production by Jurkat cells and proliferation by normal T cells requires anti-CD3 stimulation with antibody on a solid support, such as Sepharose beads or a plastic dish. Thus, we examined phosphorylation of pp60c-src after stimulation of Jurkat cells with anti-CD3 in solution or on solid phase. Both of these caused serine phosphorylation of pp60c-src that was indistinguishable even after 4 h of stimulation. These results indicate that the mode of anti-CD3 stimulation (in solution or on solid phase) controls a cellular function that modifies the consequences of signal transduction through phosphatidylinositol turnover.
Pachydermodactyly (1985)

Pachydermodactyly is a rare distinct form of fibromatosis characterized by dense fibrosis and fibroblastic proliferation around one or more proximal interphalangeal joints. Pachydermodactyly affects the appositional and dorsal aspects of proximal digits II-V. The lateral aspects of the index fingers, the medial aspect of the fifth digits, and the thumbs are usually unaffected. A typical patient was a young adult man with a long history of idiopathic asymptomatic swelling in the fingers. Skin biopsy specimens obtained from three patients with pachydermodactyly showed marked thickening of the dermis with extension of collagenous fibers into the subcutaneous tissues. There was poor demarcation between the papillary and reticular dermis. The cytology of the fibroblasts appeared benign. Isolation of collagen from the involved sites revealed collagen Types I, III, and V in a pattern typical of fibromatoses; i.e. increased Types III and V. Compared with the collagen profile of normal reticular dermis, increased numbers of fine-diameter collagen fibers were notable in electron micrographs.
Improvements to the UMF assay (2008)

With the increasing price of manuka honey there are increasing calls for a more precise measurement of UMF activity. Two years ago i gave to the AMHA executive a written report on some work they had commissioned me to do investigating variation in the results in the essay. In this report I made some recommendations for improvements, but these were never adopted. Instead their approach has been to seek an alternative method, firstly assay by MIC, and then assay MGO content, despite my explaining why these methods would not be more accurate.
Metallomacrocycles as anion receptors: combining hydrogen bonding and ion pair based hosts formed from Ag(i) salts and flexible bis- and tris-pyrimidine ligands (2013)

Two self-assembled hosts are formed from Ag(I) salts and bis-pyrimidyl ligands and X-ray characterized. Both are able to incorporate two anions into the structure combining hydrogen bonding and electrostatic interactions.
Supplementary Table 1 from A Small-Molecule Inhibitor of Glucose Transporter 1 Downregulates Glycolysis, Induces Cell-Cycle Arrest, and Inhibits Cancer Cell Growth <i>In Vitro</i> and <i>In Vivo</i> (2023)

&lt;p&gt;PDF file, 122KB, Body composition of WZB117 treated tumor-bearing mice.&lt;/p&gt;
Intracellular Localization of a Trypanosoma cruzi kDNA Minicircle Transcript Using RNA: RNA In Situ Hybridization (1994)

Using RNA: RNA in situ hybridization, the intracellular location of a transcript encoded by and spanning the entire length of a Trypanosoma cruzi kinetoplast DNA minicircle was determined. In axenically cultured T. cruzi epimastigotes, the hybridization signal was restricted to the kinetoplast, which was situated in the perinuclear region of the cell. Following conversion of epimastigotes to culture-derived metacyclic trypomastigotes, the kinetoplast moved to an acentric position in the metacyclic trypomastigote. Again, the hybridization signal co-localized with the position of the kinetoplast. These results suggested that the transcript remained closely associated with the T. cruzi kinetoplast within the mitochondrion in each of the morphological forms. Using specific oligonucleotide probes derived from a cDNA encoding the transcript, the entire native kDNA minicircle encoding the transcript was cloned and its nucleotide sequence was determined. The nucleotide sequence of the intact native minicircle was identical to that of the full-length cDNA corresponding to the minicircle transcript, indicating that the transcript was not modified prior to the time of cDNA synthesis and cloning.
Membrane-Interactive Compounds From Pistacia lentiscus L. Thwart Pseudomonas aeruginosa Virulence (2020)

