gebhart/patrepeval huggingface dataset:
Monolithic transformers in a five metal CMOS process (2003)

Four monolithic transformers and an inductor are fabricated in a 5 metal CMOS process with varying number of turns and metal thicknesses. The S-parameters are measured from 500 MHz to 5.5 GHz, and equivalent lumped element models are extracted to calculate the differential quality factor vs. frequency. The transformers demonstrated significantly higher quality factors peaking at higher frequencies compared to the inductor.
Assessing the Fidelity of Ancient DNA Sequences Amplified From Nuclear Genes (2005)

To date, the field of ancient DNA has relied almost exclusively on mitochondrial DNA (mtDNA) sequences. However, a number of recent studies have reported the successful recovery of ancient nuclear DNA (nuDNA) sequences, thereby allowing the characterization of genetic loci directly involved in phenotypic traits of extinct taxa. It is well documented that postmortem damage in ancient mtDNA can lead to the generation of artifactual sequences. However, as yet no one has thoroughly investigated the damage spectrum in ancient nuDNA. By comparing clone sequences from 23 fossil specimens, recovered from environments ranging from permafrost to desert, we demonstrate the presence of miscoding lesion damage in both the mtDNA and nuDNA, resulting in insertion of erroneous bases during amplification. Interestingly, no significant differences in the frequency of miscoding lesion damage are recorded between mtDNA and nuDNA despite great differences in cellular copy numbers. For both mtDNA and nuDNA, we find significant positive correlations between total sequence heterogeneity and the rates of type 1 transitions (adenine --> guanine and thymine --> cytosine) and type 2 transitions (cytosine --> thymine and guanine --> adenine), respectively. Type 2 transitions are by far the most dominant and increase relative to those of type 1 with damage load. The results suggest that the deamination of cytosine (and 5-methyl cytosine) to uracil (and thymine) is the main cause of miscoding lesions in both ancient mtDNA and nuDNA sequences. We argue that the problems presented by postmortem damage, as well as problems with contamination from exogenous sources of conserved nuclear genes, allelic variation, and the reliance on single nucleotide polymorphisms, call for great caution in studies relying on ancient nuDNA sequences.
Functionalization of OEP-Based Benzochlorins To Develop Carbohydrate-Conjugated Photosensitizers. Attempt To Target β-Galactoside-Recognized Proteins (2003)

meso-(2-Formylvinyl)octaethylporphyrin on reaction with cyanotrimethylsilane in the presence of various catalysts [copper triflate [Cu(OTf)(2)], indium triflate [In(OTf)(3)], or magnesium bromide diethyl etherate (MgBr(2).Et(2)O)] produced a mixture of the intermediate 3-hydroxy-3-cyanopropenoporphyrin, the corresponding trimethylsilyl ether derivative, and the unexpected propenochlorins. The yields of the reaction products were found to depend on the reaction conditions and the catalysts used. The intermediate porphyrins on treatment with concentrated sulfuric acid yielded the free-base cyanobenzochlorins in major quantity along with several other novel benzochlorins as minor products. Reduction of ethyl-3-hydroxy-1-pentenoate-porphyrin with DIBAL-H/NaBH(4) and subsequent acid treatment provided the corresponding free-base 10(3)-(2-hydroxyethyl)benzochlorin, which upon a sequence of reactions gave a free-base benzochlorin bearing a carboxylic acid functionality in good yield. It was then condensed with a variety of carbohydrates (glucosamine, galactosamine, and lactosamine), and the related conjugates were screened using the galectin-binding-ability assay. Among the carbohydrate conjugates investigated, the lactose and galactose analogues displayed the galectin-binding ability with an enhancement of about 300-400-fold compared to lactose. In preliminary studies, all photosensitizers (with or without carbohydrate moieties) were found to be active in vitro [radiation-induced fibrosarcoma (RIF) tumor cells]. However, the cells incubated with lactose (known to bind to beta-galactoside-recognized proteins) prior to the addition of the photosensitizers containing the beta-galactose moiety (e.g., galactose and lactose) produced a 100% decrease in their photosensitizing efficacy. Under similar experimental conditions, benzochlorin without a beta-galactoside moiety or the related glucose conjugate did not show any inhibition in its photosensitizing efficacy. These results in combination with the galectin-binding data indicate a possible beta-galactoside-recognized protein specificity of the galactose- and lactose-benzochlorin conjugates.
Surface alignment of ferroelectric nematic liquid crystals (2021)

