gebhart/patrepeval huggingface dataset:
DNA Repair Gene Alterations and PARP Inhibitor Response in Patients With Metastatic Castration-Resistant Prostate Cancer (2018)

<b>Background:</b> PARP inhibition is a promising therapeutic strategy for the treatment of men with metastatic castration-resistant prostate cancer whose tumors harbor homologous recombination DNA repair gene alterations. However, questions remain for many practicing clinicians about which patients are ideally suited for PARP inhibitor treatment. This report details our institutional experience using PARP inhibitor therapy in patients whose tumors harbored specific DNA repair gene alterations. <b>Patients and Methods:</b> We performed a retrospective chart review to identify patients at Oregon Health & Science University who were treated with PARP inhibition. We identified 8 patients and determined the impact of the specific DNA repair gene alterations on tumor response and time on treatment with PARP inhibition. <b>Results:</b> A number of DNA repair gene alterations were identified. Three patients had pathogenic <i>BRCA2</i> mutations and one had a <i>BRCA2</i> mutation of uncertain significance. Conversely, the 4 other patients' tumors harbored alterations in other DNA repair genes, none of which were clearly pathogenic. A statistically significant difference in benefit was seen between patients whose tumors harbored <i>BRCA2</i> gene alterations and those whose tumors did not, as measured by >50% decline in prostate-specific antigen levels (100% vs 0%; <i>P</i>=.03) and duration on therapy (31.4 vs 6.4 weeks; <i>P</i>=.03). <b>Conclusions:</b> Our results demonstrate that not all DNA repair alterations are equally predictive of PARP inhibitor response. Importantly, all responding patients had tumors harboring <i>BRCA2</i> DNA repair alterations, including one without a known pathogenic mutation. Conversely, among the 4 nonresponders, several DNA repair alterations in genes other than <i>BRCA2</i> were identified that were not clearly pathogenic. This demonstrates the need to carefully examine the functional relevance of the DNA repair alterations identified, especially in genes other than <i>BRCA2</i>, when considering patients for PARP inhibitor treatment.
SARS-CoV-2 induces robust germinal center CD4 T follicular helper cell responses in rhesus macaques (2021)

CD4 T follicular helper (T<sub>fh</sub>) cells are important for the generation of durable and specific humoral protection against viral infections. The degree to which SARS-CoV-2 infection generates T<sub>fh</sub> cells and stimulates the germinal center (GC) response is an important question as we investigate vaccine induced immunity against COVID-19. Here, we report that SARS-CoV-2 infection in rhesus macaques, either infused with convalescent plasma, normal plasma, or receiving no infusion, resulted in transient accumulation of pro-inflammatory monocytes and proliferating T<sub>fh</sub> cells with a T<sub>h</sub>1 profile in peripheral blood. CD4 helper cell responses skewed predominantly toward a T<sub>h</sub>1 response in blood, lung, and lymph nodes. SARS-CoV-2 Infection induced GC T<sub>fh</sub> cells specific for the SARS-CoV-2 spike and nucleocapsid proteins, and a corresponding early appearance of antiviral serum IgG antibodies. Collectively, the data show induction of GC responses in a rhesus model of mild COVID-19.
Renewable Epoxy Thermosets from Fully Lignin-Derived Triphenols (2018)

A series of fully renewable triphenols (TPs) with various number of methoxy group substituents (n = 0–6) were synthesized using lignin-derived phenols (guaiacol and 2,6-dimethoxyphenol) and aldehydes (4-hydroxybenzaldehyde, vanillin, and syringaldehyde). The structural evolution from TPs to epoxy thermosets was followed by nuclear magnetic resonance (NMR) and Fourier transform infrared (FTIR) spectroscopy. Thermomechanical properties of the resulting epoxy thermosets were investigated by dynamic mechanical analysis (DMA), tensile analysis (TA), and thermogravimetric analysis (TGA). Increasing the content of methoxy groups decreased the glass transition temperature (132–118 °C) and glassy modulus (2.7–2.2 GPa). Thermal stability of high-methoxy-content thermosets was reduced due to electron-donating effects and higher oxygen content. Conversions and isolated yields of TPs significantly decreased as the number of methoxy substituents increased, which markedly determined the feasibility of TPs as precursors for polymers. This work widens the synthesis route of fully lignin-derived polyphenols, yielding polymers with thermomechanical properties comparable to bisphenol A (BPA) based materials. Evaluation of methoxy substitution provides insight for the selection of lignin-derived monomers.
Significant association of caveolin-1 (CAV1) genotypes with upper urothelial tract cancer. (2013)