<i>Pseudomonas aeruginosa</i> is capable to deploy a collection of virulence factors that are not only essential for host infection and persistence, but also to escape from the host immune system and to become more resistant to drug therapies. Thus, developing anti-virulence agents that may directly counteract with specific virulence factors or disturb higher regulatory pathways controlling the production of virulence armories are urgently needed. In this regard, this study reports that <i>Pistacia lentiscus</i> L. fruit cyclohexane extract (PLFE1) thwarts <i>P. aeruginosa</i> virulence by targeting mainly the pyocyanin pigment production by interfering with 4-hydroxy-2-alkylquinolines molecules production. Importantly, the anti-virulence activity of PLFE1 appears to be associated with membrane homeostasis alteration through the modulation of SigX, an extracytoplasmic function sigma factor involved in cell wall stress response. A thorough chemical analysis of PLFE1 allowed us to identify the ginkgolic acid (C17:1) and hydroginkgolic acid (C15:0) as the main bioactive membrane-interactive compounds responsible for the observed increased membrane stiffness and anti-virulence activity against <i>P. aeruginosa</i>. This study delivers a promising perspective for the potential future use of PLFE1 or ginkgolic acid molecules as an adjuvant therapy to fight against <i>P. aeruginosa</i> infections.
A Family of Generalized Diagnostic Classification Models for Multiple Choice Option-Based Scoring (2014)

This article proposes a new family of diagnostic classification models (DCM) called the Generalized Diagnostic Classification Models for Multiple Choice Option-Based Scoring (GDCM-MC). The GDCM-MC is created for multiple choice assessments with response options designed to attract particular kinds of student thinking and understanding, both desired (correct) thinking and problematic (incorrect or partially correct) thinking. Key features that combine to distinguish GDCM-MC are: (a) an expanded latent space that can include both desirable and problematic facets of thinking, (b) an expanded <b>Q</b> matrix that includes a row for each response option and that uses a three-valued coding scheme to specify which latent states are strongly attracted to that option, (c) a guessing component that responds to the forced choice aspect of multiple choice questions, and (d) a general modeling framework that can incorporate the diagnostic modeling functionality of almost any dichotomous DCM, such as deterministic input, noisy ``and'' gate (DINA), reparameterized unified model (RUM), loglinear cognitive diagnosis model (LCDM), or general diagnostic model (GDM). The article discusses these four components and presents the GDCM-MC model equation as a mixture of cognitive and guessing components. Two identifiability theorems are presented. A Bayesian Markov Chain Monte Carlo (MCMC) model estimation algorithm is discussed, and real and simulated data studies are reported.
A stable zerovalent palladium chain enveloped by a π-electron sheath of conjugated polyene ligands (2008)

A surprisingly stable homoleptic Pd(0)(4) chain complex of non-activated olefins was isolated and structurally characterized by X-ray crystallographic analysis, and the unique structure and bonding are compared to those of the corresponding dicationic [Pd(4)](2+) chain sandwich complex.
Modeling heterogeneous materials via two-point correlation functions. II. Algorithmic details and applications (2008)

In the first part of this series of two papers, we proposed a theoretical formalism that enables one to model and categorize heterogeneous materials (media) via two-point correlation functions S(2) and introduced an efficient heterogeneous-medium (re)construction algorithm called the "lattice-point" algorithm. Here we discuss the algorithmic details of the lattice-point procedure and an algorithm modification using surface optimization to further speed up the (re)construction process. The importance of the error tolerance, which indicates to what accuracy the media are (re)constructed, is also emphasized and discussed. We apply the algorithm to generate three-dimensional digitized realizations of a Fontainebleau sandstone and a boron-carbide/aluminum composite from the two-dimensional tomographic images of their slices through the materials. To ascertain whether the information contained in S(2) is sufficient to capture the salient structural features, we compute the two-point cluster functions of the media, which are superior signatures of the microstructure because they incorporate topological connectedness information. We also study the reconstruction of a binary laser-speckle pattern in two dimensions, in which the algorithm fails to reproduce the pattern accurately. We conclude that in general reconstructions using S(2) only work well for heterogeneous materials with single-scale structures. However, two-point information via S(2) is not sufficient to accurately model multiscale random media. Moreover, we construct realizations of hypothetical materials with desired structural characteristics obtained by manipulating their two-point correlation functions.
Spatially coupled ensembles universally achieve capacity under belief propagation (2012)

