gebhart/patrepeval huggingface dataset:
Inter-Frame Co-Registration of Dynamically Acquired Fluoro-Deoxyglucose Positron Emission Tomography Human Brain Data (2007)

When acquiring positron emission tomography (PET) brain scans dynamically from a patient, it would be helpful to be able to minimize confounding effects of his/her head movement. In this study, we attempted to coregister sequential frames in the dynamic fluorodeoxyglucose (FDG) PET image sequence, specifically addressing the challenge associated with the relatively low radiotracer uptake over the cortical areas in the early short frames. PET data were acquired dynamically over sixty minutes in three healthy volunteers (frame durations ranged from 2 seconds to 5 minutes). We realigned each of the early short frames to its immediate predecessor using normalized mutual information (NMI). Afterward, the same procedure was repeated to realign the summation of the early frames, as well as each of the later frames with durations of 5 minutes and sufficient cortical tracer uptake. To validate our proposed procedure, we artificially moved frames using known linear rotations and translocations and compared the 6 NMI estimated rigid-body transformation parameters to the actual misalignment parameters and compared image-derived carotid artery FDG input function in the realigned and original images. While counting statistics in the first 3 frames (22 seconds after FDG administration) precluded us from accurately addressing misalignments, the NMI reliably recovered translocations as great as 7 mm and rotations as great as 8 degrees for all other frames. Moreover, misalignment errors in the constructed input function from the carotid artery region were able to be corrected.
SeismoWatch (2017)

The current norm for measuring blood pressure (BP) at home is using an automated BP cuff based on oscillometry. Despite providing a viable and familiar method of tracking BP at home, oscillometric devices can be both cumbersome and inaccurate with the inconvenience of the hardware typically limiting measurements to once or twice per day. To address these limitations, a wrist-watch BP monitor was developed to measure BP through a simple maneuver: holding the watch against the sternum to detect micro-vibrations of the chest wall associated with the heartbeat. As a pulse wave propagates from the heart to the wrist, an accelerometer and optical sensor on the watch measure the travel time - pulse transit time (PTT) - to estimate BP. In this paper, we conducted a study to test the accuracy and repeatability of our device. After calibration, the diastolic pressure estimations reached a root-mean-square error of 2.9 mmHg. The watch-based system significantly outperformed (p<0.05) conventional pulse arrival time (PAT) based wearable blood pressure estimations - the most commonly used method for wearable BP sensing in the existing literature and commercial devices. Our device can be a convenient means for wearable BP monitoring outside of clinical settings in both health-conscious and hypertensive populations.<sup>1</sup>.
CD28 activation promotes Th2 subset differentiation by human CD4+ cells (1995)

Ligation of CD28 provides a costimulatory signal to T cells necessary for their activation resulting in increased interleukin (IL)-2 production in vitro, but its role in IL-4 and other cytokine production and functional differentiation of T helper (Th) cells remains uncertain. We studied the pattern of cytokine production by highly purified human adult and neonatal CD4+ T cells activated with anti-CD3, phorbol 12-myristate 13-acetate (PMA) and ionomycin, or phytohemagglutinin (PHA) in the presence or absence of anti-CD28 in repetitive stimulation-rest cycles. Initial stimulation of CD4+ cells with anti-CD3 (or the mitogens PHA or PMA+ionomycin) and anti-CD28 monoclonal antibodies induced IL-4, IL-5 and interferon-gamma (IFN-gamma) production and augmented IL-2 production (6- to 11-fold) compared to cells stimulated with anti-CD3 or mitogen alone. The anti-CD28-induced cytokine production corresponded with augmented IL-4 and IL-5 mRNA levels suggesting increased gene expression and/or mRNA stabilization. Most striking, however, was the progressively enhanced IL-4 and IL-5 production and diminished IL-2 and IFN-gamma production with repetitive consecutive cycles of CD28 stimulation. The enhanced Th2-like response correlated with an increased frequency of IL-4-secreting cells; up to 70% of the cells produced IL-4 on the third round of stimulation compared to only 5% after the first stimulation as determined by ELISPOT. CD28 activation also promoted a Th2 response in naive neonatal CD4+ cells, indicating that Th cells are induced to express a Th2 response rather than preferential expansion of already established Th2-type cells. This CD28-mediated response was IL-4 independent, since enhanced IL-5 production with repetitive stimulation cycles was not affected in the presence of neutralizing anti-IL-4 antibodies. These results indicate that CD28 activation may play an important role in the differentiation of the Th2 subset in humans.
Translocation of Bim to the Endoplasmic Reticulum (ER) Mediates ER Stress Signaling for Activation of Caspase-12 during ER Stress-induced Apoptosis (2004)

