gebhart/patrepeval huggingface dataset:
The Komodo dragon (Varanus komodoensis) genome and identification of innate immunity genes and clusters (2019)

Genes with important roles in host-defense and innate immunity were identified in this newly sequenced Komodo dragon genome, suggesting that these organisms have a robust innate immune system. Specifically, multiple Komodo antimicrobial peptide genes were identified. Importantly, many of the antimicrobial peptide genes were found in gene clusters. We found that these innate immunity genes are conserved among reptiles, and the organization is similar to that seen in other avian and reptilian species. Having the genome of this important squamate will allow researchers to learn more about reptilian gene families and will be a valuable resource for researchers studying the evolution and biology of the endangered Komodo dragon.
Interfering Channel Estimation in Radar-Cellular Coexistence: How Much Information Do We Need? (2018)

In this paper, we focus on the coexistence between a MIMO radar and cellular base stations. We study the interfering channel estimation, where the radar is operated in the "search and track" mode, and the BS receives the interference from the radar. Unlike the conventional methods where the radar and the cellular systems fully cooperate with each other, in this work we consider that they are uncoordinated and the BS needs to acquire the interfering channel state information (ICSI) by exploiting the radar probing waveforms. For completeness, both the line-of-sight (LoS) and Non-LoS (NLoS) channels are considered in the coexistence scenario. By further assuming that the BS has limited a priori knowledge about the radar waveforms, we propose several hypothesis testing methods to identify the working mode of the radar, and then obtain the ICSI through a variety of channel estimation schemes. Based on the statistical theory, we analyze the theoretical performance of both the hypothesis testing and the channel estimation methods. Finally, simulation results verify the effectiveness of our theoretical analysis and demonstrate that the BS can effectively estimate the interfering channel even with limited information from the radar.
Proteogenomic Characterization Reveals Therapeutic Vulnerabilities in Lung Adenocarcinoma (2020)

To explore the biology of lung adenocarcinoma (LUAD) and identify new therapeutic opportunities, we performed comprehensive proteogenomic characterization of 110 tumors and 101 matched normal adjacent tissues (NATs) incorporating genomics, epigenomics, deep-scale proteomics, phosphoproteomics, and acetylproteomics. Multi-omics clustering revealed four subgroups defined by key driver mutations, country, and gender. Proteomic and phosphoproteomic data illuminated biology downstream of copy number aberrations, somatic mutations, and fusions and identified therapeutic vulnerabilities associated with driver events involving KRAS, EGFR, and ALK. Immune subtyping revealed a complex landscape, reinforced the association of STK11 with immune-cold behavior, and underscored a potential immunosuppressive role of neutrophil degranulation. Smoking-associated LUADs showed correlation with other environmental exposure signatures and a field effect in NATs. Matched NATs allowed identification of differentially expressed proteins with potential diagnostic and therapeutic utility. This proteogenomics dataset represents a unique public resource for researchers and clinicians seeking to better understand and treat lung adenocarcinomas.
JOpera: Autonomic Service Orchestration (2006)

The increasing interest in new software engineering technologies for application integration such as Service Oriented Computing and Service Orchestration has resulted in a proliferation of workflow management systems as the underlying representation and execution platform for service composition. Workflow management system are also being applied to new domains (e.g., virtual scientific laboratories, Grid computing, service delivery and provisioning). For these new applications, workflows are seen as the modeling metaphor behind the notion of straight through processing and virtual organizations where a collection of existing heterogeneous systems are composed into an integrated solution.\n \n In all these settings workflow engines are at the core of a complex combination of applications and clustered computers. As such, they have become rather difficult to deploy and configure, let alone tune to obtain maximum performance. This problem is not unique to workflow and service composition engines but it is more difficult to address in these settings because there is only a limited understanding of the execution procedures behind a workflow engine. In this short paper we report on our ongoing work to design and develop an autonomic workflow engine that can be used for large scale service composition. The challenge we face in doing this is threefold. First, we need to design an execution procedure for service compositions that is amenable to autonomic treatment. Second, this procedure needs to be realized in an architecture that supports the deployment of different modules of the system across a computer cluster in order to achieve the desired level of performance. Third, an autonomic controller and appropriate control policies need to be developed to automatically provision the optimal amount of resources to the engine.\n \n In this paper we provide a high level description of how we have accomplished these three goals and give a brief account of the performance of the system. The implemented system is part of the JOpera project. JOpera is an advanced SOA tool for Eclipse, which provides modeling, execution, monitoring and debugging tools for workflow-based Web service orchestration.
257 Young Scholar Presentation: Using an integrated systems biology platform to determine the mode of action of feed additives in nursery pig diets (2020)

