gebhart/patrepeval huggingface dataset:
Duftvorhersage: das Computermodell des hOR17‐4‐Rezeptors auf dem Prüfstand mit Silicium‐Analoga von Bourgeonal und Lilial (2007)

Die elektronische Oberflächenstruktur eines Moleküls bestimmt die Wechselwirkungen mit seinen Geruchsrezeptoren: Unterschiede in den stereoelektronischen Eigenschaften der Silicium-Analoga der Maiglöckchen-Riechstoffe Lilial und Bourgeonal ermöglichen einen Vergleich von In-vivo-, In-vitro- und In-silico-Daten. Die Geruchsschwellenwerte und das Schwimmverhalten von Spermien stimmen gut mit den Bindungsenergien überein, die an einem Modell des hOR17-4-Rezeptors berechnet wurden. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2007/z605002_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
ChemInform Abstract: SYNTHESIS OF 5‐(DIHYDROXYBORYL)‐2′‐DEOXYURIDINE AND RELATED BORON‐CONTAINING PYRIMIDINES (1985)

Abstract Aus den Pyrimidinen (I) werden, wie angegeben, die Dihydroxybor‐ Verbindungen (II) dargestellt und zu den entsprechenden Uracilen (III) reduziert.
A machine learning approach for body part recognition based on CT images (2008)

Body part recognition based on CT slice images is very important for many applications in PACS and CAD systems. In this paper, we propose a novel approach that can recognize which body part a slice image belongs to robustly. We focus on how to effectively express and use the unique statistical information of the correlation between the CT value and the position information of each body part. We apply the machine learning method AdaBoost to express and use this statistical information. Our approach consists of a training process and a recognition process. In the training process, we first define the whole body using a set of specific classes to ensure that training images in the same class have a high similarity, and prepare a training image set (positive samples and negative samples) for each class. Second, the training images are normalized to a fixed size and rotation in each class. Third, features are calculated for each normalized training image. Finally, AdaBoosted histogram classifiers are trained. After the training process, each class has its own classifiers. In the recognition process, given a series of CT images, the scores of all classes for each slice image are calculated based on the classifiers obtained in the training process. Then, based on the scores of each slice and a simple model of body part sequence continuity, we use dynamic programming (DP) to eliminate false recognition results. Experimental results on 440 unknown series including lesions show that our approach has high a recognition rate.
Pathogenic Events in a Nonhuman Primate Model of Oral Poliovirus Infection Leading to Paralytic Poliomyelitis (2017)

Despite a great deal of prior research, the early pathogenic events in natural oral poliovirus infection remain poorly defined. To establish a model for study, we infected 39 macaques by feeding them single high doses of the virulent Mahoney strain of wild type 1 poliovirus. Doses ranging from 10<sup>7</sup> to 10<sup>9</sup> 50% tissue culture infective doses (TCID<sub>50</sub>) consistently infected all the animals, and many monkeys receiving 10<sup>8</sup> or 10<sup>9</sup> TCID<sub>50</sub> developed paralysis. There was no apparent difference in the susceptibilities of the three macaque species (rhesus, cynomolgus, and bonnet) used. Virus excretion in stool and nasopharynges was consistently observed, with occasional viremia, and virus was isolated from tonsils, gut mucosa, and draining lymph nodes. Viral replication proteins were detected in both epithelial and lymphoid cell populations expressing CD155 in the tonsil and intestine, as well as in spinal cord neurons. Necrosis was observed in these three cell types, and viral replication in the tonsil/gut was associated with histopathologic destruction and inflammation. The sustained response of neutralizing antibody correlated temporally with resolution of viremia and termination of virus shedding in oropharynges and feces. For the first time, this model demonstrates that early in the infectious process, poliovirus replication occurs in both epithelial cells (explaining virus shedding in the gastrointestinal tract) and lymphoid/monocytic cells in tonsils and Peyer's patches (explaining viremia), extending previous studies of poliovirus pathogenesis in humans. Because the model recapitulates human poliovirus infection and poliomyelitis, it can be used to study polio pathogenesis and to assess the efficacy of candidate antiviral drugs and new vaccines.<b>IMPORTANCE</b> Early pathogenic events of poliovirus infection remain largely undefined, and there is a lack of animal models mimicking natural oral human infection leading to paralytic poliomyelitis. All 39 macaques fed with single high doses ranging from 10<sup>7</sup> to 10<sup>9</sup> TCID<sub>50</sub> Mahoney type 1 virus were infected, and many of the monkeys developed paralysis. Virus excretion in stool and nasopharynges was consistently observed, with occasional viremia; tonsil, mesentery lymph nodes, and intestinal mucosa served as major target sites of viral replication. For the first time, this model demonstrates that early in the infectious process, poliovirus replication occurs in both epithelial cells (explaining virus shedding in the gastrointestinal tract) and lymphoid/monocytic cells in tonsils and Peyer's patches (explaining viremia), thereby supplementing historical reconstructions of poliovirus pathogenesis. Because the model recapitulates human poliovirus infection and poliomyelitis, it can be used to study polio pathogenesis, candidate antiviral drugs, and the efficacy of new vaccines.
Spontaneous Pattern Formation on Ion Bombarded Si(001) (1999)