Endoplasmic reticulum (ER) stress activates caspase-12 in murine cells, triggering the ER stress-specific cascade for implementation of apoptosis. In C2C12 murine myoblast cells, activation of the cascade occurs without release of cytochrome c from mitochondria, suggesting that the cascade is independent of mitochondrial damage. Stable overexpression of Bcl-xL in C2C12 cells suppressed activation of caspase-12 and apoptosis. In ER-stressed cells, but not in normal cells, Bcl-xL was co-immunoprecipitated with Bim, a pro-apoptotic member of the Bcl-2 family, suggesting that Bcl-xL sequesters Bim, thereby inhibiting the apoptotic signaling. Fractionation of C2C12 cells revealed that ER stress led to translocation of Bim from a dynein-rich compartment to the ER, while stable overexpression of Bcl-xL suppressed accumulation of Bim on the ER. Although the toxic effect of Bim had been previously observed only at the mitochondrial outer membrane, overexpression of a Bim derivative, Bim(ER), targeted at the surface of the ER led to apoptosis. A C2C12 transfectant overexpressing the caspase-12 suppressor protein was resistant to Bim(ER), suggesting that the toxic effect of Bim on the ER is dependent on activation of caspase-12. Knockdown of Bim by RNA interference provided cells resistant to ER stress. These results suggest that translocation of Bim to the ER in response to ER stress is an important step toward activation of caspase-12 and initiation of the ER stress-specific caspase cascade.
Early expression of SCIN and CHIPS drives instant immune evasion by Staphylococcus aureus (2006)

Chemotaxis inhibitory protein of staphylococci (CHIPS) and Staphylococcal complement inhibitor (SCIN) are small, excreted molecules that play a crucial role in the staphylococcal defence against the human innate immune system. Here we show that they both counteract crucial acute responses of our immune system such as complement activation, neutrophil chemotaxis and neutrophil activation. By studying gene expression via promoter-green fluorescent protein fusions, Northern blots and protein expression analyses, we show that SCIN and CHIPS are produced during the early (exponential) growth stages. Although the SCIN and CHIPS genes are expressed simultaneously, they are differently regulated by various Staphylococcus aureus regulatory loci. However, the sae locus is crucial for upregulation of both SCIN and CHIPS. This is the first study that presents the expression of two extracellular S. aureus proteins early during growth. Because SCIN and CHIPS are both efficient modulators of neutrophil chemotaxis, phagocytosis and killing, their early expression is necessary for efficient modulation of the early immune response.
Quantitative proteomics by 2‐DE, 16O/18O labelling and linear ion trap mass spectrometry analysis of lymph nodes from piglets inoculated by porcine circovirus type 2 (2011)

Porcine circovirus type 2 (PCV2) has been identified as the essential causal agent of postweaning multisystemic wasting syndrome. However, little is known regarding the mechanism(s) underlying the pathogenesis of PCV2-induced disease and the interaction of the virus with the host immune system. Here, we present a proteomics study on inguinal lymph nodes of piglets inoculated with PCV2, in order to better understand the pathogenesis of postweaning multisystemic wasting syndrome and the pathways might be affected after infection. We used two proteomics strategies, 2-DE and 1-DE followed by (16)O/(18)O peptide labelling and peptide identification and quantification by MS. More than 100 proteins were found to be differentially regulated and the results obtained by the two strategies were fairly concordant but also complementary, the (18)O labelling approach being a more robust alternative. Analysis of these proteins by systems biology tools revealed the implication of acute phase response and NrF2-mediated oxidative stress, suggesting a putative role for these pathways in the pig immune response. Besides, CD81 was found to be up-regulated, suggesting a possible role in the internalization of the virus. The use of proteomics technologies together with biology analysis systems opens up the way to gain more exhaustive and systematic knowledge of virus-pathogen interactions.
Industrial Microprocessing Applications Of Excimer Lasers (1988)

