gebhart/patrepeval huggingface dataset:
Does RSClin provide additional information over classic clinico-pathologic scores (PREDICT 2.1, Influence, CTS-5)? A TEAM Pathology substudy. (2023)

533 Background: Gene-expression profiling tests (e.g. Oncotype, Mammaprint, Prosignia, Breast Cancer Index and EndoPredict) are widely used in the care of patients with early-stage hormone positive breast cancer (node negative or 1-3 lymph nodes). However, these tests are resource intensive, and few studies have compared their value with either free and widely available clinico-pathologic risk calculators (e.g. PREDICT 2.1, INFLUENCE 2.0, and CTS-5) or tools that combine genomic testing with clinico-pathologic data (e.g. RSClin). The TEAM pathology substudy population was used to compare these different predicted model scores with outcomes. Methods: The TEAM pathology study consists of 3284 postmenopausal hormone positive breast cancer patients treated with either exemestane or tamoxifen followed by exemestane. Accrual was from 2001 to 2006. Genes comprising the multi-parametric Oncotype Dx were used to train signatures to create true assay results. Patient data was then used to calculate recurrence scores through various tools. This included clinico-pathologic models and their respective endpoints PREDICT 2.1 (overall survival at 5 years), INFLUENCE 2.0 (distant metastasis at 5 years), CTS-5 (distant recurrence risk at year 5-10), the purely genomic Oncotype Dx trained results (distant recurrence risk at 9 years), as well as the new clinico-pathologic RSClin (distant recurrence risk at 10 years). We compared the level of association between these predictive model scores using Spearman correlation coefficients. The prognostic ability of each model was contrasted for each outcome using Harrell’s C-statistic. Results: Results were available for CTS-5 (3022 patients), INFLUENCE 2.0 (3485 patients), ODx-trained (3825 patients), and RSClin (3029 patients). Correlation coefficients showed low correlation between Influence ( r= 0.25) and CTS-5 ( r= 0.17) with Oncotype-Dx trained results, and high correlation between RSClin ( r = 0.84) and Oncotype-Dx trained results. The concordance index was similar (0.65 to 0.68) for all models with distant metastasis-free survival as the outcome. Analysis is ongoing and further results will be available at the time of presentation. Conclusions: Other clinico-pathologic tools such as Influence 2.0 and CTS-5 have good prognostic ability when compared to Oncotype Dx-trained results and RSClin. [Table: see text]
(Si)5−2y(AlP)y alloys assembled on Si(100) from Al-P-Si3 building units (2012)

An original class of IV/III-V hybrid (Si)5−2y(AlP)y/Si(100) semiconductors have been produced via tailored interactions of molecular P(SiH3)3 and atomic Al yielding tetrahedral “Al-P-Si3” building blocks. Extensive structural, optical, and vibrational characterization corroborates that these units condense to assemble single-phase, monocrystalline alloys containing 60%-90% Si (y = 0.3-1.0) as nearly defect-free layers lattice-matched to Si. Spectroscopic ellipsometry and density functional theory band structure calculations indicate mild compositional bowing of the band gaps, suggesting that the tuning needed for optoelectronic applications should be feasible.
Effects of attentional focus cues on lower extremity kinematics during inside of the foot soccer trap among expert soccer players (2021)

Numerous studies have demonstrated improved performance results for sport skills through attentional focus instructions. However, few studies have examined the effects of cueing on expert kinematic performance, and this is the first to assess cueing’s kinematic effects on expert soccer players performing .common techniques This study assessed the lower extremity kinematics of an inside of the foot soccer trap via motion capture cameras under different attentional focus cues to analyze how the cues affect the movement pattern among expert performers. 10 NCAA Division 1 soccer players trapped a launched ball on a scoring mat after receiving coaching cues inducing an internal, external, holistic, or control focus of attention. Statistical analysis revealed movement differences between the internal and external cue conditions for the ankle and knee joints during the movement. The difference at the knee was a steeper flexion followed by a correction and, at the ankle, a steeper flexion, both during the internal cue condition. Attentional focus cues inducing a conscious control of the movement may disrupt the movement patterns of highly skilled expert performers. Coaches should be acutely aware of the language they use in instruction, even among expert performers.
Identification of an Rsal RFLP at the acid alpha glucosidase (GAA) locus (1990)