Abstract The mechanisms of action for antibiotic growth promotion are poorly understood, making it difficult to select effective alternatives that are capable of providing similar responses. In order to evaluate the complete impact of supplementing antibiotics and other feed additives to nursery pigs, an integrated systems biology platform encompasses the merging of traditional nutrition models with gut physiology, nutrition and omics technologies. The objective of this study was to evaluate the growth response, metabolic responses, and intestinal microbiome composition of nursery pigs fed antibiotics. Antibiotic diets containing chlortetracycline and sulfamethazine (AB), and diets containing no antibiotics (CON) were fed in 3 trials. Pigs were weighed at d 10, 21, and 42 post-weaning and ADG, ADFI, and G:F was calculated. On d 42, one pig/pen was selected for blood, cecal, and ileum content collection to assess metabolomic profiles via liquid chromatography-mass spectrometry. The composition of bacterial communities in those samples was determined by sequencing the V4 region of the 16s rRNA bacterial gene in the MiSeq platform. Metabolomics and microbiome data were analyzed using multivariate approaches and growth performance data were analyzed using a generalized mixed model. Pigs fed AB were heavier (P &amp;lt; 0.05) on day 42. There were also significant differences (P &amp;lt; 0.05) in the cecal and serum metabolite profile of pigs fed AB compared with CON. However, there were no changes in bile acid or short chain fatty acid concentrations in cecal samples when feeding AB. Although AB had no effect on alpha or beta microbiome diversity, the abundance of specific bacterial taxa shifted significantly (P &amp;lt; 0.05). These findings suggest that feeding antibiotics improve growth, alter metabolism, and affect the abundance of specific taxonomic groups of bacteria in the gut. In the future, this approach will be utilized to evaluate antibiotic alternatives for nursery pigs.
Hydrogen Production by Autothermal Reforming Reaction of Gasoline over Ni-based Catalysts and it Applications (2004)

This study focused on the development of high performance catalyst for autothermal reforming (ATR) of gasoline to produce hydrogen. The ATR was carried out over MgO/Al2O3 supported metal catalysts prepared under various experimental conditions. The catalysts before and after reaction were characterized by N2-physisorption, CO-chemisorption, SEM and XRD. The performance of supported multi-metal catalysts were better than that of supported mono-metal catalysts. Especially, it was observed that the conversion of iso-octane over prepared Ni/Fe/MgO/Al2O3 catalyst was 99.9 % comparable with commercial catalyst (ICI) and the selectivity of hydrogen over the prepared catalyst was 65% higher than ICI catalyst. Furthermore, it was identified that the sulfur tolerance of prepared catalyst was much better than ICI catalyst based on the ATR reaction of iso-octane containing sulfur of 100 ppm. Therefore, Ni/Fe/MgO/Al2O3 catalyst can be applied for a fuel reformer, hydrogen station and on-board reformer in furl cell powered vehicles.
Treatment-Related Mortality in Patients With Advanced-Stage Hodgkin Lymphoma: An Analysis of the German Hodgkin Study Group (2013)

The individual risk of TRM associated with BEACOPP(escalated) can be predicted by a simple algorithm based on age and PS. High-risk patients should receive special clinical attention.
Adhesion/decalcification mechanisms of acid interactions with human hard tissues (2001)

