gebhart/patrepeval huggingface dataset:
GenomeDiver: A platform for phenotype-guided medical genomic diagnosis (2020)

ABSTRACT Purpose Making a diagnosis from clinical genomic sequencing requires well-structured phenotypic data to guide genotype interpretation. A patient’s phenotypic features can be documented using the Human Phenotype Ontology (HPO), generating terms used to prioritize genes potentially causing the patient’s disease. We have developed GenomeDiver to provide a user interface for clinicians that allows more effective collaboration with the clinical diagnostic laboratory, with the goal of improving the success of the diagnostic process. Methods GenomeDiver is designed to prompt reverse phenotyping of patients undergoing genetic testing, enriching the amount and quality of structured phenotype data for the diagnostic laboratory, and helping clinicians to explore and flag diseases potentially causing their patient’s presentation. Results We show how GenomeDiver communicates the clinician’s informed insights to the diagnostic lab in the form of HPO terms for interpretation of genomic sequencing data. We describe our user-driven design process, the engineering of the software for efficiency, security and portability, and an example of the performance of GenomeDiver using simulated genomic testing data. Conclusions GenomeDiver is a first step in a new approach to genomic diagnostics that enhances laboratory-clinician interactions, with the goal of directly engaging clinicians to improve the outcome of genomic diagnostic testing.
Clathrochelate Metalloligands in Supramolecular Chemistry and Materials Science (2018)

The term "clathrochelate" describes a complex in which a coordinatively saturated metal ion is surrounded by a macropolycyclic ligand. First examples of clathrochelate complexes were reported 50 years ago. Meanwhile, the synthesis and reactivity of clathrochelates have been investigated in detail, and numerous applications have been explored. In this Account, we summarize work on the utilization of transition metal clathrochelates as metalloligands in supramolecular chemistry and materials science, with special focus on results from our group. First, we discuss the chemistry of boron-capped clathrochelates. These complexes are facile to synthesize by metal-templated condensation reactions. The synthesis is modular, and it is straightforward to implement structural variations. Importantly, it is possible to attach functional groups such as amines, pyridines, or carboxylic acids to the ligand periphery. Other noteworthy features of boron-capped clathrochelates are high thermodynamic and kinetic stability, tunable redox potential, and good solubility. Next, we show that clathrochelate-based metalloligands can be used to build molecularly defined metal-ligand assemblies of nanoscale dimensions. Different molecular architectures are described, including coordination cages with unusual gyrobifastigium or square orthobicupola-like structures. Metalloligands containing multiple clathrochelate complexes are particularly well suited to build large metal-ligand assemblies (>3 nm) with minimal synthetic efforts. Boron-capped clathrochelates have also been investigated in the context of materials chemistry. Linear or cross-linked clathrochelate polymers were found to display permanent porosity. Furthermore, such polymers were used to prepare conducting films on electrodes. Clathrochelate metalloligands are well suited to prepare metal-organic frameworks (MOFs). The high stability of clathrochelates ensures compatibility with harsh reaction conditions, and it mitigates potential problems such as exchange reactions. Boron-capped clathrochelates can be decorated with functional groups in lateral and apical position, and it is possible to use these complexes as multiconnected nodes in polymeric structures. Overall, we hope to convey the utility of clathrochelate complexes in supramolecular chemistry and materials science. The work published thus far gives a first glimpse of the potential of these compounds, but there are other directions, which are waiting to be explored. For example, it will be interesting to study the properties of nanostructures based on chiral clathrochelate complexes. Furthermore, the redox and magnetic properties of clathrochelates may give rise to novel functional materials. Given that clathrochelates are straightforward to prepare, we hope that others will join the efforts to explore the supramolecular and materials chemistry of these interesting molecular building blocks.
Data from Pharmacodynamic Evaluation of the Target Efficacy of SB939, an Oral HDAC Inhibitor with Selectivity for Tumor Tissue (2023)