The probe IP20K061 is a 0.8 kb Hpall fragment isolated from a X phage obtained by screening a human genomic library with a subtelomeric interspersed repeat (STIR) (1). The insert is subcloned in the pBS vector (Stratagene) and can be excised with Hindffl. Polymorphism: MspI identifies 2 allelic fragments of 0.85 kb and 0.6 kb. Frequency: Estimated from 46 parents of the CEPH panel. 0.85 kb allele: 0.55 0.60 kb allele: 0.45 Not Polymorphic For: BamHI, BglII, EcoRI, PstI, RsaI, TaqI, XbaI (studied in 5 unrelated individuals). Chromosomal Localization: Localized to 20q13.3 by in situ hybridization and genetic linkage analysis (1). Mendelian Inheritance: Codominant segregation observed in 19 CEPH families.
Molecular alterations in AKT1, AKT2 and AKT3 detected in breast and prostatic cancer by FISH (2009)

In breast cancer AKT3 amplifications and AKT1 and AKT2 deletions were seen, which, to our knowledge, have not been shown by FISH before. Although these two cohorts cannot be directly compared, only one AKT1 amplification was identified in prostatic carcinomas. This indicates differences in the genetic changes underlying development of breast and prostatic cancers. To evaluate further the role of genetic changes of AKT in breast cancer progression, a cohort of both ER+ and ER- patients should be evaluated.
Traffic Pattern of Cystic Fibrosis Transmembrane Regulator through the Early Exocytic Pathway (2000)

The pathway of transport of the cystic fibrosis transmembrane regulator (CFTR) through the early exocytic pathway has not been examined. In contrast to most membrane proteins that are concentrated during export from the ER and therefore readily detectable at elevated levels in pre-Golgi intermediates and Golgi compartments, wild-type CFTR could not be detected in these compartments using deconvolution immunofluorescence microscopy. To determine the basis for this unusual feature, we analyzed CFTR localization using quantitative immunoelectron microscopy (IEM). We found that wild-type CFTR is present in pre-Golgi compartments and peripheral tubular elements associated with the cis and trans faces of the Golgi stack, albeit at a concentration 2-fold lower than that found in the endoplasmic reticulum (ER). delta F508 CFTR, a mutant form that is not efficiently delivered to the cell surface and the most common mutation in cystic fibrosis, could also be detected at a reduced concentration in pre-Golgi intermediates and peripheral cis Golgi elements, but not in post-Golgi compartments. Our results suggest that the low level of wild-type CFTR in the Golgi region reflects a limiting step in selective recruitment by the ER export machinery, an event that is largely deficient in delta F508. We raise the possibility that novel modes of selective anterograde and retrograde traffic between the ER and the Golgi may serve to regulate CFTR function in the early secretory compartments.
Piezoelectric actuation of aluminum nitride contour mode optomechanical resonators (2015)

We present a fully-integrated monolithic aluminum nitride optomechanical device in which lateral vibrations generated by a piezoelectric contour mode acoustic ring resonator are used to produce amplitude modulation of an optical signal in a whispering gallery mode photonic ring resonator. Acoustic and optical resonances are independently characterized in this contour mode optomechanical resonator (CMOMR). Electrically driven mechanical modes are optically detected at 35MHz, 654MHz and 884MHz.
The Oxidation-sensing Regulator (MosR) Is a New Redox-dependent Transcription Factor in Mycobacterium tuberculosis (2012)

Mycobacterium tuberculosis thrives in oxidative environments such as the macrophage. To survive, the bacterium must sense and adapt to the oxidative conditions. Several antioxidant defenses including a thick cell wall, millimolar concentrations of small molecule thiols, and protective enzymes are known to help the bacterium withstand the oxidative stress. However, oxidation-sensing regulators that control these defenses have remained elusive. In this study, we report a new oxidation-sensing regulator, Rv1049 or MosR (M. tuberculosis oxidation-sensing regulator). MosR is a transcriptional repressor of the MarR family, which, similarly to Bacillus subtilis OhrR and Staphylococcus aureus MgrA, dissociates from DNA in the presence of oxidants, enabling transcription. MosR senses oxidation through a pair of cysteines near the N terminus (Cys-10 and Cys-12) that upon oxidation forms a disulfide bond. Disulfide formation rearranges a network of hydrogen bonds, which leads to a large conformational change of the protein and dissociation from DNA. MosR has been shown previously to play an important role in survival of the bacterium in the macrophage. In this study, we show that the main role of MosR is to up-regulate expression of rv1050 (a putative exported oxidoreductase that has not yet been characterized) in response to oxidants and propose that it is through this role that MosR contributes to the bacterium survival in the macrophage.
Cellular Delivery of Bioorthogonal Pretargeting Therapeutics in PSMA-Positive Prostate Cancer (2019)