In order to study adhesion/decalcification mechanisms of acid interactions with human hard tissues such as bones and teeth, the chemical interaction of five carboxylic acids (acetic, citric, lactic, maleic, and oxalic) and two inorganic acids (hydrochloric and nitric) with enamel and two synthetic hydroxyapatite (HAp) powders with, respectively, a high and a low crystallinity were analyzed using X-ray photoelectron spectroscopy (XPS), atomic absorption spectrophotometry (AAS), and spectrophotometry (S). X-ray diffraction revealed that the crystallinity of the highly crystallized HAp was considerably higher than that of enamel while the crystallinity of the poorly crystallized HAp was similar to that of dentin and bone. XPS of acid-treated enamel demonstrated for all carboxylic acids ionic bonding to calcium of HAp. AAS and S showed for both HAps that all carboxylic and inorganic acids except oxalic acid extracted Ca significantly more than P, leading to a Ca/P ratio close to that of synthetic HAp (2.16 w/w). Oxalic acid extracted hardly any Ca, but substantially more P, leading to a significantly smaller Ca/P ratio than that of HAp. AAS showed that the calcium salt of oxalic acid hardly could be dissolved, whereas the calcium salts of all the other acids were very soluble in their respective acid solution. These results confirm the adhesion/decalcification concept (AD-concept) previously advanced. Depending on the dissolution rate of the respective calcium salts, acids either adhere to or decalcify apatitic substrates. It is concluded that the AD-concept that originally dictated the interaction of carboxylic acids with human hard tissues can be extended to inorganic acids, such as hydrochloric and nitric acid. Furthermore, HAp crystallinity was found not to affect the adhesion/decalcification behavior of acids when interacting with apatitic substrates, so that the AD-concept can be applied to all human hard tissues with varying HAp crystallinity.
Toad Urinary Bladder: Intercellular Spaces (1969)

Vasopressin causes dilation of the intercellular spaces of the mucosal epithelium in toad bladder, an effect previously thought to result from enhanced net transepithelial water transport. Under conditions of zero net fluid transport, vasopressin exerted the same effect in seven tissues, which indicates that the width of the intercellular spaces cannot be taken as a reliable index of net transepithelial fluid transport.
Nano-Size Biomaterials Based on Ca-Aluminate (2006)

This study deals with the microstructure and property profile of biomaterials within the Ca-aluminate system (CA). Hydrated CA materials are stable in bone tissue, and thus not resorbable as the Ca-phosphate materials are. Identified possible applications for CA-based materials are within vertebroplasty and odontology. CA with ZrO2 particles as well as CA with glass particles were examined with regard to mechanical properties, biocompatibility and bioactivity. The hydrates formed - examined by HRTEM - are in the size range of 20-50 nm. With the studied systems it is possible to obtain a combination of high and early strength, shape stability including low expansion pressure, and in vivo bioactivity.
Oncogenic kinase NPM/ALK induces expression of the cell‐growth stimulatory receptor ICOS (2011)

Here we report that T-cell lymphoma cells carrying the NPM-ALK fusion protein (ALK+TCL) frequently express the cell-stimulatory receptor ICOS. ICOS expression is lower in ALK+TCL-derived cells compared with cells derived from cutaneous T-cell lymphoma (CTCL). ICOS expression in ALK+TCL is strictly dependent on the expression and enzymatic activity of NPM-ALK. NPM-ALK induces ICOS expression via STAT3, which triggers the transcriptional activity of the ICOS gene. In addition, STAT3 suppresses the expression of miR-219 that, in turn, selectively inhibits ICOS expression. ALK+TCL cell lines universally display extensive DNA methylation of the CpG island located within intron 1, the putative enhancer region, whereas CTCL cell lines shown no methylation of the island. Treatment of the ALK+TCL cell lines with DNA methyltransferase inhibitor reversed the CpG island methylation and markedly augmented the expression of ICOS mRNA and protein. Cross-linking of the receptor with immobilized anti-ICOS antibody markedly enhanced proliferation of the ALK+ TCL cells. These results demonstrate that NPM-ALK, acting through STAT3, induces the expression of ICOS, a cell-growth promoting receptor. These data also show that the DNA methylation status of the intronic CpG island affects transcriptional activity of the ICOS gene and, consequently, regulates the concentration of the expressed ICOS protein.
Can 3D Shape be Estimated from Focus Cues Alone (2014)