We investigate spatially coupled code ensembles. For transmission over the binary erasure channel, it was recently shown that spatial coupling increases the belief propagation threshold of the ensemble to essentially the maximum a-priori threshold of the underlying component ensemble. This explains why convolutional LDPC ensembles, originally introduced by Felström and Zigangirov, perform so well over this channel. We show that the equivalent result holds true for transmission over general binary-input memoryless output-symmetric channels. More precisely, given a desired error probability and a gap to capacity, we can construct a spatially coupled ensemble which fulfills these constraints universally on this class of channels under belief propagation decoding. In fact, most codes in that ensemble have that property. The quantifier universal refers to the single ensemble/code which is good for all channels if we assume that the channel is known at the receiver. The key technical result is a proof that under belief propagation decoding spatially coupled ensembles achieve essentially the area threshold of the underlying uncoupled ensemble. We conclude by discussing some interesting open problems.
ATP‐binding cassette member A3 (E292V) gene mutation and pulmonary morbidity in very‐low‐birth‐weight infants (2011)

Within the size limits of our study cohort, the ABCA3 missense mutation E292V had no remarkable effect on pulmonary outcome in VLBW infants. Present results do not rule out the possibility that E292V phenotype is associated with minor difference in the morbidity.
Structure and Excited‐State Interactions in Composites of CdSe Nanorods and Interface‐Compatible Polythiophene‐graft‐poly(N,N‐dimethylaminoethyl methacrylates) (2009)

Abstract We report the preparation and characterization of two comb‐like graft copolymers, polythiophene‐ graft ‐poly( N , N ‐dimethylaminoethyl methacrylates) (PT 700 ‐ g ‐PDMA 60 and PT 220 ‐ g ‐PDMA 16 , where the subscripts represent the number average degree of polymerization), and an investigation of their interaction with CdSe nanorods. Each polymer contains a regiorandom polythiophene (PT) as the backbone, from which poly( N , N ‐dimethylaminoethyl methacrylate) (PDMA) chains are densely grafted. The PDMA arms serve as multidentate ligands for CdSe semiconductor nanocrystals and increase the compatibility between the PT backbone and the nanocrystals. Using electron microscopy, we examined the morphology and the internal structure of the nanorod/polymer composites formed in toluene. The morphology and the internal structure of the composites vary with a change in the nanorod/polymer ratio as well as with the concentration of each component. The results of steady‐state fluorescence spectroscopy indicate that the presence of the nanocrystals in toluene leads to photoluminescence (PL) quenching of the PT backbone in the graft copolymer with relatively short PDMA arms (PT 220 ‐ g ‐PDMA 16 ). In contrast, no PL quenching could be detected in composites formed from a similar polymer with longer PDMA arms (PT 700 ‐ g ‐PDMA 60 ). A likely explanation of this result is that in composites formed with PT 700 ‐ g ‐PDMA 60 , the nanocrystals are held too far from the PT backbone for energy transfer or charge transfer to take place. magnified image
Progressive Osteolysis and Surface Chondrolysis of the Proximal Humerus Following Influenza Vaccination (2012)