Prostate cancer is primarily fatal after it becomes metastatic and castration-resistant despite novel combined hormonal and chemotherapeutic regimens. Hence, new therapeutic concepts and drug delivery strategies are urgently needed for the eradication of this devastating disease. Here we report the highly specific, <i>in situ</i> click chemistry driven pretargeted delivery of cytotoxic drug carriers to PSMA(+) prostate cancer cells. Anti-PSMA 5D3 mAb and its F(ab')<sub>2</sub> fragments were functionalized with <i>trans</i>-cyclooctene (TCO), labeled with a fluorophore, and used as pretargeting components. Human serum albumin (ALB) was loaded with the DM1 antitubulin agent, functionalized with PEGylated tetrazine (PEG<sub>4</sub>-Tz), labeled with a fluorophore, and used as the drug delivery component. The internalization kinetics of components and the therapeutic efficacy of the pretargeted click therapy were studied in PSMA(+) PC3-PIP and PSMA(-) PC3-Flu control cells. The F(ab')<sub>2</sub> fragments were internalized faster than 5D3 mAb in PSMA(+) PC3-PIP cells. In the two-component pretargeted imaging study, both components were colocalized in a perinuclear location of the cytoplasm of PC3-PIP cells. Better colocalization was achieved when 5D3 mAb was used as the pretargeting component. Consecutively, the <i>in vitro</i> cell viability study shows a significantly higher therapeutic effect of click therapy in PC3-PIP cells when 5D3 mAb was used for pretargeting, compared to its F(ab')<sub>2</sub> derivative. 5D3 mAb has a longer lifetime on the cell surface, when compared to its F(ab')<sub>2</sub> analogue, enabling efficient cross-linking with the drug delivery component and increased efficacy. Pretargeting and drug delivery components were cross-linked via multiple bioorthogonal click chemistry reactions on the surface of PSMA(+) PC cells forming nanoclusters, which undergo fast cellular internalization and intracellular transport to perinuclear locations.
<title>Fiber-optic delay lines for wideband signal processing</title> (1991)

New methods for wideband signal processing using fiber delay lines are described. The processors make use of fixed and programmable reflective taps, all-fiber switches, and ladder networks. A tapped delay line with over 10 GHz bandwidth has been demonstrated, as have variable-length delay lines with up to 16 different delay times.
CCR Translation on this Article from A Novel Human Her-2/neu Chimeric Molecule Expressed by <i>Listeria monocytogenes</i> Can Elicit Potent HLA-A2 Restricted CD8-positive T cell Responses and Impact the Growth and Spread of Her-2/neu-positive Breast Tumors (2023)

CCR Translation on this Article from A Novel Human Her-2/neu Chimeric Molecule Expressed by &lt;i&gt;Listeria monocytogenes&lt;/i&gt; Can Elicit Potent HLA-A2 Restricted CD8-positive T cell Responses and Impact the Growth and Spread of Her-2/neu-positive Breast Tumors
Ultralow Power Gas Sensors for Environmental and Safety Applications (2013)

Abstract not Available.
Frontispiece: Bright Electrogenerated Chemiluminescence of a Bis‐Donor Quadrupolar Spirofluorene Dye and Its Nanoparticles (2016)

Electrogenerated Chemiluminescence Thiophene-based materials have many outstanding chemical and physical properties, such as their unique variety of electronic properties and easy structure variation. A series of symmetric fluorescent dyes built from a spirofluorene core, bearing electroactive end-groups and having different conjugated linkers were prepared in view of their use as building blocks for the preparation of electrochemiluminescent dyes and nanoparticles. The molecular confinement of the luminophores within fluorescent nanoparticles allows to design highly efficient bright nano-emitters. For more details, see the Full Paper by M. Blanchard-Desce, N. Sojic et al. on page 12702 ff.
Search for s-channel single top-quark production in proton–proton collisions at s=8 TeV with the ATLAS detector (2014)