The success of nematic liquid crystals in displays and optical applications is due to the combination of their optical uniaxiality, fluidity, elasticity, responsiveness to electric fields and controllable coupling of the molecular orientation at the interface with solid surfaces. The discovery of a polar nematic phase opens new possibilities for liquid crystal-based applications, but also requires a new study of how this phase couples with surfaces. Here we explore the surface alignment of the ferroelectric nematic phase by testing different rubbed and unrubbed substrates that differ in coupling strength and anchoring orientation and find a variety of behaviors - in terms of nematic orientation, topological defects and electric field response - that are specific to the ferroelectric nematic phase and can be understood as a consequence of the polar symmetry breaking. In particular, we show that by using rubbed polymer surfaces it is easy to produce cells with a planar polar preferential alignment and that cell electrostatics (<i>e.g.</i> grounding the electrodes) has a remarkable effect on the overall homogeneity of the ferroelectric ordering.
ChucK: A Strongly Timed Computer Music Language (2015)

ChucK is a programming language designed for computer music. It aims to be expressive and straightforward to read and write with respect to time and concurrency, and to provide a platform for precise audio synthesis and analysis and for rapid experimentation in computer music. In particular, ChucK defines the notion of a strongly timed audio programming language, comprising a versatile time-based programming model that allows programmers to flexibly and precisely control the flow of time in code and use the keyword now as a time-aware control construct, and gives programmers the ability to use the timing mechanism to realize sample-accurate concurrent programming. Several case studies are presented that illustrate the workings, properties, and personality of the language. We also discuss applications of ChucK in laptop orchestras, computer music pedagogy, and mobile music instruments. Properties and affordances of the language and its future directions are outlined.
Supplementary Figures 1-6 from Combining Histone Deacetylase Inhibitor Vorinostat with Aurora Kinase Inhibitors Enhances Lymphoma Cell Killing with Repression of c-Myc, hTERT, and microRNA Levels (2023)

Supplementary Figures 1-6 from Combining Histone Deacetylase Inhibitor Vorinostat with Aurora Kinase Inhibitors Enhances Lymphoma Cell Killing with Repression of c-Myc, hTERT, and microRNA Levels
Benzosceptrins A and B with a Unique Benzocyclobutane Skeleton and Nagelamide S and T from Pacific Sponges (2009)

Four new dimeric pyrrole-2-aminoimidazole alkaloids have been isolated from the Pacific marine sponges &lt;i&gt;Agelas cf. mauritiana&lt;/i&gt; and &lt;i&gt;Phakellia&lt;/i&gt; sp. They include the unusual C2 symmetrical benzosceptrins A (&lt;b&gt;4&lt;/b&gt;) and B (&lt;b&gt;5&lt;/b&gt;), which each possess a unique benzocyclobutane skeleton and nagelamides S (&lt;b&gt;6&lt;/b&gt;) and T (&lt;b&gt;7&lt;/b&gt;). Their structures and relative configuration were elucidated from spectroscopic data. Plausible biogenetic paths for these compounds are also proposed in this paper.
Supplementary Figures 1-3 from A Small Molecule Disruptor of Rb/Raf-1 Interaction Inhibits Cell Proliferation, Angiogenesis, and Growth of Human Tumor Xenografts in Nude Mice (2023)

Supplementary Figures 1-3 from A Small Molecule Disruptor of Rb/Raf-1 Interaction Inhibits Cell Proliferation, Angiogenesis, and Growth of Human Tumor Xenografts in Nude Mice
ChemInform Abstract: THE α‐CYANO GROUP AS A SUBSTITUENT IN SOLVOLYSIS REACTIONS. AN EVALUATION OF INDUCTIVE DESTABILIZATION VS. MESOMERIC STABILIZATION OF CATIONS BY THE CYANO MOIETY (1980)

Abstract Entgegen der auf der Basis von Taft‐Substituentenkonstanten erwarteten erheblichen Verzögerung von über 10°C bei der Solvolyse von (Ib) in 2,2,2‐Trifluorethanol (bezogen auf (Ia)) wird nur eine Verzögerung von 3.5 ‐ 103 beobachtet.
Experimental Demonstration of a 100-Gbit/s 16-QAM Free-Space Optical Link Using a Structured Optical "Bottle Beam" to Circumvent Obstructions (2021)