Influenza vaccination is a common annual event among individuals in the United States. Complications, although infrequent, are usually mild and self-limiting. This article describes the case of a 46-year-old man who experienced progressive osteolysis and surface chondrolysis of the proximal humerus following routine influenza vaccination. The patient presented with shoulder pain and limited range of motion 3 weeks following vaccination in the deltoid area. No skin changes were noted, inflammatory markers were normal, and the patient's pain and disability persisted despite nonsteroidal anti-inflammatory drugs and occupational therapy. Plain radiographs revealed a small lytic area involving the greater tuberosity of the humeral head. Magnetic resonance imaging (MRI) showed abnormal uptake and cystic changes involving the greater tuberosity of the humeral head; repeat MRI at 5 months showed progression in the cystic changes. Diagnostic arthroscopy of the shoulder revealed a hyperemic joint capsule and extensive, full-thickness chondrolysis of the humeral head. Cystic biopsy demonstrated inflammatory cells and granulation tissue, consistent with foreign body response. Cultures were negative. Surgical debridement of the cystic areas and resurfacing of the humeral head yielded a good outcome. To our knowledge, this is the first reported complication of influenza vaccination requiring surgical intervention. Physicians need to be aware of the potential for osteolysis and chondrolysis, which may require aggressive forms of management.
Biological activities of an engineered tautomycetin analogue via disruption of tmcR-encoding hydroxylase in Streptomyces sp. CK4412 (2012)

Tautomycetin (TMC), originally isolated from Streptomyces griseochromogenes, has been reported to possess biological functions including T cell-specific immunosuppressive and anticancer activities through a mechanism of differential inhibition of protein phosphatases such as PP1, PP2A, and SHP2. Independently isolated Streptomyces sp. CK4412 was also reported to produce a structurally identical TMC compound. Previously, we isolated and characterized the entire TMC biosynthetic gene cluster from Streptomyces sp. CK4412. In silico database comparison revealed a 1,359-bp tmcR as a putative bacterial Cytochrome P450 hydroxylase gene in the TMC biosynthetic gene cluster. Through targeted gene disruption and complementation, the tmcR mutant was confirmed to produce a C5-deoxy-TMC, the same analogue produced by the S. griseochromogenes ttnI mutant, implying that TmcR behaves as a regiospecific C5-oxygenase in the TMC biosynthetic pathway in Streptomyces sp. CK4412. In particular, the C5-deoxy-TMC from the tmcR mutant exhibited 3.2-fold higher inhibition activity toward SHP2 with significantly reduced inhibition activities toward PP1, and human Vero and lung cancer cells. These results suggested that C5 regiospecific modification of the TMC polyketide moiety may result in a drug development target for use in preferentially enhancing immunosuppressive activity while minimizing its undesirable biological activities.
Kernel Bayesian Inference with Posterior Regularization (2016)

We propose a vector-valued regression problem whose solution is equivalent to the reproducing kernel Hilbert space (RKHS) embedding of the Bayesian posterior distribution. This equivalence provides a new understanding of kernel Bayesian inference. Moreover, the optimization problem induces a new regularization for the posterior embedding estimator, which is faster and has comparable performance to the squared regularization in kernel Bayes' rule. This regularization coincides with a former thresholding approach used in kernel POMDPs whose consistency remains to be established. Our theoretical work solves this open problem and provides consistency analysis in regression settings. Based on our optimizational formulation, we propose a flexible Bayesian posterior regularization framework which for the first time enables us to put regularization at the distribution level. We apply this method to nonparametric state-space filtering tasks with extremely nonlinear dynamics and show performance gains over all other baselines.
A pilot multicenter randomized controlled trial comparing Bankart repair and remplissage with the Latarjet procedure in patients with subcritical bone loss (STABLE): study protocol (2022)

This study has ethics approval from the McMaster University/Hamilton Health Sciences Research Ethics Board (REB) (approval #4942). Successful completion will significantly impact the global management of patients with recurrent instability. This trial will develop a network of collaboration for future high-quality trials in shoulder instability.
Supplementary Figure 2 from Novel Target for Peptide-Based Imaging and Treatment of Brain Tumors (2023)

&lt;p&gt;PDF - 8691K, MDGI expression in glioma xenografts.&lt;/p&gt;