ABSTRACT Various industrial microprocessing applications of excimer lasers will be reviewed as well as the requirement and suitability of excimer lasers for each application. 1. INTRODUCTION Excimer lasers excel in micromachining because the unique properties of pulsed ultraviolet light can be used to remove fine amounts of material or alter the properties of the product with high finesse. Typical materials which have been effectively drilled, cut and/or marked with an excimer laser beam include plastics, metals, ceramics and hard dielectrics.A diamond, for example, is a material which belongs to an unusually difficult group of materials for laser processing due to its unique optical properties. As the optical transmission curve would indicate, (Figure 1) the ArF laser at 0.19 (im is the best laser choice for finish micromachining. Testing in Lambda Physik application laboratories indicate that even KrF lasers create some charring and heat effects which are completely absent with the ArF laser.Likewise, metals, ceramics, glass, and plastics have better absorption characteristics in the ultraviolet region than in the visible or infrared. In many cases a material has absorption peaks within the UV range of 193 to 351 nm, which allows a specific excimer wavelength to be an optimum choice.Because ultraviolet light is usually absorbed in fine layers of a material, this allows less energy per unit area is used to effectively ablate off thin volumes. The combination of high peak power and short pulses can be used to remove larger interaction areas than lasers with longer absorption depths, and heat is carried away via kinetic energy of the ablated matter.The extremely clean material removal achieved with an excimer laser contrasts greatly with the rough charred and melted results produced with a YAG or CC>2 source.
Comparison of monthly intramuscular injections of Sandostatin LAR with multiple subcutaneous injections of octreotide in the treatment of acromegaly; effects on growth hormone and other markers of growth hormone secretion (1999)

These results suggest that Sandostatin LAR is well tolerated and as effective as subcutaneous octreotide. In addition, urinary growth hormone and serum free IGF-1 may prove valuable for outpatient follow-up of acromegalic patients, as both correlate well with mean 24 h serum growth hormone levels.
Properties and kinetic mechanism of recombinant mammalian protein geranylgeranyltransferase type I. (1994)

Protein geranylgeranyltransferase type I (GGTase I) catalyzes the prenylation of a number of proteins that play important roles in cellular signaling. The recent cDNA cloning of this enzyme (Zhang, F. L., Diehl, R. E., Kohl, N. E., Gibbs, J. B., Giros, B., Casey, P. J., and Omer, C. A. (1994) J. Biol. Chem. 269, 3175-3180) has allowed us to develop an expression system for obtaining large quantities of the enzyme. Co-infection of insect cells with recombinant baculoviruses encoding the two subunits of the enzyme results in GGTase I accumulation within the cells to levels of > 20% of cytosolic protein. The recombinant enzyme could be readily purified by ion-exchange chromatography and is shown to possess the activity and specificity of the enzyme obtained from mammalian tissues. Production of the recombinant enzyme allowed us to confirm its identity as a zinc metalloenzyme by direct identification of the metal using atomic absorption spectroscopy. We also identify two substrate analogs that are competitive inhibitors of GGTase I. One is a novel isoprenoid analog, 3-aza-GGPP, which inhibits the enzyme with a Ki of 15 nM. The second inhibitor is the tetrapeptide Cys-Val-Phe-Leu, which exhibits a Ki of 50 nM. The use of these inhibitors, coupled with a steady-state kinetic analysis of the enzyme, reveals that the reaction catalyzed by GGTase I proceeds through a random ordered sequential mechanism.
Multi-task Domain Adaptation for Sequence Tagging (2016)

