gebhart/patrepeval huggingface dataset:
Coupled Parallel Snakes For Segmenting Healthy and Pathological Retinal Arteries in Adaptive Optics Images (2015)

Abstract. In this paper, we propose two important improvements of an existing approach for automatically segmenting the walls of retinal arter-ies of healthy / pathological subjects in adaptive optics images. We illus-trate the limits of the previous approach and propose to (i) modify the pre-segmentation step, and (ii) embed additional information through coupling energy terms in the parallel active contour model. The interest of these new elements as well as the pre-segmentation step is then evalu-ated against manual segmentations. They improve the robustness against low contrasted walls and morphological deformations that occur along vessels in case of pathologies. Noticeably, this strategy permits to obtain a mean error of 13.4 % compared to an inter-physicians error of 17%, for the wall thickness which is the most sensitive measure used. Additionally, this mean error is in the same range than for healthy subjects.
Real-time computed tomography (1987)

The parallel and rapid processing of optical computing can be exploited for the high-speed reconstruction of computed tomography images. Our system implements the filtered backprojection algorithm using an incoherent optical system for the backprojection. A video camera integrates the filtered backprojections, and the reconstructed image can be directly displayed on a video monitor. The filtering operation can alternatively be performed by a heterodyne space-integrating acoustooptic convolver, a surface acoustic wave filter, or a digital finite impulse response filter. We present images reconstructed by our system, discuss system performance, and compare the different filtering methods. In connection with a fast CT scanner our system makes the real-time observation of dynamic events possible.
Generation of large numbers of functional NK cells without feeders or serum (2022)

Abstract Natural killer (NK) cells are innate lymphocytes that modulate immune responses by secreting proinflammatory cytokines, and provide antitumor and antivirus activity. The ability to generate therapeutically relevant numbers of functional NK cells is critical for the development of advanced cellular immunotherapies. We have developed a streamlined culture workflow that enables expansion of functional NK cells without using either feeder cells or serum. Fresh human NK cells were isolated from peripheral blood using EasySep™, then cultured in ImmunoCult™ NK Cell Expansion Medium in plates coated with ImmunoCult™ NK Cell Expansion Coating Material. NK cells were fed, harvested, and replated on days 7 and 10 – 11 prior to phenotyping and functional assessment on day 14. The average frequency of CD56+ CD3− NK cells was 88% (range 75 – 96%, n=34), 74% (range 49 – 92%) of which expressed CD16, with an average expansion of 88 fold (range 3 – 454). Expanded NK cells were stimulated with phorbol 12-myristate 13-acetate (PMA) and ionomycin, or co-cultured with K562 cells. As detected by intracellular flow cytometry, the average frequency of interferon-γ+ among NK cells was 68% (range 41 – 90%, n=7) and 43% (range 12 – 55%) when stimulated by PMA/ionomycin or K562 cells, respectively. Similarly, the frequency of degranulated NK cells (CD107a+) was 81% (range 35 – 97%, n=7) and 64% (range 35 – 97%), respectively. The ability of expanded NK cells to kill target K562 cells was visualized by activated caspase in co-cultures with labeled K562 cells using the Incucyte® imaging system. At an effector:target ratio of 1:1, an average of 50% of K562 cells were killed (range 45 – 56, n=3). These results show large numbers of functional NK cells can be generated.
Upregulation of Glycans Containing 3′ Fucose in a Subset of Pancreatic Cancers Uncovered Using Fusion-Tagged Lectins (2015)

The fucose post-translational modification is frequently increased in pancreatic cancer, thus forming the basis for promising biomarkers, but a subset of pancreatic cancer patients does not elevate the known fucose-containing biomarkers. We hypothesized that such patients elevate glycan motifs with fucose in linkages and contexts different from the known fucose-containing biomarkers. We used a database of glycan array data to identify the lectins CCL2 to detect glycan motifs with fucose in a 3' linkage; CGL2 for motifs with fucose in a 2' linkage; and RSL for fucose in all linkages. We used several practical methods to test the lectins and determine the optimal mode of detection, and we then tested whether the lectins detected glycans in pancreatic cancer patients who did not elevate the sialyl-Lewis A glycan, which is upregulated in ∼75% of pancreatic adenocarcinomas. Patients who did not upregulate sialyl-Lewis A, which contains fucose in a 4' linkage, tended to upregulate fucose in a 3' linkage, as detected by CCL2, but they did not upregulate total fucose or fucose in a 2' linkage. CCL2 binding was high in cancerous epithelia from pancreatic tumors, including areas negative for sialyl-Lewis A and a related motif containing 3' fucose, sialyl-Lewis X. Thus, glycans containing 3' fucose may complement sialyl-Lewis A to contribute to improved detection of pancreatic cancer. Furthermore, the use of panels of recombinant lectins may uncover details about glycosylation that could be important for characterizing and detecting cancer.
Identification of <i>Pseudomonas syringae</i> pv. <i>tomato</i> genes induced during infection of <i>Arabidopsis thaliana</i> (2002)

