gebhart/patrepeval huggingface dataset:
Copy number analysis to identify tumor suppressor genes associated with enzalutamide (Enza) resistance and poor prognosis in metastatic castration-resistant prostate cancer (mCRPC) patients. (2019)

5011 Background: Although enza prolongs life in mCRPC pts, the development of drug resistance and subsequent disease progression is nearly universal. Seeking to clarify molecular mechanisms that underlie enza resistance, we analyzed whole genome sequencing (WGS) and RNA sequencing (seq) of tumors obtained from patients with enza-naive or -resistant mCRPC. Methods: One hundred and one men with mCRPC who underwent image-guided biopsy and subsequent WGS were included (n = 64 with enza-naive and n = 37 with enza-resistant mCRPC). The differential copy number alteration (CNA) events enriched in enza-resistant vs. naïve samples were determined, and the prognostic significance of differential CNAs was assessed. RNA-seq data were evaluated to confirm that CNAs correlated with changes in gene expression of relevant loci and to identify potentially druggable targets selectively activated in tumors with specific CNAs. Results: Copy number loss was more common than gain in enza-resistant tumors. Specifically, we identified 123 protein-coding genes that were more commonly lost in enza-resistant samples—eight of which were previously described tumor suppressor genes. There was a strong concordance of copy number loss and reduced mRNA expression of these genes. We identified one gene from this list of eight genes whose copy number loss was associated with poor overall survival (median overall survival from date of CRPC was 19.1 months in tumors with gene loss vs. 42.0 months in intact tumors, hazard ratio 3.8 [1.46–9.8], log-rank p = 0.003). Finally, Master Regulator analysis determined that tumors with copy number loss of this poor prognosis gene had activation of several potentially targetable factors, including the kinases Akt and PLK1. Conclusions: Copy number loss of specific tumor suppressor genes is associated with enza resistance in mCRPC patients. Previously unappreciated molecular subsets of enza-resistant CRPC were identified, including one subset associated with poor clinical outcome.
Synthesis of palladium nanoclusters within spherical microdomains in films made from block copolymer/homopolymer blends (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of palladium nanoclusters within spherical microdomains in films made from block copolymer/homopolymer blendsY. Ng Cheong Chan and Richard R. SchrockCite this: Chem. Mater. 1993, 5, 4, 566–570Publication Date (Print):April 1, 1993Publication History Published online1 May 2002Published inissue 1 April 1993https://pubs.acs.org/doi/10.1021/cm00028a026https://doi.org/10.1021/cm00028a026research-articleACS PublicationsRequest reuse permissionsArticle Views92Altmetric-Citations39LEARN 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
Deuterium absorption from the D2O exposure of oxidized 4H-SiC (0001), (0001¯), and (112¯) surfaces (2015)

We report results on deuterium absorption on several oxidized 4H-SiC surfaces following D2O vapor absorption. Absorption at the oxide/semiconductor interface is strongly face dependent with an order of magnitude more deuterium on the C-face and a-face than on the Si-face, in contrast to the bulk of the oxides which show essentially no face dependence. Annealing in NO gas produces a large reduction in interfacial deuterium absorption in all cases. The reduction of the positive charge at the interface scales linearly with the interface D content. These results also scale with the variation in interface trap density (Dit) and mobility on the three faces after wet oxidation annealing.
OP24 Clinical efficacy and safety of guselkumab maintenance therapy in patients with moderately to severely active Crohn’s Disease: Week 48 analyses from the phase 2 GALAXI 1 study (2022)

