gebhart/patrepeval huggingface dataset:
Backbone Dynamics of <i>Escherichia coli</i> Adenylate Kinase at the Extreme Stages of the Catalytic Cycle Studied by <sup>15</sup>N NMR Relaxation (2000)

Adenylate kinase from Escherichia coli (AKeco), consisting of a single 23.6 kDa polypeptide chain folded into domains CORE, AMPbd, and LID, catalyzes the reaction AMP + ATP --> 2ADP. Domains LID and AMPbd execute large-scale movements during catalysis. Backbone dynamics of ligand-free and AP(5)A-inhibitor-bound AKeco were studied comparatively with (15)N NMR relaxation methods. Overall diffusion with correlation times of 15.05 (11.42) ns and anisotropy D(parallel)/D(perp) = 1.25 (1.10), and fast internal motions with correlation times up to 100 ps (50 ps), were determined for AKeco (AKecoAP(5)A). Fast internal motions affect 93% of the AKeco sites, with pronounced preference for domains AMPbd and LID, and 47% of the AKecoAP(5)A sites, with limited variability along the chain. The mean squared generalized order parameters, <S(2)>, of secondary structure elements and loops are affected by ligand binding differentially and in a domain-specific manner. Nanosecond motions predominate within AMPbd. Prominent exchange contributions, associated in particular with residue G10 of the nucleotide-binding P-loop motif, are interpreted to reflect hydrogen-bond dynamics at the inhibitor-binding site. The hypothesis of energetic counter balancing of substrate binding based on crystallographic data is strongly supported by the solution NMR results. Correlations between backbone dynamics and domain displacement are established.
Abstract 4510: Pulmonary Hypertension before Transcatheter Aortic Valve Implantation Is Reversible and Lacks Prognostic Significance (2008)

The prognostic significance of pulmonary hypertension (PH) and the potential for reversibility in the setting of aortic stenosis (AS) have been debated. We examined the clinical correlates and prognostic significance of PH in high risk elderly patients with symptomatic severe AS undergoing transcatheter aortic valve implantation (AVI). AVI was performed in 143 patients. Adequate echocardiographic estimation of baseline pulmonary artery systolic pressure was available in 115 (80%). Patients were divided into 3 groups according to baseline pulmonary artery pressure estimated by transthoracic echocardiogram: I: &lt;30 mmHg, II: 30 –50 mmHg and III: &gt;50 mmHg. Clinical and echocardiographic follow-up was obtained at 1, 6 and 12 months after AVI. Group I consisted of 17 patients (15%), group II 58 patients (50%) and group III 40 patients (35%). At baseline the three groups were similar in terms of age, functional status, presence of severe pulmonary disease, aortic valve area and mean gradient. Patients with severe PH (group III) were more likely to have left ventricular dysfunction (LVEF &lt;50%) than patients with mild to moderate PH (groups I and II) (52% vs. 21%, p=0.002) and had more severe mitral regurgitation (grade ≥ 3 in 68% vs. 41%, p =0.0002). At one month, systolic pulmonary artery pressure fell significantly in group III (11.0 ± 14.3 mmHg, p=0.0008) and this reduction was maintained at 6 months. However, the changes in group I (increase of 7.1 ± 8.7 mmHg, p=0.07) and group II (decrease of 0.9 ± 9.3 mmHg, p=0.53) were not significant. Mortality at one year following AVI was 21%, but was not related to severity of PH. Using group III as a reference, hazard ratios were 0.83 (95% CI: 0.24 –2.9) for group I and 0.88 (95% CI: 0.4 –1.9) for group II. In elderly patients with severe AS treated with transcatheter AVI, severe PH is associated with more depressed left ventricular function and more severe mitral regurgitation. Severe PH is associated with a significant and greater fall in pulmonary pressure following AVI and does not influence one year survival.
Influence of farnesol on the morphogenesis of <i>Aspergillus niger</i> (2008)