Our results suggest that individual and combined CAV1 rs3807987/rs7804372 genotypes are involved in predisposition to upper urothelial tract cancer in the Taiwanese population.
Poly[(N-acryloyl glycinamide)-co-(N-acryloyl l-alaninamide)] and Their Ability to Form Thermo-Responsive Hydrogels for Sustained Drug Delivery (2019)

In the presence of water, poly(<i>N</i>-acryloyl glycinamide) homopolymers form highly swollen hydrogels that undergo fast and reversible gel↔sol transitions on heating. According to the literature, the transition temperature depends on concentration and average molecular weight, and in the case of copolymers, composition and hydrophilic/hydrophobic character. In this article, we wish to introduce new copolymers made by free radical polymerization of mixtures of <i>N</i>-acryloyl glycinamide and of its analog optically active <i>N</i>-acryloyl l-alaninamide in various proportions. The <i>N</i>-acryloyl l-alaninamide monomer was selected in attempts to introduce hydrophobicity and chirality in addition to thermo-responsiveness of the Upper Critical Solubilization Temperature-type. The characterization of the resulting copolymers included solubility in solvents, dynamic viscosity in solution, Fourrier Transform Infrared, Nuclear Magnetic Resonance, and Circular Dichroism spectra. Gel→sol transition temperatures were determined in phosphate buffer (pH = 7.4, isotonic to 320 mOsm/dm³). The release characteristics of hydrophilic Methylene Blue and hydrophobic Risperidone entrapped in poly(<i>N</i>-acryloyl glycinamide) and in two copolymers containing 50 and 75% of alanine-based units, respectively, were compared. It was found that increasing the content in <i>N</i>-acryloyl-alaninamide-based units increased the gel→sol transition temperature, decreased the gel consistency, and increased the release rate of Risperidone, but not that of Methylene Blue, with respect to homo poly(<i>N</i>-acryloyl glycinamide). The increase observed in the case of Risperidone appeared to be related to the hydrophobicity generated by alanine residues.
Cleavage of Isoxazolines with Tricarbonyltris(acetonitrile)molybdenum and Silica Gel. Synthesis of 1-(2-Oxoalkyl)cyclopropanols from lsoxazoline-5-spirocyclopropanes (1989)

An efficient synthesis of 1-(2-oxoalkyl)cyclopropanols [or (1-hydroxycyclopropyl)methyl ketones] from isoxazoline-5-spirocyclopropanes by selective N-O cleavage effected by Mo(CO)3(MeCN)3 and silica gel is described.
Pseudoxanthomonas mexicana sp. nov. and Pseudoxanthomonas japonensis sp. nov., isolated from diverse environments, and emended descriptions of the genus Pseudoxanthomonas Finkmann et al. 2000 and of its type species (2004)

Three mesophilic bacteria (strains AMX 26B(T), UR374_02 and 12-3(T)) isolated respectively from an anaerobic digester, human urine and urban riverside soil were characterized. Cells were Gram-negative, motile, non-sporulating, straight to curved rods with one polar flagellum and had a strictly respiratory metabolism with O(2) as the preferential terminal electron acceptor. Phylogenetic analysis based on 16S rRNA gene sequences revealed that all strains clustered within the Xanthomonadaceae branch of the Proteobacteria. Isolates AMX 26B(T) and UR374_02 exhibited 100 % 16S rRNA gene sequence similarity and both were related to strain 12-3(T) (99.6 % similarity). The closest relative of all the isolates was Pseudoxanthomonas broegbernensis DSM 12573(T) (similarity 97.1-97.5 %), and they were equidistantly related to Xanthomonas species (95.4-96.6 %), Stenotrophomonas species (95.3-96.1 %) and Pseudoxanthomonas taiwanensis ATCC BAA-4040(T) (95.3-95.4 %). Chemotaxonomic and biochemical data (branched-chain cellular fatty acid pattern without C(13 : 0) iso 3-OH, ubiquinone with eight isoprenoid units, limited range of substrates used, ability to reduce nitrite but not nitrate with the production of N(2)O) supported their affiliation to the genus Pseudoxanthomonas. The results of DNA-DNA hybridization and/or phenotypic analysis allowed them to be differentiated from the two Pseudoxanthomonas species with validly published names and showed that strain 12-3(T) was genomically and phenotypically distinct from the other two isolates. On the basis of these results, two novel species of the genus Pseudoxanthomonas are proposed: Pseudoxanthomonas mexicana sp. nov., consisting of strains AMX 26B(T) (=ATCC 700993(T)=CIP 106674(T)=JCM 11524(T)) (type strain) and UR374_02 (=DSM 15133), and Pseudoxanthomonas japonensis sp. nov., consisting of strain 12-3(T) (=CCUG 48231(T)=CIP 107388(T)=JCM 11525(T)). The report of these two novel species leads to the emendation of the description of the genus Pseudoxanthomonas and the re-evaluation of the phenotype of P. broegbernensis DSM 12573(T) necessitates the emendation of its description.
Silicon nitride PECVD at low temperature: film properties and plasma analysis (2002)