Phytopathogenic bacteria possess a large number of genes that allow them to grow and cause disease on plants. Many of these genes should be induced when the bacteria come in contact with plant tissue. We used a modified in vivo expression technology (IVET) approach to identify genes from the plant pathogen Pseudomonas syringae pv. tomato that are induced upon infection of Arabidopsis thaliana and isolated over 500 in planta-expressed (ipx) promoter fusions. Sequence analysis of 79 fusions revealed several known and potential virulence genes, including hrp/hrc, avr and coronatine biosynthetic genes. In addition, we identified metabolic genes presumably important for adaptation to growth in plant tissue, as well as several genes with unknown function that may encode novel virulence factors. Many ipx fusions, including several corresponding to novel genes, are dependent on HrpL, an alternative RNA polymerase sigma factor that regulates the expression of virulence genes. Expression analysis indicated that several ipx fusions are strongly induced upon inoculation into plant tissue. Disruption of one ipx gene, conserved effector locus (CEL) orf1, encoding a putative lytic murein transglycosylase, resulted in decreased virulence of P. syringae. Our results demonstrate that this screen can be used successfully to isolate genes that are induced in planta, including many novel genes potentially involved in pathogenesis.
Use of artificial intelligence in computed tomography dose optimisation (2020)

The field of artificial intelligence (AI) is transforming almost every aspect of modern society, including medical imaging. In computed tomography (CT), AI holds the promise of enabling further reductions in patient radiation dose through automation and optimisation of data acquisition processes, including patient positioning and acquisition parameter settings. Subsequent to data collection, optimisation of image reconstruction parameters, advanced reconstruction algorithms, and image denoising methods improve several aspects of image quality, especially in reducing image noise and enabling the use of lower radiation doses for data acquisition. Finally, AI-based methods to automatically segment organs or detect and characterise pathology have been translated out of the research environment and into clinical practice to bring automation, increased sensitivity, and new clinical applications to patient care, ultimately increasing the benefit to the patient from medically justified CT examinations. In summary, since the introduction of CT, a large number of technical advances have enabled increased clinical benefit and decreased patient risk, not only by reducing radiation dose, but also by reducing the likelihood of errors in the performance and interpretation of medically justified CT examinations.
Mammalian Δ-6 Fatty Acid Desaturase : (2000)

Δ-6 Fatty acid desaturase was noted to catalyze the conversion of linoleic acid to γ-linolenic acid and α-linolenic acid to n-3 octadecatetraenoic acid through the insertion of a double bond at the Δ-6 position of the fatty acid substrate. In mammals and paticularly in humans, this is the first rate-limiting step in the biosynthesis of polyunsaturated fatty acids such as dihomo-γ-linolenic, arachidonic, and eicosapentaenoic acids, all known as precursors of eicosanoids. Δ-6 desaturating activity has been shown associated with physiological and clinical observation findings. Expression cloning of plant and mammalian Δ-6 desaturase genes has recently been achieved and has provided indication of a new group of cytochrome b5-fusion proteins. The key role of this enzyme in lipid metabolism is presently being studied at the molecular level.
ChemInform Abstract: Synthesis of 2,5‐Disubstituted‐3‐cyanoindoles. (2012)

Abstract A three‐step sequence including selective iodination and ring closure with KOtBu via a Modified Madelung reaction yields iodo precursors of type (VI), which can be coupled with arylboronic acids.
Serology for human papillomavirus (2003)