Many domain adaptation approaches rely on learning cross domain shared representations to transfer the knowledge learned in one domain to other domains. Traditional domain adaptation only considers adapting for one task. In this paper, we explore multi-task representation learning under the domain adaptation scenario. We propose a neural network framework that supports domain adaptation for multiple tasks simultaneously, and learns shared representations that better generalize for domain adaptation. We apply the proposed framework to domain adaptation for sequence tagging problems considering two tasks: Chinese word segmentation and named entity recognition. Experiments show that multi-task domain adaptation works better than disjoint domain adaptation for each task, and achieves the state-of-the-art results for both tasks in the social media domain.
Antiandrogenic agents as monotherapy in advanced prostatic carcinoma (1993)

Pure antiandrogens have a quality-of-life advantage over other androgen ablation methods in the treatment of patients with prostatic cancer because they do not reduce the serum testosterone and therefore do not have a marked inhibitory effect on libido and potency. The long half-life of two of the three currently studied pure antiandrogens permits once-a-day administration, which should enhance patient compliance. With continued administration, there is a gradual rise in serum testosterone, and the clinical impact of this requires additional study using randomized Phase III trials. Proper stratification of patients at entry into such studies with documentation of various prognostic factors will add statistical value and enable physicians to draw better conclusion on the relative efficacy of these agents.
Role of the D-alanyl carrier protein in the biosynthesis of D-alanyl-lipoteichoic acid (1994)

D-Alanyl-lipoteichoic acid (D-alanyl-LTA) is a widespread macroamphiphile which plays a vital role in the growth and development of gram-positive organisms. The biosynthesis of this polymer requires the enzymic activation of D-alanine for its transfer to the membrane-associated LTA (mLTA). A small, heat-stable, and acidic protein that is required for this transfer was purified to greater than 98% homogeneity from Lactobacillus casei ATCC 7469. This protein, previously named the D-alanine-membrane acceptor ligase (V. M. Reusch, Jr., and F. C. Neuhaus, J. Biol. Chem. 246:6136-6143, 1971), functions as the D-alanyl carrier protein (Dcp). The amino acid composition, beta-alanine content, and N-terminal sequence of this protein are similar to those of the acyl carrier proteins (ACPs) of fatty acid biosynthesis. The isolation of Dcp and its derivative, D-alanyl approximately Dcp, has allowed the characterization of two novel reactions in the pathway for D-alanyl-mLTA biosynthesis: (i) the ligation of Dcp with D-alanine and (ii) the transfer of D-alanine from D-alanyl approximately Dcp to a membrane acceptor. It has not been established whether the membrane acceptor is mLTA or another intermediate in the pathway for D-alanyl-mLTA biosynthesis. Since the D-alanine-activating enzyme (EC 6.1.1.13) catalyzes the ligation reaction, this enzyme functions as the D-alanine-Dcp ligase (Dcl). Dcl also ligated the ACPs from Escherichia coli, Vibrio harveyi, and Saccharopolyspora erythraea with D-alanine. In contrast to the relaxed specificity of Dcl in the ligation reaction, the transfer of D-alanine to the membrane acceptor was highly specific for Dcp and did not occur with other ACPs. This transfer was observed by using only D-[14C]alanyl approximately Dcp and purified L. casei membranes. Thus, D-alanyl approximately Dcp is an essential intermediate in the transfer of D-alanine from Dcl to the membrane acceptor. The formation of D-alanine esters of mLTA provides a mechanism for modulating the net anionic charge in the cell wall.
Shape-dependent electrocatalysis: methanol and formic acid electrooxidation on preferentially oriented Pt nanoparticles (2008)

Reactivity towards methanol and formic acid electrooxidation on Pt nanoparticles with well characterised surfaces were studied and compared with the behaviour of single crystal electrodes with basal orientations. Polyoriented and preferential (100), (111) and (100)-(111) Pt nanoparticles were synthesised, cleaned preserving its surface structure, characterised and employed to evaluate the influence of the surface structure/shape of the Pt nanoparticles on these two relevant electrochemical reactions. The results pointed out that, in agreement with fundamental studies with Pt single crystal electrodes, the surface structure of the electrodes plays an important role on the reactivity of both oxidation processes, and thus the electrocatalytic properties strongly depend on the surface structure/shape of the nanoparticles, in particular on the presence of sites with (111) symmetry. These findings open the possibility of designing new and better electrocatalytic materials using decorated shape-controlled Pt nanoparticles as previously described with Pt single crystal electrodes.
Highly diverse variable number tandem repeat loci in the E. coli O157:H7 and O55:H7 genomes for high-resolution molecular typing (2005)

