gebhart/patrepeval huggingface dataset:
Coronary artery disease (CAD) in chronic kidney disease patients (2016)

There is a great deal of data demonstrating a close association between chronic kidney disease (CKD) and cardiovascular disease, particularly coronary artery disease (CAD). About one half of deaths in patients with end-stage renal disease (ESRD) are of cardiovascular causes. The association between CKD and ischemic heart disease can be explained in part because both conditions are related to the traditional risk factors for atherosclerotic vascular disease. However, CKD might also have a casual role in the development and progression of CAD, with several mechanisms potentially involved. Among CAD patients, those with CKD have systematically a worse prognosis than those without CKD irrespective of the clinical presentation or the treatments applied. Current therapy is based on small trials and observational data and on the extrapolation of the strategies that have been proved useful in the general population, although many treatments that have been shown to improve the prognosis of CAD patients are underused in those with renal impairment.&nbsp;(Cardionephrology)
Immersion resist process for 32-nm node logic devices (2008)

Key issues of resist process design for 32nm node logic device were discussed in this paper. One of them is reflectivity control in higher 1.3NA regime. The spec for the reflectivity control is more and more severe as technology node advances. The target of reflectivity control over existent substrate thickness variation is 0.4%, which was estimated from our dose budget analysis. Then, single BARC process or stacked mask process (SMAP) was selected to each of the critical layers according to the substrate transparency. Another key issue in terms of material process was described in this paper, that is spin-on-carbon (SOC) pattern deformation during substrate etch process. New SOC material without any deformation during etch process was successfully developed for 32nm node stacked mask process (SMAP). 1.3NA immersion lithography and pattern transfer performance using single BARC
Study of corneal scattering for the optimization of femtosecond keratoplasty (2009)

The specular transmittance spectrum of human corneas is studied using a confocal geometry set-up. The comparison of the obtained spectrum with the total transmittance spectrum permits the determination of the stromal scattering spectrum of pathological corneas. The dependence of the scattering cross section on wavelength dependence is analyzed.
Design and Synthesis of Bitopic 2-Phenylcyclopropylmethylamine (PCPMA) Derivatives as Selective Dopamine D3 Receptor Ligands (2020)

2-Phenylcyclopropylmethylamine (PCPMA) analogues have been reported as selective serotonin 2C agonists. On the basis of the same scaffold, we designed and synthesized a series of bitopic derivatives as dopamine D3R ligands. A number of these new compounds show a high binding affinity for D3R with excellent selectivity. Compound (1<i>R</i>,2<i>R</i>)-<b>22e</b> and its enantiomer (1<i>S</i>,2<i>S</i>)-<b>22e</b> show a comparable binding affinity for the D3R, but the former is a potent D3R agonist, while the latter acts as an antagonist. Molecular docking studies revealed different binding poses of the PCPMA moiety within the orthosteric binding pocket of the D3R, which might explain the different functional profiles of the enantiomers. Compound (1<i>R</i>,2<i>R</i>)-<b>30q</b> shows a high binding affinity for the D3R (<i>K</i><sub>i</sub> = 2.2 nM) along with good selectivity, as well as good bioavailability and brain penetration properties in mice. These results reveal that the PCPMA scaffold may serve as a privileged scaffold for the design of aminergic GPCR ligands.
Use of lidocaine-prilocaine patch to decrease intramuscular injection pain does not adversely affect the antibody response to diphtheria-tetanus-acellular pertussis-inactivated poliovirus -Haemophilus influenzae type b conjugate and hepatitis B vaccines in infants from birth to six months of age (2002)

The EMLA patch has no adverse effect on the antibody response to the vaccine antigens, is effective in reducing pain associated with DTaP-IPV-Hib and hepatitis B immunizations and does not result in any significant or unexpected adverse reactions.
Phase II Study of a HER-2/Neu (HER2) Intracellular Domain (ICD) Vaccine Given Concurrently with Trastuzumab in Patients with Newly Diagnosed Advanced Stage Breast Cancer. (2009)