Abstract Background GALAXI 1 is a Phase 2, double-blind, placebo (PBO)-controlled, multicenter study evaluating efficacy/safety of guselkumab (GUS), a selective IL-23 p19 antagonist, in patients (pts) with moderately to severely active Crohn’s disease (CD) with inadequate response/intolerance to conventional therapies (corticosteroids, immunomodulators) and/or biologics (tumor necrosis factor antagonists, vedolizumab). At Week (Wk) 12, all GUS induction doses (200, 600, and 1200mg IV) had greater improvements vs PBO for key clinical/endoscopic outcomes. We report clinical efficacy and safety of maintenance treatment through Wk48. Methods GALAXI employed a treat-through design over 48 wks. In induction pts were randomized to GUS 200, 600, or 1200mg IV, ustekinumab (UST) ~6mg/kg IV, or PBO IV. Pts transitioned to maintenance dosing as follows: PBO non-responders to UST ~6mg/kg IV to 90mg SC q8w, PBO responders to PBO SC q4w, GUS 200mg IV to 100mg SC q8w, GUS 600mg IV to 200mg SC q4w, GUS 1200mg IV to 200mg SC q4w, and UST ~6mg/kg IV to 90mg SC q8w. Pts randomized to PBO were not included in Wk48 efficacy analyses. Primary and major secondary endpoints evaluated efficacy of GUS vs PBO at Wk12. Evaluations of Wk48 endpoints were prespecified but not multiplicity controlled. UST was a reference arm; the study was not powered to evaluate differences between treatment groups with respect to efficacy at Wk48. Results Through Wk48, 248 pts in the primary efficacy analysis set were randomized and evaluated. Baseline demographics were similar across groups (Table 1). Discontinuation rates were low across active treatment groups. No dose response was observed across clinical efficacy assessments (Table 2). Proportions of pts achieving clinical remission at Wk48 ranged from 57.4–73.0% among GUS dose groups. The vast majority of pts in clinical remission were also in corticosteroid-free remission at Wk48; with rates ranging from 55.7–71.4% among GUS dose groups. PRO-2 remission rates ranged from 50.8–69.8%, and proportions of pts achieving clinical response ranged from 67.2–84.1% among GUS dose groups. Proportions of pts achieving abdominal pain scores ≤1 or daily average number of liquid or very soft stools ≤3 are presented in Table 2. Outcomes in the reference UST group are also shown in Table 2. Key safety event rates were similar among GUS dose groups (Table 3); no opportunistic infections, cases of tuberculosis, or deaths were reported in any group. Conclusion In this treat-through Phase 2 study of pts with moderately to severely active CD, GUS was safe and effective. GUS induction followed by SC maintenance achieved high rates of clinical efficacy at Wk48. Safety results were consistent with the known safety profile in approved indications.
High efficiency digitally linearized GaN based power amplifier for 3G applications (2008)

In this paper, a high efficiency GaN based power amplifier is designed using multi-harmonics load pull measurements. A load matching network that independently controls the load impedance at the fundamental, second and third harmonic frequencies is used for straightforward implementation. The continuously driven single-ended deep class AB biased power amplifier achieves a peak power added efficiency of 68% at saturation. It is found that the designed power amplifier exhibit highly non linear characteristics with 7 dB gain compression at saturation. Digital predistortion based linearizer is used to improve the linearity performance of the power amplifier under a WCDMA excitation (PAPR=9.8 dB). At a 10 dB output power back-off, 21% power added efficiency was measured along with 53 dBc adjacent channel leakage ratio.
High-temperature oxygen sensing behavior of perovskite films on the optical fiber platform (2019)

Real time gas sensing in high temperature energy conversion devices can enable optimal and efficient operation at both component and system levels, and the optical fiber based sensing platform shows significant advantages for harsh environment applications. In this research, (La<sub>0.8</sub>Sr<sub>0.2</sub>)<sub>0.95</sub>MnO<sub>3-&delta;</sub> (LSM), (La<sub>0.8</sub>Sr<sub>0.2</sub>)<sub>0.95</sub>CoO<sub>3-&delta;</sub> (LSC) and (La<sub>0.8</sub>Sr<sub>0.2</sub>)<sub>0.95</sub>Co<sub>0.2</sub>Fe<sub>0.8</sub>O<sub>3-&delta;</sub> (LSCF) films with thicknesses of several tens of nm are integrated with the optical fiber sensing platform as a functional sensor layer using a finely tuned-RF sputtering system designed for the fiber substrate deposition. Oxygen sensitivities, stabilities and overall feasibilities of these representative perovskite materials on the optical fiber platform are evaluated in the solid oxide fuel cell operational temperature regime at the oxygen concentration up to 19%, relevant for in-cell cathode stream gas composition sensing through optical transmission measurement which covers visible and near infrared wavelength ranges. Various sensitivity comparisons are carried out as a function of thickness, oxide composition, and deposition conditions. In general, the LSM sensor shows a stepwise absorption response to increasing levels of O<sub>2</sub> in a N<sub>2</sub> background, but also exhibits relatively slow kinetics including a continuous baseline drift. In contrast, LSCF based sensors exhibited enhanced transmittance responses in O<sub>2</sub> containing gas and a more rapid recovery and response, presumably due to the enhanced oxygen ion diffusion kinetics as compared to LSM. The results presented here are promising for the broad application areas of high temperature O<sub>2</sub> sensor research and a concomitantly wide range of energy related applications including combustion, solid oxide fuel cells, and others.
Optimized Liquid and Gas Phase Fractionation Increases HLA-Peptidome Coverage for Primary Cell and Tissue Samples (2021)