Spectroscopic light scattering was used to monitor periodic ripple evolution on Si(001) in situ during ${\mathrm{Ar}}^{+}$ sputtering. Analysis indicates that under high flux the concentration of mobile species on the surface is temperature and ion flux independent. This is due to an effect of ion collision cascades on the concentration of mobile species. We thereby measure the migration energy on the surface to be $1.2\ifmmode\pm\else\textpm\fi{}0.1\mathrm{eV}$. The technique is generalizable to any material, including high temperature and insulating materials for which surface migration energies are notoriously difficult to measure.
Supplementary Figure 1 from Glioblastoma Cell Enrichment Is Critical for Analysis of Phosphorylated Drug Targets and Proteomic–Genomic Correlations (2023)

&lt;p&gt;PDF file - 197K, Protein/Phosphoprotein comparison between matched LCM and non-LCM samples by unsupervised hierarchical clustering.&lt;/p&gt;
APPLICATION OF PAN/PANI COMPOSITE MEMBRANES IN PURIFICATION OF INDUSTRIAL WASTEWATER GENERATED DURING PROCESSING OF METALS (2017)

The paper presents results of research on the use of composite membranes of polyacrylonitrile (PAN) doped polyaniline (PANI) to remove contaminations of industrial wastewater generated during the processing of metals. Wastewater obtained from industry was pre-treated with the flocculant Magnafloc<sup>®</sup>336, and then the supernatant solution was introduced into the ultrafiltration cell, AMICON (Millipore) equipped in the previously prepared polymer membrane. Using spectrophotometer UV-Vis (HACH) and atomic absorption spectrometry (AAS) pollution indicators was marked before and after the integrated purification proces, to determine the degree of removal of selected ions from wastewater. As a result of flocculation from wastewater there have been removed phosphates (79%), chlorides (11-14%), sulfates (2-10%) and iron (36-92%), cobalt (~ 80%), cadmium (~ 31% ) and nickel (~ 25%). However, the pressure membrane process almost completely removed zinc, copper and cadmium (~ 100%), iron (by a further 43-69%) and phosphate anions, which was a little.
SufA – a bacterial enzyme that cleaves fibrinogen and blocks fibrin network formation (2008)

Finegoldia magna is a member of the normal human bacterial flora on the skin and other non-sterile body surfaces, but this anaerobic coccus is also an important opportunistic pathogen. SufA was the first F. magna proteinase to be isolated and characterized. Many bacterial pathogens interfere with different steps of blood coagulation, and here we describe how purified SufA efficiently and specifically cleaves fibrinogen in human plasma. SufA is both secreted by F. magna and associated with the bacterial surface. Successful gene targeting has previously not been performed in anaerobic cocci, but in order to study the role of the SufA that is present at the bacterial surface, we constructed an F. magna mutant that expresses a truncated SufA lacking proteolytic activity. In contrast to wild-type bacteria that delayed the coagulation of human plasma, mutant bacteria had no such effect. Wild-type and mutant bacteria adhered to keratinocytes equally well, but in a plasma environment only wild-type bacteria blocked the formation of fibrin networks surrounding adherent bacteria. The effective cleavage of fibrinogen by SufA suggests that the interference with fibrin network formation represents an adaptive mechanism of F. magna with potential implications also for pathogenicity.
Photothermal Genetic Engineering (2012)