This Letter presents a search at the LHC for s-channel single top-quark production in proton-proton collisions at a centre-of-mass energy of 8 TeV. The analyzed data set was recorded by the ATLAS detector and corresponds to an integrated luminosity of 20.3 fb -1 . Selected events contain one charged lepton, large missing transverse momentum and exactly two b-tagged jets. A multivariate event classifier based on boosted decision trees is developed to discriminate s-channel single top-quark events from the main background contributions. The signal extraction is based on a binned maximum-likelihood fit of the output classifier distribution. The analysis leads to an upper limit on the s-channel single topquark production cross-section of 14.6 pb at the 95% confidence level. The fit gives a cross-section of s = 5.0 4.3 pb, consistent with the Standard Model expectation.
Photoinduced Multistep Energy and Electron Transfer in an Oligoaniline−Oligo(p-phenylene vinylene)−Fullerene Triad (2003)

A donor−donor−acceptor triad, OAn−OPV−C60, with a redox gradient has been synthesized by covalently linking an oligoaniline (OAn), an oligo(p-phenylene vinylene) (OPV), and a fullerene (C60) in a nonconjugated linear array. Photoluminescence and femtosecond pump−probe spectroscopy studies reveal that photoexcitation of any of the three chromophores of this triad in a polar solvent results in formation of the OAn−OPV+−C60- charge-separated state, after an efficient ultrafast (<190 fs) singlet-energy transfer to the fullerene singlet-excited state. The initial OAn−OPV+−C60- state can rearrange to the low-energy OAn+−OPV−C60- charge-separated state via an intramolecular redox reaction. Because the competing charge recombination of the OAn−OPV+−C60- state to the ground state is fast and increases with increasing polarity of the solvent, the quantum yield for this charge shift is the highest (∼0.4) in weakly polar solvents such as chlorobenzene. Once formed, the OAn+−OPV−C60- state has a long lifetime (>1 ns) due to weak electronic coupling between the distant redox sites in the excited state. The stabilization gained is more than 1 order of magnitude in time. The experimental results are found to be in qualitative agreement with Marcus theory. In thin films, the OAn+−OPV−C60- state is formed at a higher rate and in higher quantum yield than in solution.
pH Rate Profiles of FnY356−R2s (n = 2, 3, 4) in Escherichia coli Ribonucleotide Reductase:  Evidence that Y356 Is a Redox-Active Amino Acid along the Radical Propagation Pathway (2006)

The Escherichia coli ribonucleotide reductase (RNR), composed of two subunits (R1 and R2), catalyzes the conversion of nucleotides to deoxynucleotides. Substrate reduction requires that a tyrosyl radical (Y(122)*) in R2 generate a transient cysteinyl radical (C(439)*) in R1 through a pathway thought to involve amino acid radical intermediates [Y(122)* --> W(48) --> Y(356) within R2 to Y(731) --> Y(730) --> C(439) within R1]. To study this radical propagation process, we have synthesized R2 semisynthetically using intein technology and replaced Y(356) with a variety of fluorinated tyrosine analogues (2,3-F(2)Y, 3,5-F(2)Y, 2,3,5-F(3)Y, 2,3,6-F(3)Y, and F(4)Y) that have been described and characterized in the accompanying paper. These fluorinated tyrosine derivatives have potentials that vary from -50 to +270 mV relative to tyrosine over the accessible pH range for RNR and pK(a)s that range from 5.6 to 7.8. The pH rate profiles of deoxynucleotide production by these F(n)()Y(356)-R2s are reported. The results suggest that the rate-determining step can be changed from a physical step to the radical propagation step by altering the reduction potential of Y(356)* using these analogues. As the difference in potential of the F(n)()Y* relative to Y* becomes >80 mV, the activity of RNR becomes inhibited, and by 200 mV, RNR activity is no longer detectable. These studies support the model that Y(356) is a redox-active amino acid on the radical-propagation pathway. On the basis of our previous studies with 3-NO(2)Y(356)-R2, we assume that 2,3,5-F(3)Y(356), 2,3,6-F(3)Y(356), and F(4)Y(356)-R2s are all deprotonated at pH > 7.5. We show that they all efficiently initiate nucleotide reduction. If this assumption is correct, then a hydrogen-bonding pathway between W(48) and Y(356) of R2 and Y(731) of R1 does not play a central role in triggering radical initiation nor is hydrogen-atom transfer between these residues obligatory for radical propagation.
High-$Q$ Above-IC Inductors Using Thin-Film Wafer-Level Packaging Technology Demonstrated on 90-nm RF-CMOS 5-GHz VCO and 24-GHz LNA (2006)