"Difficulties with serology for papillomavirus are associatedwith the large number of human papillomavirus, crossreactionsbetween papillomavirus, and to the diversity oflesions and target sites for infection. In addition, theexpression of the papillomavirus in the superficial layers ofthe epithelium gives rise to the weak presentation toimmunocompetent cells of viral antigens, which in turn givesrise to a weak serological response. Distinct efforts havebeen made in previous decades to develop more specificand sensitive serological assays. These former studies usefusion proteins and synthetic peptides, although they remainon the whole uninteresting, due to their lack of sensitivityand specificity. Only in the last few years, and principallydue to the advent of various virus-like particles (VLP), havemore sensitive and specific assays become available. Thispaper is available too at: http://www.insp.mx/salud/index.html"
General health checks in adults for reducing morbidity and mortality from disease (2012)

General health checks did not reduce morbidity or mortality, neither overall nor for cardiovascular or cancer causes, although the number of new diagnoses was increased. Important harmful outcomes, such as the number of follow-up diagnostic procedures or short term psychological effects, were often not studied or reported and many trials had methodological problems. With the large number of participants and deaths included, the long follow-up periods used, and considering that cardiovascular and cancer mortality were not reduced, general health checks are unlikely to be beneficial.
Minimally invasive aortic valve replacement (AVR) with Edwards Odyssey Quick-connect system (2011)

Objective: The purpose of this study was to evaluate the feasibility, safety and performance of the Odyssey aortic valve replacement system (Edwards Lifesciences), that merges the performance and durability of traditional valve technology with latest transcatheter technology to offer the advantages of more efficient implantation through a minimally invasive technique.
Web accessibility and people with dyslexia (2012)

Although the dyslexia has significant occurrence in the global population, ranging from 15 to 20%, not much is known about how developers, designers, and content producers should respect differences and consider people with dyslexia in the Web. In this paper we present a survey regarding the state of the art on dyslexia and Web Accessibility. From the results, we present a set of 41 guidelines that may support website stakeholders (i.e., people directly involved with the design, development, and content) in phases involving design, coding, and Web content insertion. Moreover, we propose a mapping of these guidelines considering the responsibilities of different roles of websites stakeholders. Informed by this survey we expect development teams to objectively consider abilities of people with dyslexia in order to remove accessibility barriers.
Improved enzymatic syntheses of valuable β-arylalkyl-β-amino acid enantiomers (2009)

The enantioselective (E approximately 200) Burkholderia cepacia-catalysed hydrolyses of beta-amino esters with H(2)O (0.5 equiv.) in t-BuOMe or in i-Pr(2)O at 45 degrees C are described. The enantiomers of biologically relevant beta-arylalkyl-substituted beta-amino acids, and especially (R)-3-amino-3-(2,4,5-trifluorophenyl)butanoic acid, the intermediate of the new antidiabetic drug sitagliptine, were prepared with high enantiomeric excesses (ee>or=96%) and in good yields (>or=42%).
Mild Arming and Derivatization of Natural Products via an In(OTf)<sub>3</sub>-Catalyzed Arene Iodination (2010)

Iodination of arene-containing natural products employing N-iodosuccinimide catalyzed by In(OTf)(3) at ambient temperature is reported as a versatile and mild method for natural product derivatization amenable to small scale. This process facilitates natural product derivatization of arene moieties for SAR studies, homo- and heterodimerization of natural products, and also conjugation with reporters such as biotin via subsequent metal-mediated coupling reactions.
Radial Extracorporeal Shock Wave Therapy is Safe and Effective in the Treatment of Chronic Recalcitrant Plantar Fasciitis (2008)

Radial extracorporeal shock wave therapy significantly improves pain, function, and quality of life compared with placebo in patients with recalcitrant plantar fasciitis.
The Capture of a Disabled Proteasome Identifies Erg25 as a Substrate for Endoplasmic Reticulum Associated Degradation (2020)