Optical methods for manipulation of cellular function have enabled deconstruction of genetic and neural circuits in vitro and in vivo. Plasmonic gold nanomaterials provide an alternative platform for external optical manipulation of genetic circuits. The tunable absorption of gold nanoparticles in the infrared spectral region and straightforward surface functionalization has led to applications in intracellular delivery and photorelease of short RNAs, recently enabling bidirectional photothermal modulation of specific genes via RNA interference (RNAi). We discuss recent advances in optical gene circuit engineering and plasmonic nanomaterials, as well as future research opportunities and challenges in photothermal gene manipulation.
Automated quantitative assessment of cardiovascular magnetic resonance-derived atrioventricular junction velocities (2015)

The assessment of atrioventricular junction (AVJ) deformation plays an important role in evaluating left ventricular systolic and diastolic function in clinical practice. This study aims to demonstrate the effectiveness and consistency of cardiovascular magnetic resonance (CMR) for quantitative assessment of AVJ velocity compared with tissue Doppler echocardiography (TDE). A group of 145 human subjects comprising 21 healthy volunteers, 8 patients with heart failure, 17 patients with hypertrophic cardiomyopathy, 52 patients with myocardial infarction, and 47 patients with repaired Tetralogy of Fallot were prospectively enrolled and underwent TDE and CMR scan. Six AVJ points were tracked with three CMR views. The peak systolic velocity (Sm1), diastolic velocity during early diastolic filling (Em), and late diastolic velocity during atrial contraction (Am) were extracted and analyzed. All CMR-derived septal and lateral AVJ velocities correlated well with TDE measurements (Sm1: r = 0.736; Em: r = 0.835; Am: r = 0.701; Em/Am: r = 0.691; all p &lt; 0.001) and demonstrated excellent reproducibility [intrastudy: r = 0.921–0.991, intraclass correlation coefficient (ICC): 0.918–0.991; interstudy: r = 0.900–0.970, ICC: 0.887–0.957; all p &lt; 0.001]. The evaluation of three-dimensional AVJ motion incorporating measurements from all views better differentiated normal and diseased states [area under the curve (AUC) = 0.918] and provided further insights into mechanical dyssynchrony diagnosis in HF patients (AUC = 0.987). These findings suggest that the CMR-based method is feasible, accurate, and consistent in quantifying the AVJ deformation, and subsequently in diagnosing systolic and diastolic cardiac dysfunction.
AAVrh.10-Mediated Expression of an Anti-Cocaine Antibody Mediates Persistent Passive Immunization That Suppresses Cocaine-Induced Behavior (2012)

Cocaine addiction is a major problem affecting all societal and economic classes for which there is no effective therapy. We hypothesized an effective anti-cocaine vaccine could be developed by using an adeno-associated virus (AAV) gene transfer vector as the delivery vehicle to persistently express an anti-cocaine monoclonal antibody in vivo, which would sequester cocaine in the blood, preventing access to cognate receptors in the brain. To accomplish this, we constructed AAVrh.10antiCoc.Mab, an AAVrh.10 gene transfer vector expressing the heavy and light chains of the high affinity anti-cocaine monoclonal antibody GNC92H2. Intravenous administration of AAVrh.10antiCoc.Mab to mice mediated high, persistent serum levels of high-affinity, cocaine-specific antibodies that sequestered intravenously administered cocaine in the blood. With repeated intravenous cocaine challenge, naive mice exhibited hyperactivity, while the AAVrh.10antiCoc.Mab-vaccinated mice were completely resistant to the cocaine. These observations demonstrate a novel strategy for cocaine addiction by requiring only a single administration of an AAV vector mediating persistent, systemic anti-cocaine passive immunity.
Saliva Urea Nitrogen Continuously Reflects Blood Urea Nitrogen after Acute Kidney Injury Diagnosis and Management: Longitudinal Observational Data from a Collaborative, International, Prospective, Multicenter Study (2016)

SUN reflects BUN especially in severe AKI. It also allows monitoring treatment responses. Video Journal Club 'Cappuccino with Claudio Ronco' at http://www.karger.com/?doi=445041.
Gelation of Ionic Liquids Using a Cross-Linked Poly(Ethylene Glycol) Gel Matrix (2004)

