gebhart/patrepeval huggingface dataset:
A genome-wide scan for common alleles affecting risk for autism (2010)

Although autism spectrum disorders (ASDs) have a substantial genetic basis, most of the known genetic risk has been traced to rare variants, principally copy number variants (CNVs). To identify common risk variation, the Autism Genome Project (AGP) Consortium genotyped 1558 rigorously defined ASD families for 1 million single-nucleotide polymorphisms (SNPs) and analyzed these SNP genotypes for association with ASD. In one of four primary association analyses, the association signal for marker rs4141463, located within MACROD2, crossed the genome-wide association significance threshold of P < 5 × 10(-8). When a smaller replication sample was analyzed, the risk allele at rs4141463 was again over-transmitted; yet, consistent with the winner's curse, its effect size in the replication sample was much smaller; and, for the combined samples, the association signal barely fell below the P < 5 × 10(-8) threshold. Exploratory analyses of phenotypic subtypes yielded no significant associations after correction for multiple testing. They did, however, yield strong signals within several genes, KIAA0564, PLD5, POU6F2, ST8SIA2 and TAF1C.
1300 nm VCSELs with Integrated Optical Pump for High-Speed Fiber-Optic Communications (1999)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text V. Jayaraman, F. H. Peters, J. C. Geske, M. H. MacDougal, T. T. Char, T. Goodwin, D. Van Deusen, T. D. Lowes, M. H. Donhowe, T. J. Goodnough, S. P. Kilcoyne, and D. Welch, "1300 nm VCSELs with Integrated Optical Pump for High-Speed Fiber-Optic Communications," in Spatial Light Modulators and Intgrated Optoelectronic Arrays, OSA Technical Digest (Optica Publishing Group, 1999), paper SMD2. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Analysis of 3D and multiview extensions of the emerging HEVC standard (2012)

Standardization of a new set of 3D formats has been initiated with the goal of improving the coding of stereo and multiview video, and also facilitating the generation of multiview output needed for auto-stereoscopic displays. Part of this effort will develop 3D and multiview extensions of the emerging standard for High Efficiency Video Coding (HEVC). This paper outlines some of the key technologies and architectures being considered for standardization, and analyzes the viability, benefits and drawbacks of different codec designs.
Degradation of lignin β‐aryl ether units in Arabidopsis thaliana expressing LigD, LigF and LigG from Sphingomonas paucimobilis SYK‐6 (2016)

Lignin is a major polymer in the secondary plant cell wall and composed of hydrophobic interlinked hydroxyphenylpropanoid units. The presence of lignin hampers conversion of plant biomass into biofuels; plants with modified lignin are therefore being investigated for increased digestibility. The bacterium Sphingomonas paucimobilis produces lignin-degrading enzymes including LigD, LigF and LigG involved in cleaving the most abundant lignin interunit linkage, the β-aryl ether bond. In this study, we expressed the LigD, LigF and LigG (LigDFG) genes in Arabidopsis thaliana to introduce postlignification modifications into the lignin structure. The three enzymes were targeted to the secretory pathway. Phenolic metabolite profiling and 2D HSQC NMR of the transgenic lines showed an increase in oxidized guaiacyl and syringyl units without concomitant increase in oxidized β-aryl ether units, showing lignin bond cleavage. Saccharification yield increased significantly in transgenic lines expressing LigDFG, showing the applicability of our approach. Additional new information on substrate specificity of the LigDFG enzymes is also provided.
Different Spectral Signatures of Octapeptide 310- and α-Helices Revealed by Two-Dimensional Infrared Spectroscopy (2006)

Femtosecond two-dimensional infrared (2D IR) spectroscopy is applied to the amide I modes of the terminally protected homo-octapeptide Z-[L-(alphaMe)Val](8)-OtBu in CDCl(3), 2,2,2-trifluoroethanol (TFE), and 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) solutions to acquire 2D spectral signatures that distinguish between 3(10)- and alpha-helix structures. Suppression of diagonal peaks by controlling polarizations of IR pulses clearly reveals cross-peak patterns that are crucial for structural determination. A doublet feature is observed when the peptide ester forms a 3(10)-helix in CDCl(3) and TFE and when it is at the initial stage of 3(10)- to alpha-helix transition in HFIP. In contrast, the 2D IR spectrum shows a multiple peak pattern after the peptide ester has acidolyzed and become an alpha-helix in HFIP. Electronic circular dichroism spectra accompanying the acidolysis-driven conformational change are also reported. This is the first report on the experimental 2D IR signature of a 3(10)-helical peptide. These results, using a model octapeptide, demonstrate the powerful capability of 2D IR spectroscopy to discriminate between different helical structures.
Electroluminescence of 2,4-bis(4-(2′-thiophene-yl)phenyl)thiophene in organic light-emitting field-effect transistors (2005)