&lt;div&gt;Abstract&lt;p&gt;SB939 is an oral histone deacetylase (HDAC) inhibitor currently in phase II clinical trials potently inhibiting class I, II, and IV HDACs with favorable pharmacokinetic properties, resulting in tumor tissue accumulation. To show target efficacy, a Western blot assay measuring histone H3 acetylation (acH3) relative to a loading control was developed, validated on cancer cell lines, peripheral blood mononuclear cells (PBMC), and in animal tumor models. Exposure of cells to 60 nmol/L (22 ng/mL) SB939 for 24 hours was sufficient to detect an acH3 signal in 25 μg of protein lysate. AcH3 levels of liver, spleen, PBMCs, bone marrow and tumor were measured in BALB/c mice, HCT-116 xenografted BALB/c nude mice, or in SCID mice orthotopically engrafted with AML (HL-60) after oral treatment with SB939. AcH3 could only be detected after treatment. In all tissues, the highest signal detected was at the 3-hour time point on day 1. On day 15, the signal decreased in normal tissues but increased in cancerous tissues and became detectable in the bone marrow of leukemic mice. In all tissues, acH3 correlated with SB939 dose levels (&lt;i&gt;r&lt;/i&gt;&lt;sup&gt;2&lt;/sup&gt; = 0.76–0.94). When applied to PBMCs from 30 patients with advanced solid malignancies in a phase I clinical trial, a dose-dependent (10–80 mg) increase in relative acH3 was observed 3-hour postdose on day 1, correlating with C&lt;sub&gt;max&lt;/sub&gt; and AUC of SB939 concentrations in plasma (&lt;i&gt;r&lt;/i&gt; = 0.97, &lt;i&gt;P&lt;/i&gt; = 0.014). Our data show that the favorable pharmacokinetic and pharmacodynamic properties of SB939 are translated from preclinical models to patients. &lt;i&gt;Mol Cancer Ther; 10(7); 1207–17. ©2011 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Transposon Tn5: Specific Sequence Recognition and Conservative Transposition (1984)

Transposable elements are discrete DNA segments that move to new sites in a genome without requiring extensive DNA sequence homology (for reviews, see Kleckner 1981; Berg and Berg 1983; Shapiro 1983). The current interest in transposable elements can be attributed to: (1) their ubiquity; (2) the novel DNA sequence recognition, cleavage, and joining reactions that their movement entails; (3) the insertion mutations, genome rearrangements, and changes in gene expression they cause; (4) their roles in genome evolution; and finally (5) their usefulness in the genetic analysis and manipulation of many different organisms.
The homeobox gene Siamois is a target of the Wnt dorsalisation pathway and triggers organiser activity in the absence of mesoderm (1996)

Siamois, a Xenopus zygotic homeobox gene with strong dorsalising activity, is expressed in the dorsal-vegetal organiser known as the Nieuwkoop centre. We show that, in contrast to Spemann organiser genes such as goosecoid, chordin and noggin, Siamois gene expression is not induced following overexpression of mesoderm inducers in ectodermal (animal cap) cells. However, Siamois is induced by overexpressing a dorsalising Wnt molecule. Furthermore, like Wnt, Siamois can dorsalise ventral mesoderm and cooperate with Xbrachyury to generate dorsal mesoderm. These results suggest that Siamois is a mediator of the Wnt-signalling pathway and that the synergy between the Wnt and mesoderm induction pathways occurs downstream of the early target genes of these two pathways. Overexpression of Siamois in animal cap cells reveals that this gene can act in a non vegetal or mesodermal context. We show the following. (1) Animal cap cells overexpressing Siamois secrete a factor able to dorsalise ventral gastrula mesoderm in tissue combination experiments. (2) The Spemann organiser-specific genes goosecoid, Xnr-3 and chordin, but not Xlim.1, are activated in these caps while the ventralising gene Bmp-4 is repressed. However, the dorsalising activity of Siamois-expressing animal caps is significantly different from that of noggin- or chordin-expressing animal caps, suggesting the existence of other dorsalising signals in the embryo. (3) Ectodermal cells overexpressing Siamois secrete a neuralising signal and can differentiate into cement gland and, to a lesser extent, into neural tissue. Hence, in the absence of mesoderm induction, overexpression of Siamois is sufficient to confer organiser properties on embryonic cells.
Preparation and Ultraviolet Absorption Spectra of Some Derivatives of Phosphafluorinic Acid1 (1959)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPreparation and Ultraviolet Absorption Spectra of Some Derivatives of Phosphafluorinic Acid1LEON D. FREEDMAN and G. O. DOAKCite this: J. Org. Chem. 1959, 24, 5, 638–641Publication Date (Print):May 1, 1959Publication History Published online1 May 2002Published inissue 1 May 1959https://pubs.acs.org/doi/10.1021/jo01087a016https://doi.org/10.1021/jo01087a016research-articleACS PublicationsRequest reuse permissionsArticle Views192Altmetric-Citations15LEARN 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 Other access optionsGet e-Alertsclose Get e-Alerts
Direct behavioral evidence for hydrocarbons as nestmate recognition cues in Formica japonica (Hymenoptera: Formicidae) (2004)