MS is the most effective method to directly identify peptides presented on human leukocyte antigen (HLA) molecules. However, current standard approaches often use 500 million or more cells as input to achieve high coverage of the immunopeptidome, and therefore, these methods are not compatible with the often limited amounts of tissue available from clinical tumor samples. Here, we evaluated microscaled basic reversed-phase fractionation to separate HLA peptide samples offline followed by ion mobility coupled to LC-MS/MS for analysis. The combination of these two separation methods enabled identification of 20% to 50% more peptides compared with samples analyzed without either prior fractionation or use of ion mobility alone. We demonstrate coverage of HLA immunopeptidomes with up to 8107 distinct peptides starting with as few as 100 million cells. The increased sensitivity obtained using our methods can provide data useful to improve HLA-binding prediction algorithms as well as to enable detection of clinically relevant epitopes such as neoantigens.
Commutativity in the Random Walk formulation of the Lovasz Local Lemma. (2015)

Recently, Achlioptas and Iliopoulos [1] proposed a new Random Walk framework for finding objects that avoid bad features, or flaws. It extends the Moser-Tardos resampling algorithm [12] to more general discrete spaces. At each step the method picks a flaw present in the current state and resamples it. However, it is less flexible than the Moser-Tardos method since [1] requires a specific flaw selection rule, whereas [12] allows an arbitrary rule (and thus can potentially be implemented more efficiently). 
We formulate a new commutativity condition, and prove that it is sufficient for an arbitrary rule to work. It also enables an efficient parallelization under an additional assumption. We then show that existing resampling oracles for perfect matchings and permutations do satisfy this condition. Finally, we observe that the bound in [1] on the expected runtime of the algorithm can be improved in some cases.
Analysis of networks of coupled spins by multiple quantum N.M.R. (1983)

It is shown that multiple quantum N.M.R. allows straightforward identification of networks of scalar coupled spins. The information obtained is particularly useful for the identification of magnetic equivalence when multiplet splittings are not fully resolved. The interpretation of multiple quantum spectra is based on a set of simple selection rules which restrict coherence transfer between multiple quantum and single quantum transitions.
Hypoxia Regulates DPP4 Expression, Proteolytic Inactivation, and Shedding from Ovarian Cancer Cells (2020)

The treatment of ovarian cancer has not significantly changed in decades and it remains one of the most lethal malignancies in women. The serine protease dipeptidyl peptidase 4 (DPP4) plays key roles in metabolism and immunity, and its expression has been associated with either pro- or anti-tumour effects in multiple tumour types. In this study, we provide the first evidence that DPP4 expression and enzyme activity are uncoupled under hypoxic conditions in ovarian cancer cells. Whilst we identified strong up-regulation of <i>DPP4</i> mRNA expression under hypoxic growth, the specific activity of secreted DPP4 was paradoxically decreased. Further investigation revealed matrix metalloproteinases (MMP)-dependent inactivation and proteolytic shedding of DPP4 from the cell surface, mediated by at least MMP10 and MMP13. This is the first report of uncoupled DPP4 expression and activity in ovarian cancer cells, and suggests a previously unrecognized, cell- and tissue-type-dependent mechanism for the regulation of DPP4 in solid tumours. Further studies are necessary to identify the functional consequences of DPP4 processing and its potential prognostic or therapeutic value.
J0330301 Fabrication of functionally graded porous aluminum by tool-traversing friction powder sintering process (2015)