We succeeded in observing electroluminescence (EL) of 2,4-bis(4-(2′-thiophene-yl)phenyl)thio-phene (TPTPT) as an active layer in an organic field-effect transistor (OFET). In particular, an OFET with a short channel of dSD=0.8μm demonstrated higher EL efficiency than one with a much longer channel (dSD=9.8μm). We observed a maximum EL quantum efficiency (ηmax) of 6.4×10−3% in the short-channel-length device at an applied source-drain voltage of Vd=−100V and a gate voltage of Vg=−40V. From the OFET characteristics, although the TPTPT layer demonstrated typical p-type operation, the occurrence of EL clearly indicated simultaneous hole and electron injection from the source and drain electronics, respectively, under high Vd and Vg.
Supplementary Data from Targeting Superficial or Nodular Basal Cell Carcinoma with Topically Formulated Small Molecule Inhibitor of Smoothened (2023)

&lt;p&gt;Supplementary Materials and Methods; Supplementary Tables S1-S4.&lt;/p&gt;
Open versus Endoscopic Medial Orbital Decompression: Utilization, Cost, and Operating Room Time (2016)

In the study sample, endoscopic orbital decompression was performed in 22.9% of patients, with significant variation in surgical technique based on geography and indication. Procedures that used endoscopic compared with open decompression techniques had no significant difference in charge on bivariate analysis. The OR time for open procedures was shorter on bivariate but not on multivariate analysis. Further research is required regarding the relative effectiveness of open versus endoscopic surgical techniques for various indications.
Classification of Order-Disorder Transitions in Common Adsorbed Systems: Realization of the Four-State Potts Model (1977)

Order-disorder transitions on square, triangular, and honeycomb arrays are classified according to whether they can be continuous or must be first order by applying a criterion of Landau. In particular, the transitions to 2 \ifmmode\times\else\texttimes\fi{} 2 arrays on triangular and honeybomb lattices are predicted to be in the universality class of the four-state Potts model. A physical realization of this model, ${\mathrm{N}}_{2}$ on Kr-plated graphite, is proposed.
Texas Two-Step: A Framework for Optimal Multi-Input Single-Output Deconvolution (2007)

Multi-input single-output deconvolution (MISO-D) aims to extract a deblurred estimate of a target signal from several blurred and noisy observations. This paper develops a new two step framework--Texas Two-Step--to solve MISO-D problems with known blurs. Texas Two-Step first reduces the MISO-D problem to a related single-input single-output deconvolution (SISO-D) problem by invoking the concept of sufficient statistics (SSs) and then solves the simpler SISO-D problem using an appropriate technique. The two-step framework enables new MISO-D techniques (both optimal and suboptimal) based on the rich suite of existing SISO-D techniques. In fact, the properties of SSs imply that a MISO-D algorithm is mean-squared-error optimal if and only if it can be rearranged to conform to the Texas Two-Step framework. Using this insight, we construct new wavelet- and curvelet-based MISO-D algorithms with asymptotically optimal performance. Simulated and real data experiments verify that the framework is indeed effective.
20-Gb/s QPSK transmission over 10-km-long holey fiber using a wavelength tunable quantum dot light source in O-band (2015)

We successfully demonstrate 20-Gb/s quadrature phase-shift keying (QPSK) signal transmission. The transmission was carried out over endlessly single-mode holey fiber in the waveband of 1276.02–1304.26 nm, whose bandwidth of 5.09- THz is broader than the traditional C-band. A wavelength-tunable quantum dot (QD) laser with broad wavelength tunability helps realize bandwidth availability. A single InAs/InGaAs QD optical gainchip was grown using a sandwiched sub-nanometer separator technique in the wavelength of 1.3-&mu;m band. Using this gain chip, the QD light source has good wavelength stability, compactness and wavelength tunablility. The measured transmission results show bit error rates within a forward error correction limit of 2&times;10<sup>–3</sup> using intradyne coherent detection with offline digital signal processing. In this study, it is expected that abundant frequency resources such as the O-band are coherently enhanced by the use of a large number of wavelength channels by effectively using the QD- laser.
Solvent-Dependent Stereoselectivity of Bis-2-pyridone [4 + 4] Photocycloaddition Is Due to H-Bonded Dimers (1999)