Abstract HER2 is a tumor antigen in breast cancer and several trials have demonstrated that breast cancer patients can be immunized against this protein. We have developed HER2 peptide based vaccines that are aimed at eliciting CD4+ Th1 tumor antigen specific T cell responses. Th1 effectors provide immunologic memory, enhance cross priming which will allow the elaboration of tumor specific CD8+ T cells, and stimulate epitope spreading which we have shown to be a potential biomarker of clinical response. 52 patients will be enrolled with the primary objective to determine relapse free survival after active immunization. Eligible patients are newly diagnosed with Stage III (B or C) or Stage IV breast cancer and begin vaccination within 6 months of starting maintenance trastuzumab. This interim report will present data on the first 25 patients enrolled; 21 stage IV and 4 locally advanced patients. The vaccine is well tolerated with all adverse events (AE) being Grade I or 2. The most common AE is injection site reaction. Moreover, the combination of HER2 vaccination with trastuzumab did not result in additive cardiac toxicity in these patients. Immune responses were evaluated by IFN-gamma ELISPOT. To date, 88% of patients immunized developed significant immunity to the components of the ICD vaccine. The majority, 75%, developed robust immunity to the HER2 protein. Our group has recently demonstrated that a broadening of immunity throughout the HER2 protein, to components of the protein that weren't in the vaccine, i.e. epitope spreading, may be associated with improved survival in vaccinated patients. 63% of immunized patients demonstrated evidence of intramolecular epitope spreading. We questioned whether such high frequencies of homing Type 1 T cells might modulate the immunosuppressive tumor microenvironment, so we evaluated whether circulating serum immunosuppressive cytokines were impacted by immunization. TGF-beta is an immunosuppressive cytokine secreted by tumor stroma and regulatory T cells. We found that the levels of serum TGF-beta decreased significantly in the majority of patients after vaccination. We further analyzed the correlation between the change of serum levels of TGF-beta post vaccination and HER2 ICD vaccine-induced T cell responses. We found that the greater the magnitude of the HER2 specific T cell response, as demonstrated by IFN-gamma secretion, the greater the decrease in serum TGF-beta (p=0.0045, r=0.742). The correlation between the increased epitope spreading T cell response and decreased levels of TGF-beta was even more significant (p=0.0003). The median overall survival has not been reached with 100% of patients alive at this time. Relapse free survival data will be presented. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 5102.
Analyte detection in complex samples using a biomimetic, non-spectroscopic sensing method (2017)

Optical sensing techniques for organic and biological molecules traditionally require the collection of complete, well-defined, vibrational spectra of a sample. The vibrational absorption bands of the spectra are identified, and statistical methods are then utilized to determine the moieties and concentration of target analytes present in a given sample. In this work, we present a new, non-spectroscopic alternative technique to molecular vibrational sensing. This biomimetic method, based on human color vision, uses only three broad, overlapping infrared (IR) optical filters to discriminate between chemicals with similar vibrational absorption bands. Unique detection vectors are defined by the interaction of a given chemical’s absorption bands with the three filter channels. Identification of the analytes present in a sample are then determined based on these detection vectors. We present multiple studies that demonstrate the ability of this approach to clearly discriminate between molecules with similar infrared vibrational absorption bands. We show that this method has the ability to precisely identify specific analytes in the presence of potential interferents with similar infrared absorption bands in the same sample. An optical filter based sensor that operates in the mid-IR using low power components, requiring no spectral scanning has been developed using this technique, and results using this sensor are shown. This method has the potential to lead the development of small, rugged optical sensors for non-invasive diagnostics and sensing of biological fluids.
Quantifying factors determining the rate of CTL escape and reversion during acute and chronic phases of HIV infection (2010)

