gebhart/patrepeval huggingface dataset:
Characterization of the ligand structure and stoichiometry on quantum dots and gold nanocrystals using NMR spectroscopy (2018)

Using a few solution phase NMR spectroscopy techniques, including 1H NMR and 31P NMR, we have characterized the organic shell on CdSe-ZnS core-shell quantum dots and tracked changes in its composition when the QD dispersions are subjected to varying degrees of purification. Combining solution phase NMR with diffusion ordered spectroscopy (DOSY), we were able to distinguish between freely diffusing ligands in the sample from those bound on the surfaces. Additionally, matrix assisted laser desorption ionization (MALDI) and FTIR measurements were used to provide complementary and supporting information on the organic ligand coating for these nanocrystals. We found that the organic shell is dominated by monomeric or oligomeric n-hexylphosphonic acid (HPA), along with small portion of 1-hexadecyl amine (HDA). The presence of TOP/TOPO (tri-n-octylphosphine / tri-noctylphosphine oxide) molecules is much smaller, even though large excess of TOP/TOPO were used during the QD growth. These results indicate that HPA (alkyl phosphonate) exhibits the strongest coordination affinity to ZnS-rich QD surfaces grown using the high temperature injection route.
Bromodomain and Extraterminal Protein Inhibition Blocks Growth of Triple-negative Breast Cancers through the Suppression of Aurora Kinases (2016)

Bromodomain and extraterminal (BET) proteins are epigenetic "readers" that recognize acetylated histones and mark areas of the genome for transcription. BRD4, a BET family member protein, has been implicated in a number of types of cancer, and BET protein inhibitors (BETi) are efficacious in many preclinical cancer models. However, the drivers of response to BETi vary depending on tumor type, and little is known regarding the target genes conveying BETi activity in triple-negative breast cancer (TNBC). Here, we show that BETi repress growth of multiple in vitro and in vivo models of TNBC by inducing two terminal responses: apoptosis and senescence. Unlike in other cancers, response to BETi in TNBC is not dependent upon suppression of MYC Instead, both end points are preceded by the appearance of polyploid cells caused by the suppression of Aurora kinases A and B (AURKA/B), which are critical mediators of mitosis. In addition, AURKA/B inhibitors phenocopy the effects of BETi. These results indicate that Aurora kinases play an important role in the growth suppressive activity of BETi in TNBC. Elucidating the mechanism of response to BETi in TNBC should 1) facilitate the prediction of how distinct TNBC tumors will respond to BETi and 2) inform the rational design of drug combination therapies.
Clinical images - a quarterly column: chance fracture of the lumbar spine. (2014)

Background: House staff play a key role in patient care but are not optimally involved in efforts to improve care. Current assessment procedures do not always include resident input, which can lead to lack of engagement. To help meet ACGME requirements, we planned to develop an interdisciplinary, interprofessional resident quality council (RQC) to engage residents in QI culture, teach them about QI, and enhance communication with administrators. Methods: We initiated the RQC in 2012 and selected the chiefs of all 10 residency programs in the hospital as the first class. Our primary focus was teaching the teacher through monthly didactic sessions, allowing us to disseminate information and knowledge about QI science to all residencies. The secondary focus was to form parallel quality tracks in all residencies to perform at least 1 quality project per year, as well as to develop participation criteria and interest for the RQC. Results: We saw significant improvement and comfort with interdisciplinary communication among the 10 participants. We were able to identify QI champion attendings within each program to support the council and connected the psychiatry chief resident to a psychiatry attending to develop a QI track. Participants also generated multiple interdisciplinary project ideas for the future. Residents were chosen to participate without gauging their level of interest, which led to lack of engagement. Residents also had a variety of responsibilities, so scheduling time for the RQC meetings was difficult. The initiative lacked a strong emphasis on the main goal of RQC participation. Conclusions: Although the RQC did not reach all of the initial goals, it successfully formed interdisciplinary working relationships and gauged the house staff9s interest in and knowledge of QI. Moving forward, the council will consist of residents who have applied and have shown interest in QI as recognized by their programs.
Prospect and challenge of detecting dynamic gene copy number increases in stem cells by whole genome sequencing (2019)