Focus� cues—blur� and� accommodation—have� generally� been� regarded� as� very� coarse,� ordinal� cues� to� depth.� This� assessment� has� been� largely� determined� by� the� inability� to� display� these� cues� correctly� with� conventional� displays.� For� example,� when� a� 3D� shape� is� displayed� with� sharp� rendering� (i.e.,� pinhole� camera),� the� expected� blur� variation� is� not� present� and� accommodation� does� not� have� an� appropriate� effect� on� the� retinal� image.� When� a� 3D� shape� with� rendered� blur� (i.e.,� camera� with� non�괂Ġpinhole� aperture)� is� displayed,� the� viewer�适s� accommodation� does� not� have� the� appropriate� retinal� effect.� We� asked� whether� the� information� provided� by� correct� blur� and� accommodation� can� be� used� to� determine� shape.� We� conducted� a� shape�괂Ġdiscrimination� experiment� in� which� subjects� indicated� whether� a� hinge� stimulus� was� concave� or� convex.� The� stimuli� were� presented� monocularly� in� a� unique� volumetric� display� that� allows� us� to� present� correct� or� nearly� correct� focus� cues.� The� hinge� was� textured� using� a� back�괂Ġprojection� technique,� so� the� stimuli� contained� no� useful� shape� cues� except� blur� and� accommodation.� We� used� four� rendering� methods� that� vary� in� the� validity� of� focus� information.� Two� single�괂Ġplane� methods� mimicked� a� conventional� display� and� two� volumetric� methods� mimicked� natural� viewing.� A� pinhole� camera� model� was� used� in� one� single�괂Ġplane� condition,� so� image� sharpness� was� independent� of� depth.� In� the� other� single�괂Ġplane� condition,� natural� blur� was� rendered� thereby� creating� an� appropriate� blur� gradient.� In� one� volumetric� condition,� a� linear� blending� rule� was� used� to� assign� intensity � to� image� planes.� In� the� other� volumetric� condition,� an� optimized� blending� rule� was� used� that� creates� a� closer� approximation� to� real�괂Ġworld� viewing.� Subject� performance� was� at� chance� in� the� single�괂Ġplane� conditions.� Performance� improved� substantially� when� in� the� volumetric� conditions,� slightly� better� in� the� optimized�괂Ġblending� condition.� This� is� direct� evidence� that� 3D� shape� judgments� can� be� made� from� the� information� contained� in� blur� and� accommodation� alone.�
Carbon−Fluorine Reductive Elimination from a High-Valent Palladium Fluoride (2008)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionCarbon−Fluorine Reductive Elimination from a High-Valent Palladium FluorideTakeru Furuya and Tobias Ritter*Cite this: J. Am. Chem. Soc. 2008, 130, 38, 12834Publication Date (Web):August 28, 2008Publication History Published online28 August 2008Published inissue 24 September 2008https://pubs.acs.org/doi/10.1021/ja8065013https://doi.org/10.1021/ja8065013correctionACS PublicationsCopyright © 2008 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views2125Altmetric-Citations4LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail PDF (41 KB) Get e-AlertscloseSUBJECTS:Anions,Atmospheric chemistry,Palladium,Reagents,Reductive elimination Get e-Alerts
Intracranial pressure estimated non-invasively in non-human primates and pediatric critical care (Conference Presentation) (2020)

Intracranial pressure (ICP) is an important metric in the management of severe head injury. We show alternatives to today’s standard of highly invasive measurement devices using near-infrared spectroscopy and diffuse correlation spectroscopy to create a real-time ICP monitor. The algorithms were developed and tested in an animal model. First results of a clinical validation will be presented.
Septum resection for women of reproductive age with a septate uterus (2017)

Hysteroscopic septum resection in women of reproductive age with a septate uterus is performed worldwide to improve reproductive outcomes. At present, there is no evidence to support the surgical procedure in these women. Randomised controlled trials are urgently needed. Two trials are currently underway.
Parasporin-1, a Novel Cytotoxic Protein to Human Cells from Non-Insecticidal Parasporal Inclusions of Bacillus thuringiensis (2005)