High-Q inductors are important for the realization of high-performance, low-power RF-circuits. In this paper, on-chip inductors with Q-factors above 40 have been realized above the passivation of a 90-nm RF-CMOS process using wafer-level packaging (WLP) techniques . The influence of a patterned polysilicon and metal ground shield on the inductor-Q is compared and the influence of highly doped active area underneath the inductors is shown. A 5-15 GHz above-IC balun has been realized on 20 Omegamiddotcm silicon with the use of patterned ground shield. The technology is demonstrated by a low-power 90-nm RF-CMOS 5-GHz VCO with a core current consumption of only 150 muA with a 1.2-V supply, and a 10% tuning range with a worst case phase noise of -111 dBc/Hz at 1-MHz offset. A 24-GHz single-stage common-source low-noise amplifier has been realized, with a noise figure of 3.2 dB, a gain of 7.5 dB, and a low power consumption of 10.6 mW
A 15×15 mm/sup 2/ single-chip fingerprint sensor and identifier using pixel-parallel processing (2003)

User authentication using fingerprints is strongly needed to prevent IC cards and mobile equipment from being used illegally. Some semiconductor sensor chips for fingerprint identification have been presented. However, they require a high-performance microprocessor and large memories, which makes it difficult to embed these chips in small, thin devices. Moreover, it is easy to tamper with the personal data in the microprocessor, memory and sensor chips because they are separate. Incorporating a sensor and identifier in a single chip solves these problems. The LSI architecture integrates the sensor and identifier in a single chip, and provides a sensor-unified fingerprint identifying LSI.
Direct detection of unamplified genomic DNA based on photo-induced silver ion reduction by DNA molecules (2013)

A label-free, colorimetric method has been developed for ultrasensitive detection of nucleic acids that is based on photoinduced silver ion (Ag(+)) reduction around DNA bases. The assay system is capable of directly detecting bacterial genomic DNA without the need for PCR amplification.
Studies on the Unique RNA Duplex Destabilization by an Azoniacyclophane − NMR Titrations with Mono- and Oligonucleotides of the RNA and DNA Types (2002)

The mechanism of the unique destabilization of a folded RNA by the azoniacyclophane CP66 has been investigated by complexation studies with mono- and short single-stranded oligonucleotides as models. For the mononucleotides, NMR titrations revealed only a slight difference of binding free energy ΔG between RNA-type nucleotides compared to DNA analogues, with ΔΔG values of up to 1.3 kJ/mol. The complexation-induced NMR shifts (CIS values) both in the ligand and in the cyclophane were also similar for deoxyribo- and ribonucleotides, suggesting similar inclusion geometries in both series. Similar observations had been made earlier on the CIS effects of denatured single-strand polymers. Titrations with dinucleotides showed a slight preference for ribose derivatives, with ΔG = −11.2 kJ/mol for ApA and −13.2 kJ/mol for ApG, and −9.9 kJ/mol for dApdA. With the dinucleotides and with selected tri- and tetranucleotides, the NMR shielding effects indicated stronger binding to adenine amongst the nucleobases, with a preference for the 5′-end position where available. In view of the small affinity decrease from ribose to deoxyribose derivatives, possible differences in the geometric disposition of the cyclophane towards the major groove of the duplexes were analysed with a simplified point charge model. The phosphates in the RNA groove indeed matched the cationic ammonium centres of the ligand less well than did those in the larger B-DNA groove. The conclusion from these results is that the destabilization of duplex RNA relative to that of duplex DNA is caused at least in part by the differences in interaction between CP66 and the duplex species and not the single-stranded species. (© Wiley-VCH Verlag GmbH, 69451 Weinheim, Germany, 2002)
PeptideRanger: An R Package to Optimize Synthetic Peptide Selection for Mass Spectrometry Applications (2023)

Targeted and semitargeted mass spectrometry-based approaches are reliable methods to consistently detect and quantify low abundance proteins including proteins of clinical significance. Despite their potential, the development of targeted and semitargeted assays is time-consuming and often requires the purchase of costly libraries of synthetic peptides. To improve the efficiency of this rate-limiting step, we developed PeptideRanger, a tool to identify peptides from protein of interest with physiochemical properties that make them more likely to be suitable for mass spectrometry analysis. PeptideRanger is a flexible, extensively annotated, and intuitive R package that uses a random forest model trained on a diverse data set of thousands of MS experiments spanning a variety of sample types profiled with different chromatography setups and instruments. To support a variety of applications and to leverage rapidly growing public MS databases, PeptideRanger can readily be retrained with experiment-specific data sets and customized to prioritize and filter peptides based on selected properties.