We experimentally demonstrate a 100-Gbit/s 16-QAM free-space optical link using/tailoring an optical bottle beam to circumvent obstructions with different sizes and locations. Experimental results show ~10-dB less obstruction-induced power penalty compared to using a Gaussian beam for the obstruction with a diameter of ~4.5 mm.
Supplementary Dataset S1 from Expansion of a BDCA1<sup>+</sup>CD14<sup>+</sup> Myeloid Cell Population in Melanoma Patients May Attenuate the Efficacy of Dendritic Cell Vaccines (2023)

&lt;p&gt;The detailed composition of all gene sets used in GSEA.&lt;/p&gt;
A phage-linked immunoabsorbant system for the detection of pathologically relevant antigens. (1990)

This report describes a novel system for the immunological detection of immobilized antigen. The detection of herpes simplex virus (HSV) antigen was used as an example. Bacteriophage M13, containing the E. coli lac Z gene, was used as the "reporter" molecule in an immunoassay which is otherwise analogous to the enzyme-linked immunoabsorbant assay (ELISA). Briefly, HSV infected cells were incubated with a mouse monoclonal antibody specific for HSV antigen, followed by rabbit anti-mouse serum and mouse anti-M13 serum. Immune complexes were incubated with viable M13 phage. M13 binding was due to the presence of M13 antibodies, whose presence ultimately depended on the binding of monoclonal antibody to HSV. Phage was recovered by elution in pH = 11. Recovered phage was used to infect E. coli. M13 was quantitated by either plaque assay or by an assay for phage-induced beta-galactosidase activity in appropriate E. coli strains. The amount of M13 recovered was proportional to the number of HSV infected cells probed. Therefore, M13 served as a "bio-amplifiable tag" to antibody, as enzymes do in the ELISA. Since M13 is viable, its signal can be amplified by infection of susceptible bacteria, and the promise for an enormously sensitive immunoassay exists. The sensitivity of the assay described here is compared to the ELISA in the detection of HSV infection cells, as an example of the novel assay's potential. Significantly, the novel assay was more sensitive than the ELISA when samples were tested under identical circumstances. This technique is called the phage-linked immunoabsorbant assay (PHALISA), by analogy to the ELISA.
First Clinical Photon-counting Detector CT System: Technical Evaluation (2021)

Background The first clinical CT system to use photon-counting detector (PCD) technology has become available for patient care. Purpose To assess the technical performance of the PCD CT system with use of phantoms and representative participant examinations. Materials and Methods Institutional review board approval and written informed consent from four participants were obtained. Technical performance of a dual-source PCD CT system was measured for standard and high-spatial-resolution (HR) collimations. Noise power spectrum, modulation transfer function, section sensitivity profile, iodine CT number accuracy in virtual monoenergetic images (VMIs), and iodine concentration accuracy were measured. Four participants were enrolled (between May 2021 and August 2021) in this prospective study and scanned using similar or lower radiation doses as their respective clinical examinations performed on the same day using energy-integrating detector (EID) CT. Image quality and findings from the participants' PCD CT and EID CT examinations were compared. Results All standard technical performance measures met accreditation and regulatory requirements. Relative to filtered back-projection reconstructions, images from iterative reconstruction had lower noise magnitude but preserved noise power spectrum shape and peak frequency. Maximum in-plane spatial resolutions of 125 and 208 µm were measured for HR and standard PCD CT scans, respectively. Minimum values for section sensitivity profile full width at half maximum measurements were 0.34 mm (0.2-mm nominal section thickness) and 0.64 mm (0.4-mm nominal section thickness) for HR and standard PCD CT scans, respectively. In a 120-kV standard PCD CT scan of a 40-cm phantom, VMI iodine CT numbers had a mean percentage error of 5.7%, and iodine concentration had root mean squared error of 0.5 mg/cm<sup>3</sup>, similar to previously reported values for EID CT. VMIs, iodine maps, and virtual noncontrast images were created for a coronary CT angiogram acquired with 66-msec temporal resolution. Participant PCD CT images showed up to 47% lower noise and/or improved spatial resolution compared with EID CT. Conclusion Technical performance of clinical photon-counting detector (PCD) CT is improved relative to that of a current state-of-the-art CT system. The dual-source PCD geometry facilitated 66-msec temporal resolution multienergy cardiac imaging. Study participant images illustrated the effect of the improved technical performance. © RSNA, 2022 <i>Online supplemental material is available for this article.</i> See also the editorial by Willemink and Grist in this issue.
First measurement of the ${\mathbf{|\textit t|}}$-dependence of coherent $\mathbf{\rm{J/\psi}}$ photonuclear production (2021)