Human immunodeficiency virus (HIV) often evades cytotoxic T cell (CTL) responses by generating variants that are not recognized by CTLs. However, the importance and quantitative details of CTL escape in humans are poorly understood. In part, this is because most studies looking at escape of HIV from CTL responses are cross-sectional and are limited to early or chronic phases of the infection. We use a novel technique of single genome amplification (SGA) to identify longitudinal changes in the transmitted/founder virus from the establishment of infection to the viral set point at 1 year after the infection. We find that HIV escapes from virus-specific CTL responses as early as 30-50 days since the infection, and the rates of viral escapes during acute phase of the infection are much higher than was estimated in previous studies. However, even though with time virus acquires additional escape mutations, these late mutations accumulate at a slower rate. A poor correlation between the rate of CTL escape in a particular epitope and the magnitude of the epitope-specific CTL response suggests that the lower rate of late escapes is unlikely due to a low efficacy of the HIV-specific CTL responses in the chronic phase of the infection. Instead, our results suggest that late and slow escapes are likely to arise because of high fitness cost to the viral replication associated with such CTL escapes. Targeting epitopes in which virus escapes slowly or does not escape at all by CTL responses may, therefore, be a promising direction for the development of T cell based HIV vaccines.
Plasmonic Random Lasing in Strongly Scattering Regime with Slanted Silver Nanorod Array (2015)

We present a plasmonic approach employing a slanted silver nanorod array for achieving controllable random lasing in a strongly scattering regime. Such random lasers can serve as a bright optical source for speckle-free imaging.
FDMA-FSK star network with a tunable optical filter demultiplexer (1988)

An optical frequency-division-multiple-access (FDMA) star network is analyzed and demonstrated experimentally using two 45-Mb/s frequency-shift-keyed (FSK) laser channels at 1.5 mu m. A tunable fiber Fabry-Perot (FFP) filter is used to select channels and convert FSK to intensity modulation for direct detection. The analysis predicts and experiment supports a minimum channel spacing of about six times bit rate B for a single FFP. These constraints are similar to those for more complex heterodyne demultiplexing. Estimates show that a network with 1000 users, independent of bit rate, is feasible with a tandem FFP. For B=1 Gb/s per channel the network capacity would be 1 Tb/s.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The multi-mind effect (2007)

Courtesy of experiments carried out by such thinkers as Wason, Johnson-Laird, and Kahneman & Tversky, there is overwhelming empirical evidence that the vast majority of logically untrained humans are unable to reason in context-independent, normatively correct fashion. However, the multi-mind effect, which is predicted by our earlier success at teaching this kind of reasoning, and also by our general theory of human and machine reasoning, shows that while individual persons (with rare exceptions) are unable to solve problems that demand context-independent reasoning, groups of persons can often solve such problems.
Stereoselective Synthesis of Orthogonally Protected β-Hydroxy-α-,γ-diamino Butyric Acids (2011)

A synthesis of all four stereoisomers of the unnatural amino acid β-OH Dab (α,γ-diamino butyric acid) in orthogonally protected form is described. The synthetic strategy relies on a three-step sequence comprising stereoselective dihydroxylation, sulfite formation, and regioselective sulfite opening with azide to build the densely functionalized carbon skeleton.
Direct observation of phase transformations in the simulated heat-affected zone of a 9Cr martensitic steel (2008)

Abstract An experimental test melt of a boron alloyed 9Cr-3W-3Co-V,Nb steel for high temperature applications in the thermal power generation industry was produced by vacuum induction melting. This grade of steel typically displays a homogeneous tempered martensitic microstructure in the as-received, i. e. normalised and tempered, condition. However, after welding, this microstructure is significantly altered, resulting in a loss of its desired properties. The phase transformations during simulated thermal cycles typical of those experienced in the weld heat-affected zone were directly observed by in-situ X-ray diffraction experiments using synchrotron radiation. Heating rates of 10 K s −1 and 100 K s −1 up to a peak temperature of 1300°C are investigated here. The final microstructures observed after both simulated weld thermal cycles are primarily composed of martensite with approximately 4% retained delta ferrite and 4% retained austenite, by volume. With the temporal resolution of the in-situ X-ray diffraction technique, phase transformations from tempered martensite to austenite to delta ferrite during heating and to martensite during cooling were monitored. With this technique, the evolution of the final microstructure through both heating and cooling is monitored, providing additional context to the microstructural observations.
The Changing Face of Web Search (2006)