Summary form only given. Recently there has been growing interest in the development of materials and processes at low temperatures compatible with transparent plastics for use in more rugged and flexible flat panel displays. Silicon nitride is a commonly used dielectric in thin film transistors (TFTs), the active switching element for each pixel in a display. We used plasma enhanced chemical vapor deposition (PECVD) at temperatures <150/spl deg/C with SiH/sub 4/, N/sub 2/ and He to deposit silicon nitride. Process analysis was done using in-situ mass spectroscopy and optical emission spectroscopy. Nitrogen instead of NH/sub 3/ was used to inhibit hydrogen incorporation which has been found to increase as temperature decreases in PECVD materials. Our films had an atomic hydrogen concentration near 20% at 50/spl deg/C vs. 30% in films deposited with NH/sub 3/. He dilution was used to engineer the distribution of hydrogen to obtain equal amounts bonded to Si and N, a physical property that has been associated with good quality films deposited at high temperatures. We found that increasing N/sub 2/:SiH/sub 4/ flow rate ratio from 50 to 150 resulted in a decrease in N atom incorporation relative to Si atoms in the films from N/Si=1.37 to 1.27. To examine the possibility of an increasing Si incorporation causing an apparent decrease in N atom fraction, we obtained the silane consumption fraction from mass spectrometry as a function of N/sub 2//SiH/sub 4/ flow rate ratio. The silane consumption fraction decreased from 97% at N/sub 2/ /SiH/sub 4/=50 to 93% at N/sub 2//SiH/sub 4/=150, which means increased Si incorporation as N/sub 2/ flow is increased is unlikely. Optical emission was used to observe nitrogen excited states, and detailed correlations between emission intensities, gas phase species distribution, and Si/N ratio in the deposited films will be reported.
Optical Fiber Amplifiers and Their Applications. Optical Fiber Amplifier for Multi-Channel Transmission. (1997)

This paper discusses our EDFA module for multi-channel transmission systems. This EDFA module has flat gain characteristics in l5nm (from 1546 to 1561nm) and +20dBm signal output power. We improved gain flatness by optimizing EDF and using gain equalizers, which passively equalize gain variance of EDF.
Decomposition of [2-Pyr(SiMe<sub>3</sub>)<sub>2</sub>C]<sub>2</sub>SbCl into the Stibaalkene [2-Pyr(SiMe<sub>3</sub>)<sub>2</sub>C−SbC(SiMe<sub>3</sub>)2-Pyr]:  Solid, Solution, and ab Initio Study (2004)

The disubstituted antimony chloride complex [2-Pyr(SiMe3)2C]2SbCl (Pyr = C5H4N), formed from the 2:1 reaction of [2-Pyr(SiMe3)2CLi·tmeda] with SbCl3, readily decomposes into the stibaalkene species [2-Pyr(SiMe3)2CSbC(SiMe3)2-Pyr] via β-elimination of Me3SiCl. The stibaalkene species is an intensely colored, highly air and moisture sensitive, deep red oil. In thf solution the elimination of Me3SiCl occurs at temperatures ca. −40 °C; however, orange crystals of [2-Pyr(SiMe3)2C]2SbCl were obtained from an Et2O solution maintained at −25 °C and the structure was determined by single-crystal X-ray diffraction. 1H and 13C NMR spectra of the crystals of [2-Pyr(SiMe3)2C]2SbCl have been obtained in d8-toluene at −30 °C, and its decomposition to the stibaalkene was followed by recording spectra as the sample was warmed to 30 °C. DFT ab initio calculations have been conducted to investigate the role of the pyridyl groups in Me3SiCl elimination as well as the structure and stability of the final stibaalkene. These indicate that the formation of strong Sb−N bonds effectively localizes much of the double-bond character in a CC rather than SbC bond, increasing its overall stability.
Capacity of a noisy quantum channel (1996)