Pro-parasporin-1 is a parasporal inclusion protein of the non-insecticidal Bacillus thuringiensis strain A1190. Cytotoxic fragments, named parasporin-1, were generated from pro-parasporin-1 by trypsin digestion. Parasporin-1 was purified by a combination of chromatography procedures based on the cytotoxic activity to HeLa cells. Two different fragments of 15-kDa and 56-kDa were detected in the purified parasporin-1 fraction. These fragments were tightly associated with each other and could not be separated by chromatography under conditions that preserve cytotoxic activity, indicating that the active form of parasporin-1 is a heterodimer of the 15- and 56-kDa fragments. Amino acid sequencing and MALDI-TOF mass spectrometric analysis revealed that parasporin-1 is generated from pro-parasporin-1 by trypsin digestion at Arg 93 and Arg 231. Of 12 human cell lines tested, parasporin-1 showed strong cytotoxicity to four cell lines derived from cancer tissues, but low to no cytotoxicity to the other cell lines. The time-courses of cytotoxicity indicated that the mode of action of parasporin-1 to sensitive cells differs from that shown for previously isolated cytotoxic proteins from Bacillus thuringiensis, Cyt proteins, and other bacterial pore-forming toxins. Thus, parasporin-1 is a novel cytotoxic protein to human cancer cells produced by B. thuringiensis, and may be useful as a tool to recognize and destroy specific cancer cells.
Cell surface carbohydrates for targeting studies (1980)

Syntheses of a series of glycolipids with 6-(5-cholesten-3β-yloxy)-1-thiohexane as the aglycon and the following carbohydrates as surface determinants are described: D-glucose, D-mannose, D-galactose, 2-acetamido-2-deoxy-D-glucose, 2-acetamido-2-deoxy-D-galactose, L-fucose, L-arabinose, D-xylose, N-acetyl-D-neuraminic acid, lactose, and cellobiose. These 6-(5-cholesten-3β-yloxy)hexyl 1-thioglycopyranosides have been incorporated into phospholipid vesicles for invivo tissue distribution studies.
Qualitative and Quantitative Imaging Evaluation of Renal Cell Carcinoma Subtypes with Grating-based X-ray Phase-contrast CT (2017)

Current clinical imaging methods face limitations in the detection and correct characterization of different subtypes of renal cell carcinoma (RCC), while these are important for therapy and prognosis. The present study evaluates the potential of grating-based X-ray phase-contrast computed tomography (gbPC-CT) for visualization and characterization of human RCC subtypes. The imaging results for 23 ex vivo formalin-fixed human kidney specimens obtained with phase-contrast CT were compared to the results of the absorption-based CT (gbCT), clinical CT and a 3T MRI and validated using histology. Regions of interest were placed on each specimen for quantitative evaluation. Qualitative and quantitative gbPC-CT imaging could significantly discriminate between normal kidney cortex (54 ± 4 HUp) and clear cell (42 ± 10), papillary (43 ± 6) and chromophobe RCCs (39 ± 7), p < 0.05 respectively. The sensitivity for detection of tumor areas was 100%, 50% and 40% for gbPC-CT, gbCT and clinical CT, respectively. RCC architecture like fibrous strands, pseudocapsules, necrosis or hyalinization was depicted clearly in gbPC-CT and was not equally well visualized in gbCT, clinical CT and MRI. The results show that gbPC-CT enables improved discrimination of normal kidney parenchyma and tumorous tissues as well as different soft-tissue components of RCCs without the use of contrast media.
Comparison of Observer Variation in Conventional and Three Digital Radiographic Methods Used in the Evaluation of Patients With Adolescent Idiopathic Scoliosis (2008)

Measurements made on conventional and digital radiographs using manual and computer-based techniques have similar good to excellent interobserver reliability. Interobserver reliability was lower for digital radiographs when printed onto 2 unstitched films. The results suggest that different observers will obtain similar measurements when viewing the same image, but care should be taken when interpreting images printed on 2 unstitched films.
Effect of the equivalent refractive index on intraocular lens power prediction with ray tracing after myopic laser in situ keratomileusis (2015)

For IOL power determination in post-LASIK patients, custom ray tracing including a modified ERI was an accurate procedure that exceeded the current standards for normal eyes.