Gene amplification is an evolutionarily well-conserved and highly efficient mechanism to increase the amount of specific proteins. In humans, gene amplification is a hallmark of cancer and has recently been found during stem cell differentiation. Amplifications in stem cells are restricted to specific tissue areas and time windows, rendering their detection difficult. Here, we report on the performance of deep WGS sequencing (average 82-fold depth of coverage) on the BGISEQ with nanoball technology to detect amplifications in human mesenchymal and neural stem cells. As reference technology, we applied array-based comparative genomic hybridization (aCGH), fluorescence in situ hybridization (FISH), and qPCR. Using different in silico strategies for amplification detection, we analyzed the potential of WGS for amplification detection. Our results provide evidence that WGS accurately identifies changes of the copy number profiles in human stem cell differentiation. However, the identified changes are not in all cases consistent between WGS and aCGH. The results between WGS and the validation by qPCR were concordant in 83.3% of all tested 36 cases. In sum, both genome-wide techniques, aCGH and WGS, have unique advantages and specific challenges, calling for locus-specific confirmation by the low-throughput approaches qPCR or FISH. KEY MESSAGES: WGS allows for the identification of dynamic copy number changes in human stem cells. Less stringent threshold setting is crucial for detection of copy number increase. Broad knowledge of dynamic copy number is pivotal to estimate stem cell capabilities.
Supplementary Data from A Randomized Phase II Preoperative Study of Autophagy Inhibition with High-Dose Hydroxychloroquine and Gemcitabine/Nab-Paclitaxel in Pancreatic Cancer Patients (2023)

&lt;p&gt;Supplementary Data&lt;/p&gt;
Deep Learning with Apache SystemML (2018)

Enterprises operate large data lakes using Hadoop and Spark frameworks that (1) run a plethora of tools to automate powerful data preparation/transformation pipelines, (2) run on shared, large clusters to (3) perform many different analytics tasks ranging from model preparation, building, evaluation, and tuning for both machine learning and deep learning. Developing machine/deep learning models on data in such shared environments is challenging. Apache SystemML provides a unified framework for implementing machine learning and deep learning algorithms in a variety of shared deployment scenarios. SystemML's novel compilation approach automatically generates runtime execution plans for machine/deep learning algorithms that are composed of single-node and distributed runtime operations depending on data and cluster characteristics such as data size, data sparsity, cluster size, and memory configurations, while still exploiting the capabilities of the underlying big data frameworks.
Cross Domain Robot Imitation with Invariant Representation (2022)

Animals are able to imitate each others' behavior, despite their difference in biomechanics. In contrast, imitating other similar robots is a much more challenging task in robotics. This problem is called cross domain imitation learning (CDIL). In this paper, we consider CDIL on a class of similar robots. We tackle this problem by introducing an imitation learning algorithm based on invariant representation. We propose to learn invariant state and action representations, which align the behavior of multiple robots so that CDIL becomes possible. Compared with previous invariant representation learning methods for similar purposes, our method does not require human-labeled pairwise data for training. Instead, we use cycle-consistency and domain confusion to align the representation and increase its robustness. We test the algorithm on multiple robots in the simulator and show that unseen new robot instances can be trained with existing expert demonstrations successfully. Qualitative results also demonstrate that the proposed method is able to learn similar representations for different robots with similar behaviors, which is essential for successful CDIL.
ChemInform Abstract: Diastereofacial Selectivity in the Diels‐Alder Reaction of 2,3‐Dialkoxy‐1,3‐butadienes. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Retinoic acid (RA) receptor transcriptional activation correlates with inhibition of 12-O-tetradecanoylphorbol- 13-acetate-induced ornithine decarboxylase (ODC) activity by retinoids: A potential role fortrans-RA-induced ZBP-89 in ODC inhibition (2000)