Here we report direct evidence that cuticular hydrocarbons are responsible for nestmate recognition in Formica japonica distributing in Southern Honshu in Japan. Workers showed aggressive behavior against foreign workers but not against nestmates. A similar response was observed when a glass dummy was treated with isolated hydrocarbons from foreign workers or nestmates. Among the isolated hydrocarbons, ten hydrocarbon components were identified: five n-alkanes and five (Z)-9-alkenes with odd number of carbons from 25 to 33, in different ratios in different colonies. When synthetic hydrocarbons blended in the same ratio as natural blends were presented to workers, they showed aggressive responses against foreign blends but paid less attention to those of nestmates. Neither n-alkane nor (Z)-9-alkene blends, however, caused aggression response in foreign workers. Thus, both n-alkanes and (Z)-9-alkenes are necessary to discriminate nestmates from foreign conspecifics.
Cs[CB10H13] at 293 K (1995)

The unit cell of the room-temperature phase of Cs[CB 10 H 13 ], caesium 8,9:10,11-di-μ-hydro-undecahydro-7-carba-nido-undecaborate(1−), is found to be very similar to that of γ-Cs[C 2 B 9 H 12 ] at 299 K reported previously [Rius, Romerosa, Teixidor, Casabo & Miravitlles (1991). Inorg. Chem. 30, 1376-1379], but the packing of the carborane anion cages around the Cs + ions is distorted further from ideal octahedral geometry and the uncapped pentagonal faces of the cages lie parallel to the a axis. No evidence of increased conductivity in two higher-temperature phases has been found for this compound
Flow Cytometric Detection of CD79a Expression in T-Cell Acute Lymphoblastic Leukemias (2000)

We evaluated the lineage specificity of CD79a in acute leukemias using 3-color flow cytometry in 58 consecutive cases. A panel of cell-surface antigens, including myeloid-associated markers, B-cell-associated markers, and T-cell-associated markers, was used. All cases of acute myeloid leukemia were CD79a-, whereas all cases of B-lineage acute lymphoblastic leukemia (ALL) were CD79a+. Three of 8 cases of T-cell ALL showed variable CD79a expression, indicating the presence of a blast subset expressing a relatively high level of CD79a. We investigated the clinical and pathologic characteristics of these 3 cases. All 3 cases had L1 or L2 morphology and expressed surface CD3. None of the other B-cell-associated markers were positive, although 1 case expressed CD13 and CD33. Uncommon random karyotypic abnormalities were identified in all 3 cases. Molecular studies demonstrated monoclonal gene rearrangement of T-cell receptor gamma in 2 of 3 cases. All 3 patients were 18 years old or younger; 1 patient did not enter remission, and 1 had disease relapse in 8 months. Our findings provide further support for the existence of a subset of T-cell ALL coexpressing CD3 and CD79a. Further study of the clinical and biologic significance of this subset may be warranted.
Early results of a Canadian laparoscopic sleeve gastrectomy experience (2011)

Preliminary analysis of our experience with LSG indicates that this is an effective and safe procedure for the treatment of obesity.
Creasing severity and reverse-side cracking (2020)