Farnesol was the first quorum-sensing regulator to be found in eukaryotic cells. In Candida albicans, a dimorphic fungal human pathogen, farnesol blocks the yeast-to-filamentous growth transition. Here we show that in Aspergillus niger farnesol acts as an inhibitor of conidiation: Colonies grown on media containing farnesol were unable to develop conidia. Although farnesol treated A. niger cultures exhibited a colony morphology resembling the "fluffy" phenotype of A. nidulans, which is caused by a hyperactive G-protein/cAMP pathway, the intracellular level of cAMP in A. niger mycelia grown in presence of farnesol is greatly diminished. Furthermore, whereas inhibiting adenylyl cyclase led to a farnesol-like effect, the addition of external cAMP inhibited conidiation without causing a "fluffy" phenotype. This suggests that the mechanisms regulating conidiation in A. niger and A. nidulans are different.
Dual polarized phased array antenna for airborne L-band SAR (2006)

This paper describes the design and initial results of an L band dual polarized phased array antenna for the Argentine SARAT project. The dual polarized L band antenna consists on 24 short circuit annular slots in a 2/spl times/12 configuration. The antenna elements are fed using sequential rotation in order to improve the polarization purity and the port to port isolation of the whole antenna.
The glucocorticoid dexamethasone programs human dendritic cells for enhanced phagocytosis of apoptotic neutrophils and inflammatory response (2011)

GCs are powerful anti-inflammatory compounds inhibiting inflammatory cell recruitment and production of proinflammatory cytokines. We have recently found that DCs, the key players of T cell priming and polarization, respond to allogeneic apoptotic neutrophils with proinflammatory cytokine release and Th1 cell activation. Here, we show that monocyte-derived human DCs develop their capacity to engulf apoptotic cells by up-regulating a set of apoptophagocytic genes. This gene expression pattern was reprogrammed when differentiation took place in the presence of the synthetic GC Dex, which increased the expression of phagocytosis receptors MERTK and CD14, the bridging molecule C1QA, DNASE2, and ADORA3. The increased phagocytosis was attenuated by the addition of ADORA3 antagonist and could not be observed when bone marrow-derived DCs of ADORA3 KO mice were treated with Dex. The GC-treated human DCs loaded with allogeneic apoptotic neutrophils secreted, in response to LPS and IFN-γ, the inflammatory cytokine TNF-α. Furthermore, the Dex-treated DCs could activate autologous T lymphocytes toward Th1 effector cells, and this was enhanced by their exposure to allogeneic apoptotic neutrophils.
Genome‐wide linkage scan, fine mapping, and haplotype analysis in a large, inbred, Arab Israeli pedigree suggest a schizophrenia susceptibility locus on chromosome 20p13 (2007)

Linkage and association studies in schizophrenia have repeatedly drawn attention to several chromosomal regions and to genes within them. Conflicting patterns of association and the lack of a clear functional significance of the associated variants limit the interpretation of these results. The use of rare pedigrees, where genes with a major effect cause the disorder, has been proven beneficial in studies of other complex disorders. Our objective was to use this advantage by performing a genome wide linkage analysis for schizophrenia in a large, multiplex Israeli Arab pedigree. We genotyped 346 microsatellite markers in 24 pedigree members affected with schizophrenia spectrum disorders and 32 unaffected relatives. Two-point linkage analysis with SUPERLINK demonstrated a LOD score of 2.47 for D20S116 on chromosome 20p13 under an autosomal dominant mode of inheritance. Further fine mapping yielded a two-point LOD score of 2.56 for the adjacent marker D20S193 and narrowed down the linked region to 2-5 cM. A haplotype containing the markers D20S193, D20S889, and D20S116, 0.7 Mb in length, was found to be shared by most affected pedigree members. Genotyping of 43 SNPs in the interval supported these results with a multipoint LOD score of 2.7 around D20S193. We were also able to better define the boundaries of the shared haplotype which contains strong candidate genes for schizophrenia. Our study exemplifies the power of rare and unique pedigrees in drawing attention to novel regions for genetic studies of schizophrenia.
The NutriChip project – translating technology into nutritional knowledge (2012)