Studies in the yeast <i>Saccharomyces cerevisiae</i> have helped define mechanisms underlying the activity of the ubiquitin-proteasome system (UPS), uncover the proteasome assembly pathway, and link the UPS to the maintenance of cellular homeostasis. However, the spectrum of UPS substrates is incompletely defined, even though multiple techniques-including MS-have been used. Therefore, we developed a substrate trapping proteomics workflow to identify previously unknown UPS substrates. We first generated a yeast strain with an epitope tagged proteasome subunit to which a proteasome inhibitor could be applied. Parallel experiments utilized inhibitor insensitive strains or strains lacking the tagged subunit. After affinity isolation, enriched proteins were resolved, in-gel digested, and analyzed by high resolution liquid chromatography-tandem MS. A total of 149 proteasome partners were identified, including all 33 proteasome subunits. When we next compared data between inhibitor sensitive and resistant cells, 27 proteasome partners were significantly enriched. Among these proteins were known UPS substrates and proteins that escort ubiquitinated substrates to the proteasome. We also detected Erg25 as a high-confidence partner. Erg25 is a methyl oxidase that converts dimethylzymosterol to zymosterol, a precursor of the plasma membrane sterol, ergosterol. Because Erg25 is a resident of the endoplasmic reticulum (ER) and had not previously been directly characterized as a UPS substrate, we asked whether Erg25 is a target of the ER associated degradation (ERAD) pathway, which most commonly mediates proteasome-dependent destruction of aberrant proteins. As anticipated, Erg25 was ubiquitinated and associated with stalled proteasomes. Further, Erg25 degradation depended on ERAD-associated ubiquitin ligases and was regulated by sterol synthesis. These data expand the cohort of lipid biosynthetic enzymes targeted for ERAD, highlight the role of the UPS in maintaining ER function, and provide a novel tool to uncover other UPS substrates via manipulations of our engineered strain.
Selective Recognition of G-Quadruplex Telomeric DNA by a Bis(quinacridine) Macrocycle (2003)

The interaction of G-quadruplex DNA with the macrocyclic compound BOQ1, which possesses two dibenzophenanthroline (quinacridine) subunits, has been investigated by a variety of methods. The oligonucleotide 5'-A(GGGT(2)A)(3)G(3), which mimics the human telomeric repeat sequence and forms an intramolecular quadruplex, was used as one model system. Equilibrium binding constants measured by biosensor surface plasmon resonance (SPR) methods indicate a high affinity of the macrocycle for the quadruplex conformation (K > 1 x 10(7) M(-)(1)) with two equivalent binding sites. The affinity of BOQ1 for DNA duplexes is at least 1 order of magnitude lower. In addition, the macrocycle is more selective than the monomeric control compound (MOQ2), which is not able to discriminate between the two DNA structures (K(duplex) approximately K(quadruplex) approximately 10(6) M(-)(1)). Strong binding of BOQ1 to G4 DNA sequences was confirmed by fluorometric titrations with a tetraplex-forming oligonucleotide. Competition dialysis experiments with a panel of different DNA structures, from single strands to quadruplexes, clearly established the quadruplex binding specificity of BOQ1. Fluorescence resonance energy transfer (FRET) T(m) experiments with a doubly labeled oligonucleotide also revealed a strong stabilization of the G4 conformation in the presence of BOQ1 (DeltaT(m) = +28 degrees C). This DeltaT(m) value is one of the highest values measured for a G-quadruplex ligand and is significantly higher than observed for the monomer control compounds (DeltaT(m) = +10-12 degrees C). Gel mobility shift assays indicated that the macrocycle efficiently induces the formation of G-tetraplexes. Strong inhibition of telomerase was observed in the submicromolar range (IC(50) = 0.13 microM). These results indicate that macrocycles represent an exciting new development opportunity for targeting DNA quadruplexes.
A preliminary survey of extended-spectrum Î²-lactamases (ESBLs) in clinical isolates of<i>Klebsiella pneumoniae</i>and<i>Escherichia coli</i>in Japan (2000)

We conducted a survey of extended-spectrum beta-lactamases (ESBLs) among 16805 Escherichia coli and 9794 Klebsiella pneumoniae clinical isolates recovered from 196 separate medical institutions during the period January 1997 to January 1998. Using the criteria for minimal inhibitory concentrations (MICs) of oxyimino-cephalosporins of >/=8 microg ml(-1) and confirmation by double-disk test, we detected 15 E. coli and 34 K. pneumoniae isolates producing ESBLs. Genotypes of ESBLs determined by PCR with type-specific primers included one TEM-derived and 24 SHV-derived ESBLs, in addition to 24 Toho-1-type ESBLs, one of the major types of ESBLs reported in Japan. Nucleotide sequence analysis of SHV-specific PCR products revealed that SHV-12 was the dominant type of SHV-derived ESBL. In addition, we also identified TEM-26 and SHV-2. This is the first report characterizing TEM- and SHV-derived ESBLs in Japan.
Amplification of short pulses in tunable solid-state materials (1991)