Porous aluminum (Al) was fabricated by a tool traversing friction powder sintering process. In this process, a mixture of Al powder and sodium chloride (NaCl) powder as spacer particles was used as a starting material. The powder mixture was placed in a mold, compaction and sintering of the mixture was conducted only by the traversing of a rotating tool as in friction stir welding. In this study, functionally graded porous aluminum was fabricated by a tool traversing friction powder sintering process which had different range of porosity of 60%, 70% and 80%. By X-ray computing tomography observation, it was found that the fabricated functionally graded porous Al had uniform pore distribution in each porosity range. By a compression test, it was shown that the plateau stress was decreased with the increased in porosity. Consequently, it was shown that functionally graded porous Al can be fabricated by changing of NaCl mixing rate and tool traversing friction powder sintering process.
Potent anti-viral activity of a trispecific HIV neutralizing antibody in SHIV-infected monkeys (2022)

Broadly neutralizing antibodies (bNAbs) represent an alternative to drug therapy for the treatment of HIV-1 infection. Immunotherapy with single bNAbs often leads to emergence of escape variants, suggesting a potential benefit of combination bNAb therapy. Here, a trispecific bNAb reduces viremia 100- to 1000-fold in viremic SHIV-infected macaques. After treatment discontinuation, viremia rebounds transiently and returns to low levels, through CD8-mediated immune control. These viruses remain sensitive to the trispecific antibody, despite loss of sensitivity to one of the parental bNAbs. Similarly, the trispecific bNAb suppresses the emergence of resistance in viruses derived from HIV-1-infected subjects, in contrast to parental bNAbs. Trispecific HIV-1 neutralizing antibodies, therefore, mediate potent antiviral activity in vivo and may minimize the potential for immune escape.
Cryogenic Insulation Bondline Studies for Reusable Launch Vehicles (2003)

Cryogenic insulations bonded to metallic substrates were characterized under simulated mission conditions representative for a reusable launch vehicle. The combined thermal and mechanical test consisted of 50 to a 100 cycles. These combined thermal and mechanical cycles simulated flight missions with temperatures ranging from -423 F to 450 F and a maximum mechanical tension load ranging from 20,000 lbs. to 97,650 lbs. The combined thermal and mechanical (uniaxial tension) test apparatus (1 ft. by 2 ft. Test Apparatus) developed at the NASA Langley Research Center, was used to perform cyclic tests on cryogenic insulations bonded to tank wall substrates. No visual delamination or degradation was observed in the cryogenic insulation-to-metallic substrate bondline or butt joints between cryogenic insulation panels. In addition, after cyclic testing was performed, residual property results from tension-pull and closed-cell content tests of the cryogenic insulations indicated a decrease in the bondline strength and closed-cell content.
InP/InGaAs photodetector on SOI circuitry (2009)

We present the design, fabrication and characterization of an InP-based membrane photodetector on an SOI wafer containing a Si-wiring photonic circuit. Measured detector responsivity and 3 dB bandwidth are 0.45 A/W and 33 GHz, respectively. The photonic device fabrication is compatible with wafer scale processing steps, guaranteeing compatibility towards future generation electronic IC processing.
Remarkable sequence signatures in archaeal genomes (2002)

Complete archaeal genomes were probed for the presence of long (> or = 25 bp) oligonucleotide repeats (words). We detected the presence of many words distributed in tandem with narrow ranges of periodicity (i.e., spacer length between repeats). Similar words were not identified in genomes of non-archaeal species, namely Escherichia coli, Bacillus subtilis, Haemophilus influenzae, Mycoplasma genitalium and Mycoplasma pneumoniae. BLAST similarity searches against the GenBank nucleotide sequence database revealed that these words were archaeal species-specific, indicating that they are of a signature character. Sequence analysis and genome viewing tools showed these repeats to be restricted to non-coding regions. Thus, archaea appear to possess a non-coding genomic signature that is absent in bacterial species. The identification of a species-specific genomic signature would be of great value to archaeal genome mapping, evolutionary studies and analyses of genome complexity.
FBMC-based Physical Random Access Channel (2017)