Web search has emerged from being a starting point for exploring the web, to being a proving ranking algorithms and large-scale distributed systems, to its current form in which it is a fast-growing advertising medium. This talk reviews the background of web search, the finally its emerging prospects and technical directions including ubiquitous access across mobile devices. Along the way, we also discuss challenges arising in using the web as an advertising medium.
Meta-analysis of gestational duration and spontaneous preterm birth identifies new maternal risk loci (2022)

Abstract Background Preterm birth (&lt;37 weeks of gestation) is a major cause of neonatal death and morbidity. Up to 40% of the variation in timing of birth results from genetic factors, mostly due to the maternal genome. Methods We conducted a genome-wide meta-analysis of gestational duration and spontaneous preterm birth in 68,732 and 98,371 European mothers, respectively. Results We detected 19 associated loci of which seven were novel. The loci mapped to several biologically plausible genes, including HAND2 whose expression was previously shown to decrease during gestation, associated with gestational duration, and GC encoding Vitamin D-binding protein, associated with preterm birth. Downstream in silico -analysis suggested regulatory roles as underlying mechanisms for the associated loci. LD score regression found birth weight measures as the most strongly correlated traits, highlighting the unique nature of spontaneous preterm birth phenotype. Tissue expression and colocalization analysis revealed reproductive tissues and immune cell types as the most relevant sites of action. Conclusion We report novel genetic risk loci that associate with preterm birth or gestational duration, and reproduce findings from previous genome-wide association studies. Altogether, our findings provide new insight into the genetic background of preterm birth. Better characterization of the causal genetic mechanisms will be important to public health as it could suggest new strategies to treat and prevent preterm birth.
On Preserving Views in Evolving Environments (1997)

The construction and maintenance of data warehouses (views) in large-scale environments composed of numerous distributed information sources (ISs) such as the WWW has received great attention recently. Such environments are plagued with continuously changing information because ISs tend to continuously evolve by modifying not only their content but also their query capabilities and interface and by joining or leaving the environment at any time. In this paper, we outline our position on issues related to the challenging new problem of how to adapt views in such evolving environments. We first present a taxonomy of view adaptation problems by describing the dimensions along which view adaptation problems can be classified. Based on this taxonomy, we identify a new view adaptation problem for view evolution in the context of ISs capability changes, which we call View Synchronization. We also outline the Evolvable View Environment (EVE) that we propose as framework for solving the view sy...
Controlled conductivity at low pH in Protein L chromatography enables separation of bispecific and other antibody formats by their binding valency (2019)

The complex molecular formats of recent therapeutic antibodies, including bispecific antibodies, antibody fragments, and other fusion proteins, makes the task of purifying the desired molecules in a limited number of purification steps more and more challenging. Manufacturing these complicated biologics can be substantially improved in the affinity capture stage if the simple bind-and-elute mode is accompanied by targeted removal of the impurities, such as mis-paired antibodies and oligomers or aggregates. Here, we report a method, based on the binding valency to Protein L resin, of separating proteins during the elution step by simply controlling the conductivity at low pH. We show that the method efficiently separated targeted antibodies from mis-paired and aggregated species. Notably, the number of Protein L binding sites can be built into the molecule by design to facilitate the purification. This method may be useful for purifying various antibody formats at laboratory and manufacturing scales.
Plasma epinephrine levels in resuscitation with cardiopulmonary bypass (1990)

Since the highest plasma epinephrine levels have been recorded during resuscitation, we evaluated the isolated effect of cardiac arrest upon adrenomedullary secretion. We determined plasma epinephrine in dogs resuscitated with cardiopulmonary bypass (CPB) after cardiac arrest periods of 12 (CPB-12; n = 4) or 16 min (CPB-16; n = 5). Through 2 h of CPB and the following 6 h of critical care, there was no difference between CPB-12 and CPB-16 regarding most cardiopulmonary functional variables. Plasma epinephrine was markedly elevated immediately after initiation of CPB (p less than .01 at 1 min CPB vs. basal) and returned rapidly to basal concentrations. Comparison of plasma epinephrine levels between CPB and standard CPR groups showed that responses to cardiac arrest were similar (p greater than .05 at 1 min CPB vs. 11.5 min CPR). We conclude that cardiac arrest is the main or sole determinant of the plasma epinephrine elevation of resuscitation.
The Combined Percentage of Gleason Patterns 4 and 5 Is the Best Predictor of Cancer Progression After Radical Prostatectomy (2005)