Evaluation of retinoic acid receptor (RAR) subtype-selective alpha and gamma agonists and antagonists and a retinoid X receptor (RXR) class-selective agonist for efficacy at inhibiting both induction of ornithine decarboxylase (ODC) by the tumor promoter 12-O-tetradecanoylphorbol-13-acetate (TPA) in mouse epidermis and rat tracheal epithelial cells and the appearance of papillomas in mouse epidermis treated in the 2-stage tumor initiation-promotion model indicated that (i) RXR class-selective transcriptional agonists, such as MM11246, were not involved in ODC inhibition; (ii) RAR-selective agonists that induce gene transcription from RA-responsive elements (RAREs) were active at low concentrations; (iii) RAR-selective antagonists that bind RARs and inhibit AP-1 activation on the collagenase promoter but do not activate RAREs to induce gene transcription were less effective inhibitors; and (iv) RARgamma-selective retinoid agonists were more effective inhibitors of TPA-induced ODC activity than RARalpha-selective agonists. These results suggest that RARE activation has a more important role in inhibition of ODC activity than RXR activation or AP-1 inhibition and that RARgamma-selective agonists would be the most useful inhibitors of epithelial cell proliferation induced by tumor promoters. The natural retinoid all-trans-RA induced expression of transcription factor ZBP-89, which represses activation of the GC box in the ODC promoter by the transcription factor Sp1.
Characteristics and Functionality Enhancement by Glycosylation of Bitter Melon ( Momordica charantia ) Seed Protein (2014)

Seeds of ripe bitter melon (Momordica charantia) contain approximately 30% protein. However, this protein, which is less functional than soy protein, may have desirable functionalities as a food ingredient after modification. Bitter melon seed protein isolate (BMSPI) was prepared under optimal extraction conditions (defatted meal to 1.3 M NaCl was 1:10 w/v; pH 9.0) and its functional properties were investigated before and after modification by glycosylation. Glycosylation was conducted at varying relative humidities (50%/65%/80%) and temperatures (40 °C/50 °C/60 °C) using a response surface central composite design. Degree of glycosylation (DG) ranged from 39.3 to 52.5%, 61.7 to 70.9%, and 81.2 to 94.8% at 40 °C, 50 °C, and 60 °C, respectively (P values < 0.0001). Denaturation temperatures of all DGs ranged from 111.6 °C to 114.6 °C, while unmodified/native BMSPI had a value of 113.2 °C. Surface hydrophobicity decreased to approximately 60% when the DG was maximal (94.8%). Solubility decreased almost 90% when the DG was maximal in comparison to the native BMSPI (62.0%). Emulsifying activity increased from 0.35 to 0.80 when the DGs were ≥80%, while emulsion stability increased from 63 to 72 min when the DGs were greater than 70%. A similar trend was observed with foaming capacity and foaming stability of the glycosylated proteins. This glycosylated BMSPI with improved emulsifying and foaming properties could be used as an ingredient in food products where such properties are required.
Pausing and activating thread state upon pin assertion by external logic monitoring polling loop exit time condition (2023)

A system and method for enhancing performance of a computer which includes a computer system including a data storage device. The computer system includes a program stored in the data storage device and steps of the program are executed by a processer. The processor processes instructions from the program. A wait state in the processor waits for receiving specified data. A thread in the processor has a pause state wherein the processor waits for specified data. A pin in the processor initiates a return to an active state from the pause state for the thread. A logic circuit is external to the processor, and the logic circuit is configured to detect a specified condition. The pin initiates a return to the active state of the thread when the specified condition is detected using the logic circuit.
Development of a GIN11/FRT-based multiple-gene integration technique affording inhibitor-tolerant, hemicellulolytic, xylose-utilizing abilities to industrial Saccharomyces cerevisiae strains for ethanol production from undetoxified lignocellulosic hemicelluloses (2014)