Conductive ionic liquid−poly(ethylene glycol) (IL−PEG) gels have been prepared by gelation of the hydrophobic ionic liquid 1-hexyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([C6mim][NTf2]) by the cross-linking reaction of disuccinimidylpropyl PEG monomers with four-arm tetraamine PEG cross-linkers. This is the first time that a cross-linked PEG matrix, such as this, has been used to gel nonaqueous solvents. Initial studies screening other ionic liquids as solvents indicate that the gelation of the ionic liquid is both cation and anion dependent with smaller, coordinating cations disrupting or preventing gel formation.
Sinus Augmentation with Simultaneous, Non-Submerged, Implant Placement Using a Minimally Invasive Hydraulic Technique (2020)

<i>Background and objectives:</i> To evaluate whether sinus augmentation, using a minimally invasive implant device, via a non-submerged surgical approach, might negatively influence the outcome. <i>Materials and Methods:</i> A retrospective cohort study was conducted by evaluating patients' files, classifying them into two groups. Fifty patients (22 men 28 women) were included in the study, 25 in each group. The use of an implant device based on residual alveolar ridge height for sinus augmentation, radiographic evaluation, insertion torque, membrane perforation, post-operative healing, and a minimum of 12 months follow-up were evaluated. <i>Results:</i> The mean residual alveolar ridge height was 5.4 mm for the non-submerged group and 4.2 mm for the submerged group. There were no intraoperative or postoperative complications (including membrane perforations). The mean insertion torque was 45 N/cm for the study group and 20 N/cm for the control group. Complete soft tissue healing was observed within three weeks. Mean bone gain height was 8 mm for the study and 9.3 mm for the control group. All implants osseointegrated after 6-9 months of healing time. Mean follow-up was 17.5 months, range 12-36 months. Marginal bone loss at last follow-up was not statistically significantly different: 1 mm in the non-submerged vs. 1.2 mm in the submerged group. <i>Conclusions:</i> Submerged and non-submerged healing following maxillary sinus augmentation was comparable provided residual alveolar ridge height >5 mm and insertion torque >25 N/cm.
Inhibition of carcinoma cell‐derived VEGF reduces inflammatory characteristics in xenograft carcinoma (2006)

The stroma of carcinomas shares several characteristics with inflamed tissues including a distorted vasculature, active angiogenesis and macrophage infiltration. In addition, the tumor interstitial fluid pressure (P(IF)) of the stroma is pathologically elevated. We show here that bevacizumab [rhuMab vascular endothelial growth factor (VEGF), Avastin], a monoclonal antibody to VEGF, at a dose of 5 mg/kg modulated inflammation in KAT-4 xenograft human anaplastic thyroid carcinoma tissue. At this dose, bevacizumab reduced the density of macrophages, MHC class II antigen expression by macrophages and IL-1beta mRNA expression. Furthermore, bevacizumab lowered tumor extracellular fluid volume, plasma protein leakage from tumor vessels, the number of CD31-positive structures and tumor P(IF). The tumor plasma volume and the number of alpha-smooth muscle actin-positive vessels, however, remained unchanged. Our data suggest that carcinoma cell-derived VEGF either directly or indirectly participates in maintaining an inflammatory microenvironment in experimental KAT-4 carcinoma. Furthermore, our data indicate that the reduction of inflammation resulting in reduced vascular permeability and decrease in the tumor extracellular fluid volume by bevacizumab contributes to reduced tumor P(IF).
Epigenetic Tumor Response to Hypoxia: An Epimutation Pattern and a Method of Multi Targeted Epigenetic Therapy (MTET) (2016)

In most cases, cancer develops as a result of non-inheritable somatic mutations (epimutations), acquired by the individual adult cell, during the evolution of the cell, and propagated into an expanding clone of progeny of the cells by natural selection [1]. The role of microenvironment in selection for such acquired mutations, or epimutations, is a focus of scientific research in carcinogenesis [2]. Here we describe a defective DNA response to hypoxia due to epigenetic aberrancies, in cancer cellular biology [3]. We also summarize a literature review on hypoxia mediated epigenetic responses, and its role in carcinogenesis and metastasis. Further, we review a novel method of treating hypoxic solid tumors with a combination of epigenetic modifiers with both in vitro and in vivo results in human, translating to an improved prognosis and clinical outcome. We propose that this approach both independently and synergistically (with the current standard of care) can provide an improved outcome.
Catalytic hydrogen production by a Ni–Ru mimic of NiFe hydrogenases involves a proton-coupled electron transfer step (2013)