The first measurement of the dependence on $|t|$, the square of the momentum transferred between the incoming and outgoing target nucleus, of coherent J/$\psi$ photoproduction is presented. The data were measured with the ALICE detector in ultra-peripheral Pb-Pb collisions at a centre-of-mass energy per nucleon pair $\sqrt{s_{\rm NN}} = 5.02$ TeV with the J/$\psi$ produced in the central rapidity region $|y|<0.8$, which corresponds to the small Bjorken-$x$ range $(0.3-1.4)\times10^{-3}$. The measured $|t|$-dependence is not described by computations based only on the Pb nuclear form factor, while the photonuclear cross section is better reproduced by models including shadowing according to the leading-twist approximation, or gluon-saturation effects from the impact-parameter dependent Balitsky-Kovchegov equation. This new observable is therefore a valid tool to constrain the relevant model parameters and to investigate the transverse gluonic structure at very low Bjorken-$x$.
A Phase 3 Study to Evaluate ISIS-TTRRx in Patients with Transthyretin Familial Amyloid Polyneuropathy (TTR-FAP): Study Design and Baseline Demographics (S50.006) (2015)

Objective: A Phase 3 randomized, double-blind, placebo-controlled study to assess the efficacy and safety of ISIS-TTR Rx in patients with TTR-FAP is currently ongoing. ISIS-TTR Rx is an antisense oligonucleotide (ASO) inhibitor of TTR protein production. ISIS-TTR Rx binds to the TTR mRNA resulting in the degradation of the mRNA, thus preventing production of the TTR protein. ISIS-TTR Rx inhibits the production of wild-type TTR as well as all known TTR mutations. It is hypothesized that reduction of circulating levels of TTR (both wild-type and mutant) will slow or halt disease progression.
 Background: TTR-FAP is a rare hereditary disorder caused by mutations in the TTR protein which destabilize the liver derived TTR protein, causing it to dissociate and form fibril deposits in multiple tissues. The predominant clinical manifestation is a progressive sensorimotor and autonomic neuropathy. The worldwide prevalence of TTR-FAP has been estimated at approximately 10,000 patients.
 Design/Methods: The ongoing ISIS-TTR Rx Phase 3 study will enroll 195 patients randomized 2:1 to receive ISIS-TTR Rx or placebo for a period of 15 months. The study drug is administered once weekly as a single subcutaneous injection.
 Results: To date, subjects with 22 different TTR mutations have been enrolled. Approximately 70[percnt] of patients are Stage 1 and 30[percnt] are Stage 2, the average baseline NIS score is ~42 and roughly 2/3 of patients have been previously treated with either Tafamidis or Diflunisal. Approximately 1/2 of the enrolled patients have cardiomyopathy with a baseline LV wall thickness 蠅13 mm. Blinded safety analysis has shown ISIS-TTR Rx to be generally safe and well tolerated.
 Conclusions: An analysis of the baseline demographics for enrolled patients in the ISIS-TTR Rx Phase 3 study shows a well-balanced patient population with respect to the TTR mutation type, stage of disease, previous treatment with Tafamidis or Diflunisal, and cardiomyopathy involvement. Disclosure: Dr. Benson has nothing to disclose. Dr. Kincaid has received research support from CSL Beringer and Isis Pharmaceuticals. Dr. Ackerman has received personal compensation for activities with Isis Parmaceuticals, Inc. as an employee. Dr. Monia has received personal compensation for activities with Isis Pharmaceuticals, Inc. as an employee.
Cloning and Expression of a Novel NADP(H)-Dependent Daidzein Reductase, an Enzyme Involved in the Metabolism of Daidzein, from Equol-Producing Lactococcus Strain 20-92 (2010)