We analyze a quantum channel for information transmission and storage. In analogy to classical channels, we propose to define the quantum channel capacity as the maximum rate of mutual entanglement processed by the channel (for the transmission and storage of quantum entanglement), which reduces to the maximum mutual information processed by the channel for the transmission of classical data. The entanglement processed by the channel observes a data-processing inequality, and we derive a quantum Fano-inequality relating the loss of the channel to the fidelity of the quantum code. The latter establishes the link between quantum error-correction and the transfer of entanglement. The mutual entanglement and the capacity are calculated explicitly for the quantum ``depolarizing'' channel.
Diagrammatic Derivation of Gradient Algorithms for Neural Networks (1996)

Deriving gradient algorithms for time-dependent neural network structures typically requires numerous chain rule expansions, diligent bookkeeping, and careful manipulation of terms. In this paper, we show how to derive such algorithms via a set of simple block diagram manipulation rules. The approach provides a common framework to derive popular algorithms including backpropagation and backpropagation-through-time without a single chain rule expansion. Additional examples are provided for a variety of complicated architectures to illustrate both the generality and the simplicity of the approach.
A sensor-based navigation for a mobile robot using fuzzy logic and reinforcement learning (1995)

The proposed navigator consists of an avoidance behavior and goal-seeking behavior. Two behaviors are independently designed at the design stage and then combined them by a behavior selector at the running stage. A behavior selector using a bistable switching function chooses a behavior at each action step so that the mobile robot can go for the goal position without colliding with obstacles. Fuzzy logic maps the input fuzzy sets representing the mobile robot's state space determined by sensor readings to the output fuzzy sets representing the mobile robot's action space. Fuzzy rule bases are built through the reinforcement learning which requires simple evaluation data rather than thousands of input-output training data. Since the fuzzy rules for each behavior are learned through a reinforcement learning method, the fuzzy rule bases can be easily constructed for more complex environments. In order to find the mobile robot's present state, ultrasonic sensors mounted at the mobile robot are used. The effectiveness of the proposed method is verified by a series of simulations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Mutations affecting craniofacial development in zebrafish. (1996)

In a large-scale screen for mutations affecting embryogenesis in zebrafish, we identified 48 mutations in 34 genetic loci specifically affecting craniofacial development. Mutants were analyzed for abnormalities in the cartilaginous head skeleton. Further, the expression of marker genes was studied to investigate potential abnormalities in mutant rhombencephalon, neural crest, and pharyngeal endoderm. The results suggest that the identified mutations affect three distinct aspects of craniofacial development. In one group, mutations affect the overall pattern of the craniofacial skeleton, suggesting that the genes are involved in the specification of these elements. Another large group of mutations affects differentiation and morphogenesis of cartilage, and may provide insight into the genetic control of chondrogenesis. The last group of mutations leads to the abnormal arrangement of skeletal elements and may uncover important tissue-tissue interactions underlying jaw development.
Design and synthesis of new ruthenium-based catalysts for improved activity in challenging Z-selective metathesis reactions (2013)

Our group has recently reported a series of ruthenium-based metathesis catalysts that&#13;\ncontain a chelating NHC. These catalysts demonstrate high Z-selectivity in a variety of&#13;\nmetathesis reactions including cross metathesis, ring-closing metathesis and ring-opening&#13;\nmetathesis polymn. However, the substrate scope has so far been limited to relatively&#13;\nunhindered olefins. In order to probe the origin of this selectivity, a series of catalysts&#13;\nwith N-heterocyclic carbene (NHC) substituents of varying steric bulk were prepd. These&#13;\ncatalysts were subsequently examd. for improved reactivity in a range of olefins that&#13;\ncontain bulky substituents. In addn., the mechanism of the C-H-activation step in the&#13;\nsynthesis of such catalysts was probed through variation of the sterics and electronics of&#13;\nboth the adamantyl and aryl NHC substituents.
On Tweaking Luby-Rackoff Blockciphers. (2007)

Abstract. Tweakable blockciphers, first formalized by Liskov, Rivest, and Wagner [13], are blockciphers with an additional input, the tweak, which allows for variability. An open problem proposed by Liskov et al. is how to construct tweakable blockciphers without using a pre-existing blockcipher. This problem has yet to receive any significant study. There are many natural questions in this area: is it significantly more efficient to incorporate a tweak directly? How do direct constructions compare to existing techniques? Are these direct constructions optimal and for what levels of security? How large of a tweak can be securely added? In this work, we address these questions for Luby-Rackoff blockciphers. We show that tweakable blockciphers can be created directly from Feistel ciphers, and in some cases show that direct constructions of tweakable blockciphers are more efficient than previously known constructions. 1
Racial Differences in Trust and Regular Source of Patient Care, and Implications for Prostate Cancer Screening Utilization (2020)