Advances in food transformation have dramatically increased the diversity of products on the market and, consequently, exposed consumers to a complex spectrum of bioactive nutrients whose potential risks and benefits have mostly not been confidently demonstrated. Therefore, tools are needed to efficiently screen products for selected physiological properties before they enter the market. NutriChip is an interdisciplinary modular project funded by the Swiss programme Nano-Tera, which groups scientists from several areas of research with the aim of developing analytical strategies that will enable functional screening of foods. The project focuses on postprandial inflammatory stress, which potentially contributes to the development of chronic inflammatory diseases. The first module of the NutriChip project is composed of three in vitro biochemical steps that mimic the digestion process, intestinal absorption, and subsequent modulation of immune cells by the bioavailable nutrients. The second module is a miniaturised form of the first module (gut-on-a-chip) that integrates a microfluidic-based cell co-culture system and super-resolution imaging technologies to provide a physiologically relevant fluid flow environment and allows sensitive real-time analysis of the products screened in vitro. The third module aims at validating the in vitro screening model by assessing the nutritional properties of selected food products in humans. Because of the immunomodulatory properties of milk as well as its amenability to technological transformation, dairy products have been selected as model foods. The NutriChip project reflects the opening of food and nutrition sciences to state-of-the-art technologies, a key step in the translation of transdisciplinary knowledge into nutritional advice.
Expression of bisecting GlcNAc in pediatric brain tumors and its association with tumor cell response to vinblastine. (1999)

Increased expression of the bisecting GlcNAc has been correlated with tumor progression in several experimental tumor models. Its expression and function in brain tumors are, however, not yet known. In this study, we investigated expression of the bisecting GlcNAc structure in a series of pediatric brain tumors and its relationship to tumor response to vinblastine. A plant lectin (E-PHA) that recognizes the bisecting GlcNAc structure was used for detection of this molecule in a total of 90 pediatric brain tumors and normal brain tissue specimens. Our results showed that, whereas E-PHA staining was undetectable in the normal brain tissue, pediatric brain tumor specimens exhibited different levels of reactivity. Lectin staining was particularly prominent in high-grade astrocytomas (73%) and ependymomas (72%). In astrocytomas, there was a positive correlation with the tumor grade, which suggests that the bisecting GlcNAc may be of particular interest as a tumor marker for diagnosis and/or prognosis. By using a human glioma cell culture model, we have found that treatment of these cells with E-PHA lectin enhances their sensitivity to vinblastine. E-PHA interacted directly with the drug transporter P-glycoprotein and inhibited its drug efflux function. In a drug-resistant glioma cell line transfected with the mdr1 gene, drug resistance was reversed by E-PHA. Our findings indicate that: (a) expression of the bisecting GlcNAc in pediatric brain tumors may have a potential relevance as a tumor marker; and (b) glioma response to chemotherapy may be modulated through the bisecting GlcNAc.
Enrichment of putative stem cells from adipose tissue using dielectrophoretic field-flow fractionation (2008)

We have applied the microfluidic cell separation method of dielectrophoretic field-flow fractionation (DEP-FFF) to the enrichment of a putative stem cell population from an enzyme-digested adipose tissue derived cell suspension. A DEP-FFF separator device was constructed using a novel microfluidic-microelectronic hybrid flex-circuit fabrication approach that is scaleable and anticipates future low-cost volume manufacturing. We report the separation of a nucleated cell fraction from cell debris and the bulk of the erythrocyte population, with the relatively rare (<2% starting concentration) NG2-positive cell population (pericytes and/or putative progenitor cells) being enriched up to 14-fold. This work demonstrates a potential clinical application for DEP-FFF and further establishes the utility of the method for achieving label-free fractionation of cell subpopulations.
Endotoxin Antagonists: Possible Candidates for the Treatment of Gram‐Negative Sepsis (1995)

The acylation and phosphorylation pattern determines the effectiveness of disaccharide antagonists of lipid A (lipid A from Escherichia coli is shown on the right), the toxic principle of sepsis-inducing endotoxins from Gram-negative bacteria. These antgonists, which have not shown toxic activity for humans, have now been synthesized.
Towards annotation-efficient segmentation via image-to-image translation (2019)