A combined electrochemical and theoretical study suggests that hydrogen evolution from weak acids catalyzed by a structural mimic of the active site of NiFe hydrogenases [Ni(xbsms)Ru(C6Me6)Cl](+) proceeds through proton-coupled electron transfer steps.
CAMTOS - a software suite combining direct and indirect trajectory optimization methods (2002)

Many engineering applications involve the solution of optimal control problems. Such problems cover a wide variety of different disciplines, starting from typical aerospace applications, e.g. a fuel minimal launcher ascent trajectory, up to more exotic applications such as the optimal motion of the human body in different sport disciplines. This thesis presents a new method for solving a general class of multi-phase trajectory optimization problems. This new method uses a combination of direct multiple shooting and direct collocation. Depending on the specific demands of the problem to solve, a different kind of transcription method can be used for each phase. In addition, the method can be combined with the indirect method. Once the adjoint differential equations are available in addition to the dynamic system, one or more phases can be modeled as indirect phases. Since the transversality conditions that are usually required for solving the multi-point boundary value problem are contained in the Karush-Kuhn-Tucker conditions of the NLP-solver, they need not be formulated explicitly. The benefits of combining direct and indirect methods is demonstrated on an Ariane 5 dual payload mission. While the atmospheric parts of this mission are modelled with the direct multiple-shooting technique, the upper stage is using the indirect method. An analysis of the switching function, which is generated as a by-product of the indirect method, yields an improved mission profile. This profile involves an additional coast-arc and improves the pay-load performance by 66%. An additional example demonstrates the advantages of using direct collocation and direct multiple shooting to solve a complex branched trajectory optimization problem. The ascent and return of the suborbital Hopper vehicle is optimized such that the payload delivered to the geostationary transfer orbit by an upper stage is maximized. The robustness and large convergence radius of the direct collocation method significantly simplifies the generation of an approximate solution of the problem which is then refined by changing the transcription method of the atmospheric parts of the trajectory to the direct multiple shooting technique.
The TRIM5 Gene Modulates Penile Mucosal Acquisition of Simian Immunodeficiency Virus in Rhesus Monkeys (2011)

There is considerable variability in host susceptibility to human immunodeficiency virus type 1 (HIV-1) infection, but the host genetic determinants of that variability are not well understood. In addition to serving as a block for cross-species retroviral infection, TRIM5 was recently shown to play a central role in limiting primate immunodeficiency virus replication. We hypothesized that TRIM5 may also contribute to susceptibility to mucosal acquisition of simian immunodeficiency virus (SIV) in rhesus monkeys. We explored this hypothesis by establishing 3 cohorts of Indian-origin rhesus monkeys with different TRIM5 genotypes: homozygous restrictive, heterozygous permissive, and homozygous permissive. We then evaluated the effect of TRIM5 genotype on the penile transmission of SIVsmE660. We observed a significant effect of TRIM5 genotype on mucosal SIVsmE660 acquisition in that no SIV transmission occurred in monkeys with only restrictive TRIM5 alleles. In contrast, systemic SIV infections were initiated after preputial pocket exposures in monkeys that had at least one permissive TRIM5 allele. These data demonstrate that host genetic factors can play a critical role in restricting mucosal transmission of a primate immunodeficiency virus. In addition, we used our understanding of TRIM5 to establish a novel nonhuman primate penile transmission model for AIDS mucosal pathogenesis and vaccine research.
Mid-Infrared Detection of a Hot Molecular Core in G29.96−0.02 (2001)

We present high angular resolution (~0.5") 10 and 18 micron images of the region around G29.96-0.02 taken from the Gemini North 8-m telescope using the mid-infrared imager and spectrometer OSCIR. These observations were centered on the location of a group of water masers, which delineate the site of a hot molecular core believed to contain an extremely young, massive star. We report here the direct detection of a hot molecular core at mid-infrared wavelengths at this location. The size and extent of the core at 18 microns appears to be very similar to the morphology as seen in integrated NH3 maps. However, our observations indicate that the mid-infrared emission may not be exactly coincident with the NH3 emission.