Bioethanol produced by the yeast Saccharomyces cerevisiae is currently one of the most promising alternatives to conventional transport fuels. Lignocellulosic hemicelluloses obtained after hydrothermal pretreatment are important feedstock for bioethanol production. However, hemicellulosic materials cannot be directly fermented by yeast: xylan backbone of hemicelluloses must first be hydrolyzed by heterologous hemicellulases to release xylose, and the yeast must then ferment xylose in the presence of fermentation inhibitors generated during the pretreatment. A GIN11/FRT-based multiple-gene integration system was developed for introducing multiple functions into the recombinant S. cerevisiae strains engineered with the xylose metabolic pathway. Antibiotic markers were efficiently recycled by a novel counter selection strategy using galactose-induced expression of both FLP recombinase gene and GIN11 flanked by FLP recombinase recognition target (FRT) sequences. Nine genes were functionally expressed in an industrial diploid strain of S. cerevisiae: endoxylanase gene from Trichoderma reesei, xylosidase gene from Aspergillus oryzae, β-glucosidase gene from Aspergillus aculeatus, xylose reductase and xylitol dehydrogenase genes from Scheffersomyces stipitis, and XKS1, TAL1, FDH1 and ADH1 variant from S. cerevisiae. The genes were introduced using the homozygous integration system and afforded hemicellulolytic, xylose-assimilating and inhibitor-tolerant abilities to the strain. The engineered yeast strain demonstrated 2.7-fold higher ethanol titer from hemicellulosic material than a xylose-assimilating yeast strain. Furthermore, hemicellulolytic enzymes displayed on the yeast cell surface hydrolyzed hemicelluloses that were not hydrolyzed by a commercial enzyme, leading to increased sugar utilization for improved ethanol production. The multifunctional yeast strain, developed using a GIN11/FRT-based marker recycling system, achieved direct conversion of hemicellulosic biomass to ethanol without the addition of exogenous hemicellulolytic enzymes. No detoxification processes were required. The multiple-gene integration technique is a powerful approach for introducing and improving the biomass fermentation ability of industrial diploid S. cerevisiae strains.
Customized Consensus Spectral Library Building for Untargeted Quantitative Metabolomics Analysis with Data Independent Acquisition Mass Spectrometry and MetaboDIA Workflow (2017)

Data independent acquisition-mass spectrometry (DIA-MS) coupled with liquid chromatography is a promising approach for rapid, automatic sampling of MS/MS data in untargeted metabolomics. However, wide isolation windows in DIA-MS generate MS/MS spectra containing a mixed population of fragment ions together with their precursor ions. This precursor-fragment ion map in a comprehensive MS/MS spectral library is crucial for relative quantification of fragment ions uniquely representative of each precursor ion. However, existing reference libraries are not sufficient for this purpose since the fragmentation patterns of small molecules can vary in different instrument setups. Here we developed a bioinformatics workflow called MetaboDIA to build customized MS/MS spectral libraries using a user's own data dependent acquisition (DDA) data and to perform MS/MS-based quantification with DIA data, thus complementing conventional MS1-based quantification. MetaboDIA also allows users to build a spectral library directly from DIA data in studies of a large sample size. Using a marine algae data set, we show that quantification of fragment ions extracted with a customized MS/MS library can provide as reliable quantitative data as the direct quantification of precursor ions based on MS1 data. To test its applicability in complex samples, we applied MetaboDIA to a clinical serum metabolomics data set, where we built a DDA-based spectral library containing consensus spectra for 1829 compounds. We performed fragment ion quantification using DIA data using this library, yielding sensitive differential expression analysis.
Microstructure and superconductivity of Bi-Sr-Ca-Cu-O/Bi-Sr-Cu-O multilayer thin films (1994)

Epitaxially grown multi-layers of Bi<SUB>2</SUB>Sr<SUB>2</SUB>CaCu<SUB>2</SUB>O<SUB>y</SUB> (Bi-2212) and Bi<SUB>2</SUB>Sr<SUB>2</SUB>CuO<SUB>x</SUB> (Bi-2201) have been investigated referring to those microstructure and transport properties. Thin films have been prepared by a RF magnetron sputtering technique and laminated as the superconducting and non-superconducting layers. The samples have a variety of film thickness of each layer. The surface morphology, crystallization, diffusion and layered structures of these multi-layers were evaluated by TEM, AES, SIMS, STM-AFM and X-ray diffraction measurements. BSCO films exhibit normal conducting transport property even at 4.2 K. The superconducting properties such as change of Tc, a broadening of the transition and anisotropy in those properties under magnetic field were discussed. Those results suggested that the structural and electronic condition in N-layer seriously affect the superconducting interlayer coupling between superconducting layers through non- superconducting layers.
Unification of de novo and acquired ibrutinib resistance in mantle cell lymphoma (2017)