Escherichia coli O157:H7 MLVA offers a complimentary analysis to the more traditional PFGE approach. Application of MLVA to an outbreak cluster could generate superior molecular epidemiology and result in a more effective public health response.
Crystal structure of a designed, thermostable, heterotrimeric coiled coil (1999)

Electrostatic interactions are often critical for determining the specificity of protein-protein complexes. To study the role of electrostatic interactions for assembly of helical bundles, we previously designed a thermostable, heterotrimeric coiled coil, ABC, in which charged residues were employed to drive preferential association of three distinct, 34-residue helices. To investigate the basis for heterotrimer specificity, we have used multiwavelength anomalous diffraction (MAD) analysis to determine the 1.8 A resolution crystal structure of ABC. The structure shows that ABC forms a heterotrimeric coiled coil with the intended arrangement of parallel chains. Over half of the ion pairs engineered to restrict helix associations were apparent in the experimental electron density map. As seen in other trimeric coiled coils, ABC displays acute knobs-into-holes packing and a buried anion coordinated by core polar amino acids. These interactions validate the design strategy and illustrate how packing and polar contacts determine structural uniqueness.
Angiotensin-Converting Enzyme 2 and Angiotensin-(1-7) (2005)

This lecture summarizes the chronology and rationale that led to the discovery of angiotensin-(1-7) as a hormone that, in its own right, opposes the vasoconstrictor and proliferative actions of angiotensin II. The work discussed here additionally analyzes the newest findings on angiotensin-converting enzyme 2, the angiotensin-converting enzyme homologue that efficiently hydrolyzes angiotensin II into angiotensin-(1-7). Both components of this system may significantly influence our future perspective of the role of the renin-angiotensin system, not just in terms of its role in the regulation of cardiovascular and renal function but, moreover, as regulators of a vast array of disease processes in which inflammation and immune mechanisms play a role.
Tyrosine Kinase Inhibitors in the Treatment of Systemic Sclerosis: The Difficulty in Interpreting Proof-of-Concept Studies (2011)

Tyrosine kinase inhibitors (TKIs) have emerged as a targeted therapy of interest for the treatment of systemic sclerosis (SSc). Recently, several groups have performed pilot or "proof-of-concept" studies to determine the feasibility of this approach for the treatment of the cutaneous and pulmonary manifestations of this multisystem disease. The conclusions drawn by these different studies have been conflicting, and some controversy has arisen as to whether tyrosine kinase inhibition is a treatment approach worthy of continued study. This paper summarizes this research to date with emphasis on the challenges in interpreting proof-of-concept studies in this patient group.
Multidimensional constellations. I. Introduction, figures of merit, and generalized cross constellations (1989)

The authors discuss the major attributes desired in signal constellations, such as signal-to-noise ratio (SNR) efficiency, simplicity of mapping bits to points and vice versa, compatibility with coded modulation schemes, and compatibility with quadrature amplitude modulation (QAM). The capability of supporting a so-called opportunistic secondary channel, often used for internal control signaling, is considered. The gain in SNR efficiency of a multidimensional constellation (lattice code) consisting of the points from a lattice Lambda within a region R compared to a cubic constellation is shown to be approximately separable into the coding gain of Lambda and the shape gain of R, for large constellations. Similarly, the expansion of the associated constituent 2-D constellation is shown to be approximately separable into a constellation expansion ratio (CER) coding component CER/sub c/( Lambda ) and a shaping component CER/sub s/(R). The N sphere is the region R with the best shape gain, but N also has large constellation expansion. Bounds for the best possible shape gain versus CER/sub s/(R) or peak-to-average-power ratio (PAR) are given. Generalized cross constellations are discussed. These constellations yield a modest shape gain with very low CER/sub s/(R) or PAR, are easily implemented, are well suited for use with coded QAM modems, and can be readily adapted to support an opportunistic secondary channel.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>