Crease cracking can be detrimental to the functionality and appearance of paperboard-based pack-aging. The effect of creasing severity on the degree of reverse-side crease cracking (bead-side of the crease) of paperboard was investigated. Samples were creased with a range of rule and channel geometries, and the cracking degree was quantified as the percent of cracked length relative to the total length of the crease. The cracking degree was typically below 5% at low crease penetration depths, but was exponentially higher beyond a critical penetration depth. A rule and channel combination with a wider clearance shifted the critical depth to larger values. The creasing severity parameter, termed the creasing draw, converged the cracking degree data from different rule and channel combinations to a single curve. The creasing draw was derived from the same analytical expres-sions as the transverse shear strain and quantifies the length of paper that is drawn into the channel during creasing. The critical draw is defined as the draw at which cracking becomes greater than 5%, which corresponds with the point at which cracking becomes exponential. The critical draw is a material/system parameter that defines the level below which cracking is minimal.
Analysis of the intranasal distribution of ointment. (1997)

The results of the study raise doubts about the effectiveness of this therapy.
Research on evaluation method of composite insulators aging (2009)

This article introduces the research on composite insulator of various degrees by using Fourier transform infrared spectroscopy (FTIR). The results show there is a close relationship between absorption areas of the functional group of Si-CH <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> and Si-O-Si of silicone rubber shed and housing aging. Along with the severity of ageing in the appearance of composite insulator, the absorption areas of the functional group of Si-CH <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> and Si-O-Si would decrease. The four different aging periods of composite insulator correspond to the different absorption areas of the functional group of Si-CH <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> and Si-O-Si accordingly. FTIR can be used to judge the aging degree of the appearance of composite insulators.
The microtiter SDI test is more advantageous than the SDI test for assessing the chemosensitivity of human tumor cells (1991)

The in vitro succinate dehydrogenase inhibition (SDI) test was adapted to be used with microtiter plates and this microtiter SDI (mSDI) test was evaluated for clinical use of chemosensitivity testing, as compared to findings with the SDI test. The optimal conditions of the mSDI test were determined: (1) 2-5 x 10(4) cells/well; (2) enzymatic disaggregation of solid tumors with the use of a mixture of 0.2% pronase, 0.25% collagenase, 0.1% DNase for 20 min at 37 degrees C; (3) addition of 10 mM sodium succinate in the colorimetric reaction; and (4) use of dimethyl sulfoxide (DMSO) as a solvent for extraction of formazan product. Good correlations were observed between the mSDI and the SDI tests when S-180 cells (r = 0.890-0.996) or 16 human fresh tumor cells (r = 0.731-0.999) were exposed to six anti-cancer drugs (carboquone, adriamycin, mitomycin C, aclacinomycin A, cisplatin, 5-fluorouracil). Thus, the mSDI test facilitates testing of a large number of drugs with minimal amounts of specimens, and is expected to replace the SDI test for chemosensitivity testing of clinical tumor cells.
Introduction to Ultra Wideband (2005)

This chapter contains sections titled: Introduction Scope of the Book References
X-ray calibration of the time resolved crystal spectrometer SXDHR-1t of the Ligne d’Intégration Laser (2004)

The time resolved crystal x-ray spectrometers called SXDHR-lt of the Ligne d’Intégration laser is presented. It is necessary to calibrate all x-ray sensitive elements of diagnostics before using them in laser matter interaction experiments. In particular, crystals need to be calibrated. Measurements of the integrated coefficient of reflection of a beryl cylindrical crystal used in this spectrometer were performed with synchrotron radiation and with an x-ray tube and are presented. A test of the homogeneity of the reflection of the crystal was also performed. Aging or accidental pollution of x-ray diagnostics installed around target chambers is always possible. This happened to the DMX broadband spectrometer installed on the OMEGA Laser Facility at the University of Rochester (Laboratory for Laser Energetics) and this changed the spectral sensitivity of its channels. The evolution over time of the x-ray sensitivity needs to be critically assessed and if necessary x-ray sensitive elements will need to be recalibrated.
Microstrip antenna circuit model and linear pattern correction (2005)