Equol is a metabolite produced from daidzein by enteric microflora, and it has attracted a great deal of attention because of its protective or ameliorative ability against several sex hormone-dependent diseases (e.g., menopausal disorder and lower bone density), which is more potent than that of other isoflavonoids. We purified a novel NADP(H)-dependent daidzein reductase (L-DZNR) from Lactococcus strain 20-92 (Lactococcus 20-92; S. Uchiyama, T. Ueno, and T. Suzuki, international patent WO2005/000042) that is involved in the metabolism of soy isoflavones and equol production and converts daidzein to dihydrodaidzein. Partial amino acid sequences were determined from purified L-DZNR, and the gene encoding L-DZNR was cloned. The nucleotide sequence of this gene consists of an open reading frame of 1,935 nucleotides, and the deduced amino acid sequence consists of 644 amino acids. L-DZNR contains two cofactor binding motifs and an 4Fe-4S cluster. It was further suggested that L-DZNR was an NAD(H)/NADP(H):flavin oxidoreductase belonging to the old yellow enzyme (OYE) family. Recombinant histidine-tagged L-DZNR was expressed in Escherichia coli. The recombinant protein converted daidzein to (S)-dihydrodaidzein with enantioselectivity. This is the first report of the isolation of an enzyme related to daidzein metabolism and equol production in enteric bacteria.
Accurate video-quality estimation without video decoding (2010)

This paper proposes a video-quality estimation method which does not need video decoding. It takes into account error-concealment effectiveness and the location of video-quality degradation to estimate video-quality from only packet-header information. Error-concealment effectiveness is evaluated on the basis of motion-level information estimated by the data-size of each frame. The quality-degraded location in a frame is evaluated by the transmission-error timing. Experimental results show that a high correlation coefficient of 0.853 with a lower outlier ratio is achieved with the proposed method. The method is suitable for a low-complexity video-quality monitoring system in IPTV services due to its accurate video-quality estimation without video decoding.
ChemInform Abstract: Synthesis of Tertiary sec‐Alkylamines by the Addition of Grignard Reagents to N,N‐Dialkylformamides Mediated by Ti(OiPr)4 and Me3SiCl. (2009)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Tunable Pulse Shape DUV Photocathode Laser for X-ray Free Electron Lasers at DESY (2021)

Modern X-ray Free Electron Lasers (XFEL) enable a variety of scientific applications [1] . For driving their electron gun photocathode, they require a robust deep ultraviolet (DUV) laser source. To enable the capability for generating both 1 ps electron bunches for few femtoseconds, single spike self-amplified stimulated emission (SASE) X-ray pulses and high charge 20 ps electron bunches for standard operation, we demonstrate a 257.5 nm photocathode laser with widely tunable output pulse durations. The schematic of the set-up is shown in Fig. 1 . The laser front-end consists of a pm-Yb-fiber oscillator and 3-stage amplifier, which generates a 20 mW, 1 MHz pulse train at 1030 nm center wavelength to seed a 4-stage Yb:YAG amplifier chain. An additional nonlinear Yb-fiber amplifier generates 100 mW, 150 fs for cross-correlation reference [2] . The Yb:YAG amplifier chain boosts the laser pulse energy to more than 180 µJ. The front-end contains an additional fiber stretcher and a programmable high-resolution spectral shaper for tuning the amplifier output spectrum. This allows after passing a fixed dispersion transmissive grating compressor to tune the NIR output pulse duration between 1 ps and 20 ps.
Supplementary Figure S7 from Caspase-8 Promotes Cell Motility and Calpain Activity under Nonapoptotic Conditions (2023)

Supplementary Figure S7 from Caspase-8 Promotes Cell Motility and Calpain Activity under Nonapoptotic Conditions
Microstructural Evidence of Reconstituted Limestone Blocks in the Great Pyramids of Egypt (2006)

How the Great Pyramids of Giza were built has remained an enduring mystery. In the mid‐1980s, Davidovits proposed that the pyramids were cast in situ using granular limestone aggregate and an alkali alumino‐silicate‐based binder. Hard evidence for this idea, however, remained elusive. Using primarily scanning and transmission electron microscopy, we compared a number of pyramid limestone samples with six different limestone samples from their vicinity. The pyramid samples contained microconstituents (μc's) with appreciable amounts of Si in combination with elements, such as Ca and Mg, in ratios that do not exist in any of the potential limestone sources. The intimate proximity of the μc's suggests that at some time these elements had been together in a solution. Furthermore, between the natural limestone aggregates, the μc's with chemistries reminiscent of calcite and dolomite—not known to hydrate in nature—were hydrated. The ubiquity of Si and the presence of submicron silica‐based spheres in some of the micrographs strongly suggest that the solution was basic. Transmission electron microscope confirmed that some of these Si‐containing μc's were either amorphous or nanocrystalline, which is consistent with a relatively rapid precipitation reaction. The sophistication and endurance of this ancient concrete technology is simply astounding.