Nonmedical factors may modify biological risk of prostate cancer and contribute to differential use of early detection, curative care, and ultimately greater racial disparities in prostate cancer (CaP) mortality. This study examines patients' usual source of care, continuity of care, and mistrust of physicians and their association with racial differences in CaP screening.
Dynamic and Thermal Properties of Aluminum Alloy A356/Silicon Carbide Hollow Particle Syntactic Foams (2014)

Aluminum alloy A356 matrix syntactic foams filled with SiC hollow particles (SiCHP) are studied in the present work. Two compositions of syntactic foams are studied for quasi-static and high strain rate compression. In addition, dynamic mechanical analysis is conducted to study the temperature dependent energy dissipation and damping capabilities of these materials. The thermal characterization includes study of the coefficient of thermal expansion (CTE). A356/SiCHP syntactic foams are not strain rate sensitive as the compressive strength displayed little variation between the tested strain rates of 0.001–2100 s−1. Microscopic analysis of the high strain rate compression tested specimens showed that the fracture is initiated by the failure of hollow particles at the onset of the plastic deformation region. This is followed by plastic deformation of the matrix material and further crushing of particles. The syntactic foams showed decrease in storage modulus with increasing temperature and the trend was nearly linear up to 500 °C. The alloy shows a similar behavior at low temperature but the decrease in storage modulus increases sharply over 375 °C. The loss modulus is very small for the tested materials because of lack of viscoelasticity in metallic materials. The trend in the loss modulus is opposite, where the matrix alloy has lower loss modulus than syntactic foams at low temperature. However, over 250 °C the matrix loss modulus starts to increase rapidly and attains a peak around 460 °C. Syntactic foams have higher damping parameter at low temperatures than the matrix alloy. Incorporation of SiCHP helps in decreasing CTE. Compared to the CTE of the matrix alloy, 23.4 × 10−6 °C−1, syntactic foams showed CTE values as low as 11.67 × 10−6 °C−1.
ChemInform Abstract: ASYMMETRIC HYDROGENATION BY CHIRAL AMINOPHOSPHINE‐PHOSPHINITE RHODIUM COMPLEXES (1982)

Abstract Aus den Aminoalkoholen (I) bzw. (IV) entstehen bei der Umsetzung mit Diphenylphosphorchlorid (II) in Gegenwart von Triethylamin die Komplexbildner (III) bzw. (V).
Sensing Using Coded Communications Signals (2022)

A key challenge for common waveforms for Integrated Sensing and Communications – widely regarded as a resource-efficient way to achieve high performance for both functionalities – lies in leveraging information-bearing channel-coded communications signal(s) (c.c.s) for sensing. In this paper, we investigate the range-Doppler sensing performance of c.c.s in multi-user interference-limited scenarios, and show that it is affected by sidelobes whose form depends on whether the c.c.s modulates a single-carrier or OFDM waveform. While uncoded signals give rise to asymptotically zero sidelobes due to the law of large numbers, it is not obvious that the same holds for c.c.s, as structured codes (e.g., linear block codes) induce dependence across codeword symbols. In this paper, we show that c.c.s also give rise to asymptotically zero sidelobes – for both single-carrier and OFDM waveforms – by deriving upper bounds for the tail probabilities of the sidelobe magnitudes that decay as <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\exp ( - O(\text {code rate} \times \text {block length}))$ </tex-math></inline-formula> . Consequently, for any code rate, c.c.s are effective sensing signals that are robust to multi-user interference at sufficiently large block lengths, with negligible difference in performance based on whether they modulate a single-carrier or OFDM waveform. We verify the latter implication through simulations, where we observe the sensing performance (i.e., the detection and false-alarm probabilities) of a QPSK-modulated c.c.s (code rate = 120/1024, block length = 1024 symbols) to match that of a comparable interference-free FMCW waveform even at high interference levels (SIR of −11dB), for both single-carrier and OFDM waveforms.
Untargeted metabolomic analysis of urine samples in the diagnosis of some inherited metabolic disorders (2014)

This study showed that untargeted metabolomics can be applied in the diagnosis of mild IMDs with less clear biochemical profiles.