FilterBank MultiCarrier (FBMC) is a candidate waveform for the coming fifth generation of mobile communications. The major advantage of FBMC is its very good frequency localization, provided that a high overlapping factor is used. Obviously the drawback is the poor time localization of the signal. In this paper we nevertheless show that it is possible to design a FBMC system with quite strong time constraints. The challenge was to implement a Long Term Evolution (LTE) like Physical Random Access Channel (PRACH) based on FBMC. Frequency Spreading implementation of FBMC is used and a PRACH is designed with equivalent or better time and frequency localizations than the LTE classical PRACH.
CXCR4 in Waldenström’s Macroglobulinema: chances and challenges (2020)

It is one of the major aims in cancer research to improve our understanding of the underlying mechanisms which initiate and maintain tumor growth and to translate these findings into novel clinical diagnostic and therapeutic concepts with the ultimate goal to improve patient care. One of the greater success stories in this respect has been Waldenström's Macroglobulinemia (WM), which is an incurable B-cell neoplasm characterized by serum monoclonal immunoglobulin M (IgM) and clonal lymphoplasmacytic cells infiltrating the bone marrow. Recent years have succeeded to describe the molecular landscape of WM in detail, highlighting two recurrently mutated genes, the MYD88 and the CXCR4 genes: MYD88 with an almost constant and recurrent point mutation present in over 90% of patients and CXCR4 with over 40 different mutations in the coding region affecting up to 40% of patients. Intriguingly, both mutations are activating mutations leading in the case of CXCR4 to an indelible activation and perpetual signaling of the chemokine receptor. These data have shed light on the essential role of CXCR4 in this disease and have paved the way to use these findings for predicting treatment response to the Bruton tyrosine kinase (BTK) inhibitor ibrutinib and novel therapeutic approaches in WM, which might be transferable to other related CXCR4 positive diseases. Well known for its central role in cancer progression and distribution, CXCR4 is highlighted in this review with regard to its biology, prognostic and predictive relevance and therapeutic implications in WM.
Oxidation of Monoethylene Glycol to Glycolic Acid with Gold-Based Catalyst and Glycolic Acid Isolation by Electrodialysis (2021)

In this work, a highly selective and active gold-based catalyst for the oxidation of high concentrated monoethylene glycol (MEG) in aqueous solution (3 M, 20 wt%) is described. High glycolic acid (GA) selectivity was achieved under mild reaction conditions. The optimization of the catalyst composition and of the reaction conditions for the oxidation of MEG in semi-batch mode under alkaline conditions led to a GA yield of &gt;80% with a GA selectivity of about 90% in short reaction time. The bimetallic catalyst 0.1 wt% AuPt (9:1)/CeO2 showed very high activity (&gt;2000 mmolMEG/gmetalmin) in the oxidation of MEG and, contrary to other studies, an extremely high educt to metal mole ratio of &gt;25,000 was used. Additionally, the gold–platinum catalyst showed a high GA selectivity over more than 10 runs. A very efficient and highly selective process for the GA production from MEG under industrial relevant reaction conditions was established. In order to obtain a GA solution with high purity for the subsequent polymerization, the received reaction solution containing sodium glycolate, unreacted MEG and sodium oxalate is purified by a novel down-stream process via electrodialysis. The overall GA yield of the process exceeds 90% as unreacted MEG can be recycled.
Supplementary Figure S3 from Reduced Proteolytic Shedding of Receptor Tyrosine Kinases Is a Post-Translational Mechanism of Kinase Inhibitor Resistance (2023)

&lt;p&gt;Supplementary Figure 3. Corresponds to Fig. 3C, showing U0126 and PD325901 elicit AXL upregulation to a degree that correlates with AXLi/MEKi synergy across a panel of cell lines.&lt;/p&gt;