Often in medical imaging, it is prohibitively challenging to produce enough boundary annotations to train deep neural networks for accurate tumor segmentation. We propose the use of weak labels about whether an image presents tumor or whether it is absent to extend training over images that lack these annotations. Specifically, we propose a semi-supervised framework that employs unpaired image-to-image translation between two domains, presence vs. absence of cancer, as the unsupervised objective. We conjecture that translation helps segmentation -- both require the target to be separated from the background. We encode images into two codes: one that is common to both domains and one that is unique to the presence domain. Decoding from the common code yields healthy images; decoding with the addition of the unique code produces a residual change to this image that adds cancer. Translation proceeds from presence to absence and vice versa. In the first case, the tumor is re-added to the image and we successfully exploit the residual decoder to also perform segmentation. In the second case, unique codes are sampled, producing a distribution of possible tumors. To validate the method, we created challenging synthetic tasks and tumor segmentation datasets from public BRATS (brain, MRI) and LitS (liver, CT) datasets. We show a clear improvement (0.83 Dice on brain, 0.74 on liver) over baseline semi-supervised training with autoencoding (0.73, 0.66) and a mean teacher approach (0.75, 0.69), demonstrating the ability to generalize from smaller distributions of annotated samples.
PAEDIATRIC SURGICAL TRAINING: A SYSTEM THAT WORKS (1998)

A successful training programme requires a commitment to educate one's junior colleagues. Busy consultants can contribute actively by offering to teach and by encouraging their trainees to attend rounds and tutorials. The rewards are better-educated and well-rounded surgeons as well as, hopefully, a higher pass-rate at the Part 2 examination.
Role of competition between slip and twinning in nanoscale deformation of sapphire (2009)

Insights into the initiation of plasticity under contact loading of $A$ and $M$ planes of sapphire are provided by finite element analysis of the resolved shear stress acting on basal slip and basal twinning systems and by the evaluation of acoustic emission signals associated with the onset of plasticity. The analysis of acoustic emission activity utilizes wavelet-based signal representation in the joint time-frequency domain. The proposed model invoking loading-rate-dependent competition between basal slip and basal twinning predicts different yield-point mechanisms for $A$ and $M$ planes. The predicted mechanisms are consistent with the experimental plasticity initiation patterns. Room-temperature values of critical shear stress of 12.9--13.9 GPa for basal slip and 12.6--14.4 GPa for basal twinning derived from application of finite element analysis to the results of nanoindentation experiments are compared with the values expected from the results of theoretical modeling and extrapolation of high-temperature experimental results.
Analysis of IgG kinetic stability by differential scanning calorimetry, probe fluorescence and light scattering (2017)

Monoclonal antibodies of the immunoglobulin G (IgG) type have become mainstream therapeutics for the treatment of many life-threatening diseases. For their successful application in the clinic and a favorable cost-benefit ratio, the design and formulation of these therapeutic molecules must guarantee long-term stability for an extended period of time. Accelerated stability studies, e.g., by employing thermal denaturation, have the great potential for enabling high-throughput screening campaigns to find optimal molecular variants and formulations in a short time. Surprisingly, no validated quantitative analysis of these accelerated studies has been performed yet, which clearly limits their application for predicting IgG stability. Therefore, we have established a quantitative approach for the assessment of the kinetic stability over a broad range of temperatures. To this end, differential scanning calorimetry (DSC) experiments were performed with a model IgG, testing chaotropic formulations and an extended temperature range, and they were subsequently analyzed by our recently developed three-step sequential model of IgG denaturation, consisting of one reversible and two irreversible steps. A critical comparison of the predictions from this model with data obtained by an orthogonal fluorescence probe method, based on 8-anilinonaphthalene-1-sulfonate binding to partially unfolded states, resulted in very good agreement. In summary, our study highlights the validity of this easy-to-perform analysis for reliably assessing the kinetic stability of IgGs, which can support accelerated formulation development of monoclonal antibodies by ranking different formulations as well as by improving colloidal stability models.
Interaction of artemisinin and tetracycline or erythromycin against<i>Plasmodium falciparum in vitro</i> (1994)