Mutual coupling, among other effects, causes the element patterns in an antenna array to be different. In the practical adaptive use of the array identical element patterns are usually expected. Linear pattern correction with matrix multiplication can be used to correct the array element inputs/outputs. In this paper, a multiport model for a microstrip array and a method to find the input circuit for its ports is presented for use in the array correction.
Formation and Cleavage of Bisnoradamantane Derivatives Through SmI2 Reductions. (2001)

Abstract For Abstract see ChemInform Abstract in Full Text.
On the Performance Analysis of Multiple Access Codes for Ultra-Wideband Sensor Networks (2006)

Ultra Wideband (UWB) technology is fast emerging as a potential contender for next generation wireless sensor networks because of the inherent low power requirements and built in security. Time hopping and direct sequence based spread spectrum techniques are employed for UWB multiple access systems, which makes the correlation properties of these techniques a critical issue in a multi-user (multiple nodes) scenario. In this paper we present a comparative performance analysis of different spreading codes namely, PN, Gold and Kasami using PPM and PAM modulation schemes over AWGN and IEEE 802.15.3a channel models. We use a PRake receiver for multipath channel. We observe that DS spreading technique is more suitable than TH for multi-user systems. Simulation results show that Kasami codes perform better than Gold and PN codes for all considered cases. However, Kasami codes can accommodate less number of nodes for a given code length due to their reduced set size. Thus, for small sensor networks Kasami codes should be deployed, where as for larger sensor networks Gold and PN codes are more suitable.
Compared Ageing of Oil from Curcubitea Pepo in Two Different Storage Conditions (2011)

The aim of this study was to investigate the oil pumkin seeds of Curcubitea pepo from Congo- Brazzaville. The ageing of oil extracted from the seeds of the pumpkin Curcubitea pepo stored at two temperatures (6 and 30oC) was monitored during storage for 11 months by comparison of physical and chemical characteristics correlated with spectroscopic data. Medium infrared spectroscopy confirmed saponification index data. Ultraviolet absorption confirmed peroxide index data. Antioxidant behaviour was monitored by fluorescence and the effect of ageing on the two major fatty acid families was analysed by a study of chemical composition correlated with differential scanning calorimetry measurements. This study showed an overall lengthening of the fatty acid carbon chains and allowed preferential storage conditions to be specified for this oil.
A Decision-Theoretic Scheduling of Resource-Bounded Agents in Dynamic Environments (2005)

Markov Decision Processes (MDPs) provide a good, robust formal framework for modeling a large variety of stochastic planning and decision problems, but they are unsuitable to realistic problems, in particular, to solve problems in
CXCR4 chemokine receptor antagonists: perspectives in SCLC (2009)

Small-cell lung cancer (SCLC) is a particularly aggressive form of lung cancer characterized by early and widespread metastases and the ability to rapidly develop resistance against chemotherapeutic agents. Tumor cell migration and metastasis share many similarities with leukocyte trafficking, which is critically regulated by chemokine receptors and adhesion molecules. SCLC cells express high levels of CXCR4 (CD184), a seven-transmembrane G-protein-coupled chemokine receptor. Stromal cells within the bone marrow microenvironment and at extramedullary sites constitutively secrete stromal cell-derived factor-1 (CXCL12), the ligand for CXCR4. Activation of CXCR4 induces SCLC cell migration and adhesion to stromal cells that secrete CXCL12, which in turn provides growth- and drug resistance-signals to the tumor cells. CXCR4 antagonists, such as Plerixafor (AMD3100) and T140 analogues (TN14003/ BKT140), disrupt CXCR4-mediated SCLC cell-adhesion to stromal cells. In stromal cell co-cultures, CXCR4 antagonists also sensitize SCLC cells to cytotoxic drugs, such as etoposide, and thereby antagonize cell adhesion-mediated drug resistance. Therefore, targeting the CXCR4-CXCL12 axis is a novel, attractive therapeutic approach in SCLC. Here, we summarize preclinical data about CXCR4 in SCLC, and the current status of the preclinical and clinical development of CXCR4 antagonists.