The novel Bruton's tyrosine kinase inhibitor ibrutinib has demonstrated high response rates in B-cell lymphomas; however, a growing number of ibrutinib-treated patients relapse with resistance and fulminant progression. Using chemical proteomics and an organotypic cell-based drug screening assay, we determine the functional role of the tumour microenvironment (TME) in ibrutinib activity and acquired ibrutinib resistance. We demonstrate that MCL cells develop ibrutinib resistance through evolutionary processes driven by dynamic feedback between MCL cells and TME, leading to kinome adaptive reprogramming, bypassing the effect of ibrutinib and reciprocal activation of PI3K-AKT-mTOR and integrin-β1 signalling. Combinatorial disruption of B-cell receptor signalling and PI3K-AKT-mTOR axis leads to release of MCL cells from TME, reversal of drug resistance and enhanced anti-MCL activity in MCL patient samples and patient-derived xenograft models. This study unifies TME-mediated de novo and acquired drug resistance mechanisms and provides a novel combination therapeutic strategy against MCL and other B-cell malignancies.
Functional Pyrimidinyl Pyrazolate Pt(II) Complexes: Role of Nitrogen Atom in Tuning the Solid‐State Stacking and Photophysics (2019)

Abstract Pt(II) metal complexes are known to exhibit strong solid‐state aggregation and are promising for realization of efficient emission in fabrication of organic light emitting diodes (OLED) with nondoped emitter layer. Four pyrimidine–pyrazolate based chelates, together with four isomeric Pt(II) metal complexes, namely: [Pt(pm2z) 2 ], [Pt(tpm2z) 2 ], [Pt(pm4z) 2 ], and [Pt(tpm4z) 2 ], are isolated and systematically investigated for their structure–property relationships for practical OLED applications. Detailed single molecular and aggregated structures are revealed by photophysical and mechanochromic measurements, grazing‐incidence X‐ray diffraction, and theoretical approaches. These results suggest that these Pt(II) emitters pack like a deck of playing cards under vacuum deposition, and their emission energy is not only affected by the single molecular designs, but notably influenced by their intermolecular packing interaction, i.e., Pt···Pt separations that are arranged in the order: [Pt(tpm4z) 2 ] &gt; [Pt(pm4z) 2 ] &gt; [Pt(tpm2z) 2 ] &gt; [Pt(pm2z) 2 ]. Nondoped OLED with emission ranging from green to red are prepared, to which the best performances are recorded for [Pt(tpm2z) 2 ], giving maximum external quantum efficiency (EQE) of 27.5% at 10 3 cd m −2 , maximum luminance of 2.5 × 10 5 cd m −2 at 17 V, and with stable CIE x , y of (0.56, 0.44).
ChemInform Abstract: Synthesis of S‐Amino‐azetine. (1986)

Abstract Aus dem Azetidin (I) erhält man mit Phthalimidkalium das Substitutionsprodukt (IIa), das zum Amin (IIb) hydrolysiert werden kann.
Folding of Synthetic Homogeneous Glycoproteins in the Presence of a Glycoprotein Folding Sensor Enzyme (2014)

UDP-glucose:glycoprotein glucosyltransferase (UGGT) plays a key role in recognizing folded and misfolded glycoproteins in the glycoprotein quality control system of the endoplasmic reticulum. UGGT detects misfolded glycoproteins and re-glucosylates them as a tag for misfolded glycoproteins. A flexible model to reproduce in vitro folding of a glycoprotein in the presence of UGGT in a mixture containing correctly folded, folding intermediates, and misfolded glycoproteins is described. The data demonstrates that UGGT can re-glucosylate all intermediates in the in vitro folding experiments, thus indicating that UGGT inspects not only final folded products, but also the glycoprotein folding intermediates.
Asymmetric Hydroformylation of Heterocyclic Olefins Mediated by Supramolecularly Regulated Rhodium-Bisphosphite Complexes (2015)

Rhodium complexes derived from conformationally transformable α,ω-bisphosphite ligands combined with a suitable alkali metal BArF salt as a regulation agent (RA) provide high regio- and enantioselectivities in the asymmetric hydroformylation (AHF) of three heterocyclic olefins. The outcome of the AHF could be exquisitely regulated by choosing the appropriate RA with an increase in the ee, the reversal of the regioselectivity, or the complete suppression of one byproduct.