Antimalarial activities of tetracycline (TC) and erythromycin (EM), alone or in combination with artemisinin (Qinghaosu, QHS), were studied using chloroquine (CQ)-sensitive (D6) and -resistant (W2) strains of Plasmodium falciparum in vitro. The antimalarial potency of TC (IC50 = 9862 nM for the CQ-sensitive parasite, 32414 nM for the CQ-resistant one) or EM (IC50 = 45787 nM for the CQ-sensitive parasite, 33397 nM for the CQ-resistant one) was much less than that of QHS (IC50 ranging from 25 to 40 nM). The CQ-resistant falciparum parasite displayed a cross-resistance to TC, while both the drug-sensitive and -resistant parasites exhibited similar responses to EM. However, antimalarial potency of EM appeared to be less than that of TC against the drug-sensitive parasite. When TC was combined with QHS, an additive interaction was observed against the CQ-sensitive falciparum parasite, while synergism was found with the CQ-resistant parasite. When EM was tested in combination with QHS, a potentiating interaction occurred with both the CQ-sensitive and resistant falciparum parasite. The above results indicated that the QHS combination with either TC or EM may be a promising antimalarial preparation with low recrudescence compared to artemisinin used alone in clinical practice.
Observation of the Electromagnetically Induced Transparency and Dispersion-like Structure in Trapped Cs Atoms (2001)

We report experiemtnal results demonstrating the electromagnetically induced transparency (EIT) in trapped Cs atoms. EIT occurs at the Λ-type configuration where the re0-pumping laser simultaneously plays a role as the coupling laser in the presence of a magneto-optical trapping and weak magnetic fields. Dependences of EIT signal on both the intensity and the detuning of the coupling laser were investigated. Linear absorption spectra for cold cesium atoms in the magneto-optical trap have been observed and shown the pronounced dispersion-like structure with sub-natural linewidth of 1 MHz due to the cooling laser.
Automated crystal structure solution from powder diffraction data: Validation of the first-principles-assisted structure solution method (2017)

The authors demonstrate an automated method to solve crystal structures from powder diffraction data. Originally developed by Meredig and Wolverton in 2013, their First-Principles-Assisted Structure Solution (FPASS) method uses $a\phantom{\rule{0}{0ex}}b$ $i\phantom{\rule{0}{0ex}}n\phantom{\rule{0}{0ex}}i\phantom{\rule{0}{0ex}}t\phantom{\rule{0}{0ex}}i\phantom{\rule{0}{0ex}}o$ energetics to guide the search for reasonable structures. Here, the authors find that FPASS accurately recovers the known solution for nearly 100 crystals and employ it to solve 10 structures that were previously incomplete in crystallographic databases. The authors identified several potential semiconducting materials from these new solutions, and also have released their automation software to allow others to use FPASS.
Los estudios de Medicina en Hispano-América (1998)

Comunicacion en las IV Jornadas sobre la presencia universitaria espanola en America, Abril de 1990.
Abstract 3046: Survival of Patients with Aortic Stenosis Referred for Percutaneous Aortic Valve Replacement (2008)

Transcatheter aortic valve replacement (TAVR) has emerged as a treatment alternative for patients with severe symptomatic aortic stenosis (AS) who are poor candidates for surgical aortic valve repl...
Reduced-Order Realization of a Nonlinear Power Network Using Companion-Form State Equations with Periodic Coefficients (2002)

This paper presents a methodology for the identification of a reduced-order dynamic equivalent of a nonlinear power network for the simulation of electromagnetic transients. The equivalent is deduced from the observer companion form of the state equations with periodic coefficients and includes the effects of the nonlinearity of the power network at its operating point. A previously proposed concept, the harmonic domain dynamic transfer function (HDDTF), is used to characterize the network's transient behavior, superimposed on the steady state. The HDDTF is obtained by linearization of the nonlinear state equations of the network corresponding to harmonic perturbations applied to the steady-state operating point. Then reduced-order companion-form state equations with periodic coefficients are fitted to the HDDTF in the frequency domain using a least-squares procedure based on the SVD and QR algorithms. The fitting procedure includes sequential weighting, column scaling, and vertical partitioning to improve computational accuracy and efficiency. The SVD algorithm serves to determine an appropriate model order. A test network with nonlinear inductances is used to demonstrate the performance of the identification method as well as the time-domain simulation results.