There has been recent interest in amplifying femtosecond-range pulses to the terawatt level by the use of chirped pulse solid-state laser amplifiers. 1 In this paper, we describe our progress in amplifying short pulses to the joule level using a variety of tunable solid-state materials.
Application of a Limited-Area Short-Range Ensemble Forecast System to a Case of Heavy Rainfall in the Mediterranean Region (2004)

Severe weather risk assessment is becoming an increasing component of the daily operational activity at advanced meteorological forecasting centers. To improve its forecast capabilities and develop a severe weather warning system, the Sardinian Regional Meteorological Service (SAR) and the Centre for Advanced Studies, Research and Development in Sardinia (CRS4) have been testing a Limited-area Ensemble Prediction System (SAR-LEPS). The SAR-LEPS system is described and preliminary results of its use to predict the intense and localized flooding event of 12–13 November 1999 are discussed. Results for this specific case study indicate that SAR-LEPS provided valuable, additional information to the ECMWF ensemble system. This suggests that the operational use of SAR-LEPS could prove to be an important component in the decision making process in issuing threat warnings for severe weather conditions.
Gene Modulatory Effects, Pharmacokinetics, and Clinical Tolerance of Interferon-α1b: A Second Member of the Interferon-α Family (2007)

Interferon-alpha1 (IFN-alpha1), which may have a primary role in innate immunity, differs significantly in amino-acid sequence from IFN-alpha2, the only recombinant IFN-alpha with substantial clinical evaluation. Patients with metastatic malignancies received daily subcutaneous doses of 1.5-270 mug/m(2) of recombinant IFN-alpha1b. Gene modulation, pharmacokinetics, tolerability, and disease response were determined. Significant (P<0.01) dose and gene-dependent increases of 2-10 fold occurred in IFN-stimulated genes, including four (tumor necrosis factor-related apoptosis-inducing ligand, cig 5, p56, GEM) never previously identified as increased in patients; significant increases (P<0.01) resulted at the lowest dose (1.5 microg/m(2); 1.5 x 10(4) human antiviral units/m(2)). Increases (P<0.01) were sustainable for >4 weeks. Peak levels of IFN-alpha1b were at 3 h; an increase of approximately eightfold in both C(max) and AUC occurred between 15 microg/m(2) and 270 microg/m(2). Chronic toxicities of anorexia, weight loss, and fatigue were relatively uncommon. Eighteen patients were treated for >8 weeks; none experienced >grade 1 weight loss. Three patients at the highest dose developed grade 3 fatigue after > or =3 months, which required dose reduction or discontinuation. Patient acceptability of fatigue defined a dose for initiation of Phase II trials, 270 microg/m(2). Six patients (five with renal cell carcinoma) had progression-free survival for >1 year, including two who had partial responses. IFN-alpha1b resulted in potent stimulation of IFN-regulated genes and tumor regressions in renal cell carcinoma. Unique gene modulatory effects, when coupled with the moderate severity of side effects and a potentially central role in innate immunity, provide rationale for further clinical evaluation of IFN-alpha1 in virus infections and cancer.
One-Dimensional Ferrimagnetic Behavior of a Hetero-Spin Chain in an Organic Radical Crystal as Probed by Susceptibility and Relaxation Time Measurements (1996)

Abstract Spin state energies were calculated for a linear chain composed of a doublet radical and a biradical with a triplet ground state by numerical diagonalization of finite-size Heisenberg spin Hamiltonian. When all the intermolecular antiferromagnetic interactions couple the S=1/2 sites uniformly, a ferrimagnetic-like ground state appears. This finding is consistent with the simple picture of antiparallel alignment of different S's. On the other hand, quasidegenerate low-lying excited states appear as the spatial symmetry of intermolecular antiferromagnetic interactions is lowered. The quasi-degeneracy breaks the stability of the ferrimagnetic-like ground state. This result gives a qualitative explanation of the susceptibility and the spin-spin relaxation time measured for a nitronylnitroxide-based molecular crystal composed of an S=1/2 and S=1 molecules. The instability of the ferrimagnetic-like ground state is inherent in multi-centered antiferromagnetic interactions between the open-shell organic molecular systems, suggesting a prerequisite for purely organic ferrimagnetic ordering.
Porcine and human in vivo predictions for doxorubicin containing formulations used in locoregional HCC treatment (2017)

Porcine and human in vivo predictions for doxorubicin containing formulations used in locoregional HCC treatment