The combined percentage of Gleason patterns 4 and 5 is one of the most powerful predictors of patient outcome, and appears superior to conventional Gleason score in identifying patients at increased risk of disease progression. On the basis of our results, we recommend that the combined percentage of Gleason patterns 4 and 5 be evaluated in radical prostatectomy specimens. The amount of high-grade cancer in a prostatectomy specimen should be taken into account in therapeutic decision making and assessment of patient prognosis.
Alimentos con calidad. Nuevas estrategias rurales para nuevos consumidores (2016)

Este texto profundiza en uno de los aspectos que caracteriza a la nueva ruralidad: la progresiva especialización de los espacios rurales en producción de calidad y el uso de marcas distintivas. Este tipo de estrategia de creación de valor añadido en los productos alimentarios ha sido una de las líneas prioritarias de los Programas de Desarrollo Rural en Europa desde los inicios del siglo xxi. Esta incesante proliferación de marcas de calidad de productos agroalimentarios denota la profunda transformación con que los espacios rurales han entrado en el nuevo siglo.
Sintering Metal–Organic Framework Gels for Application as Structural Adhesives (Small 25/2023) (2023)

Metal–Organic Frameworks The zeolitic imidazolate framework-67 (ZIF-67) gel sintering technique provides a microstructure of densely aggregated, large spherical ZIF-67 crystals, resulting in bonding of Cu substrates with shear strength exceeding 30 MPa, comparable to that of conventional structural adhesives. More details can be found in article number 2300298 by Izuru Miyazaki, Mitsutaro Umehara, and co-workers.
<title>Five-dimensional fluorescence microscopy</title> (2001)

We report a whole-field fluorescence imaging microscope that combines 3-D spatial resolution by optical sectioning, using structured illumination, with fluorescence lifetime imaging and spectrally-resolved imaging. We show the potential of this technique in the elimination of common artefacts in fluorescence lifetime imaging and apply it to study the dependence of the lifetime on the emission wavelength in biological tissue.
Coarse-Grained/Molecular Mechanics of the TAS2R38 Bitter Taste Receptor: Experimentally-Validated Detailed Structural Prediction of Agonist Binding (2013)

Bitter molecules in humans are detected by ∼25 G protein-coupled receptors (GPCRs). The lack of atomic resolution structure for any of them is complicating an in depth understanding of the molecular mechanisms underlying bitter taste perception. Here, we investigate the molecular determinants of the interaction of the TAS2R38 bitter taste receptor with its agonists phenylthiocarbamide (PTC) and propylthiouracil (PROP). We use the recently developed hybrid Molecular Mechanics/Coarse Grained (MM/CG) method tailored specifically for GPCRs. The method, through an extensive exploration of the conformational space in the binding pocket, allows the identification of several residues important for agonist binding that would have been very difficult to capture from the standard bioinformatics/docking approach. Our calculations suggest that both agonists bind to Asn103, Phe197, Phe264 and Trp201, whilst they do not interact with the so-called extra cellular loop 2, involved in cis-retinal binding in the GPCR rhodopsin. These predictions are consistent with data sets based on more than 20 site-directed mutagenesis and functional calcium imaging experiments of TAS2R38. The method could be readily used for other GPCRs for which experimental information is currently lacking.
Experimental Introduction into the Atomic World. (1999)

This article describes a series of demonstration experiments, which were exhibited to general visitors in open days of our research institute. The intention is to provide the people with an opportunity to actually experience by themselves why and how atoms assemble to form various types of materials. At the same time, these experiments are designed to be an enjoyable introduction to our research activity.