[formula: see text] A solvent-dependent stereoselectivity found for intramolecular [4 + 4] photocycloaddition of tethered 2-pyridones is concentration dependent, indicating that a dimeric structure with four hydrogen bonds plays a critical role in the observed cis selectivity found for nonpolar solvents.
Evidence of protein-free homology recognition in magnetic bead force–extension experiments (2016)

Earlier theoretical studies have proposed that the homology-dependent pairing of large tracts of dsDNA may be due to physical interactions between homologous regions. Such interactions could contribute to the sequence-dependent pairing of chromosome regions that may occur in the presence or the absence of double-strand breaks. Several experiments have indicated the recognition of homologous sequences in pure electrolytic solutions without proteins. Here, we report single-molecule force experiments with a designed 60 kb long dsDNA construct; one end attached to a solid surface and the other end to a magnetic bead. The 60 kb constructs contain two 10 kb long homologous tracts oriented head to head, so that their sequences match if the two tracts fold on each other. The distance between the bead and the surface is measured as a function of the force applied to the bead. At low forces, the construct molecules extend substantially less than normal, control dsDNA, indicating the existence of preferential interaction between the homologous regions. The force increase causes no abrupt but continuous unfolding of the paired homologous regions. Simple semi-phenomenological models of the unfolding mechanics are proposed, and their predictions are compared with the data.
Supplementary Figure S5 from The CARMA3–Bcl10–MALT1 Signalosome Drives NFκB Activation and Promotes Aggressiveness in Angiotensin II Receptor–Positive Breast Cancer (2023)

&lt;p&gt;Role of Bcl10 in mediating cell migration and invasion of additional AGTR1+ breast cancer cell lines (Hs578T and Hs606T).&lt;/p&gt;
A Low Noise Chipset for Passive Millimeter Wave Imaging (2007)

Technology for passive millimeter wave imaging has been maturing over the last 4-5 years. One key piece of technology that will allow for large scale production is a low cost front-end receiver. We have developed a two chip solution that addresses this need at W-band. A four stage InP LNA with a pre-matched Sb-heterostructure diode provides a low noise equivalent temperature difference (NETD). Our fabricated chipset provides sensitivities of 10,000 mV/μW over a 22 GHz noise equivalent bandwidth and an NETD of 0.8 K. To our knowledge, this is the best performance to date of a two chip solution for a passive millimeter wave radiometer.
Photogeneration of High Pretilt Angles of Nematic Liquid Crystals by Non‐Polarized Light Irradiation of Azobenzene‐Containing Polymer Films (2004)

Abstract A vertical‐alignment (VA) cell of nematic liquid crystals (LCs) was prepared using photoirradiated thin films of a poly(methacrylate) with mesogenic moieties of 4‐trifluoromethoxyazobenzene as the side chains. Optical anisotropy was generated by oblique irradiation of the azobenzene‐containing polymer films with non‐polarized UV light, followed by annealing treatment to enhance the photodichroism, which displayed thermal stability. The combination of oblique exposure to non‐polarized UV light and subsequent annealing treatment brought about high pretilt angles of nematic LCs so that a photoaligned VA LC cell was fabricated. The photopatterned LC cell exhibited electro‐optical properties with excellent optical quality when a voltage was applied even after heating at 100 °C for several hours.
Notice of Violation of IEEE Publication Principles: Pedestrian detection and tracking through hierarchical clustering (2014)

Notice of Violation of IEEE Publication Principles <br><br>“Pedestrian Detection and Tracking through Hierarchical Clustering” <br>by Selva Raj K and R. Poovendran <br>in the Proceedings of the International Conference on Information Communication and Embedded Systems (ICICES), February 2014 <br><br>After careful and considered review of the content and authorship of this paper by a duly constituted expert committee, this paper has been found to be in violation of IEEE’s Publication Principles. <br><br>This paper is a duplication of the original text from the paper cited below. The original text was copied without attribution (including appropriate references to the original author(s) and/or paper title) and without permission. <br><br>Due to the nature of this violation, reasonable effort should be made to remove all past references to this paper, and future references should be made to the following article: <br><br>“Vision-Based Analysis of Small Groups in Pedestrian Crowds” <br>by Weina Ge, Robert T. Collins, and R. Barry Ruback <br>in the IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. 34, No. 5, May 2012<br><br> <br/> Building upon state-of-the-art algorithms for pedestrian detection and multi-object, and inspired by sociological models of human collective behavior, we automatically detect small roups of individuals who are traveling together. These groups are discovered by bottom-up hierarchical clustering using a generalized, symmetric Hausdorff distance defined with respect to pairwise proximity and velocity. We validate our results quantitatively and qualitatively on videos of real-world pedestrian scenes. Where human-coded ground truth is available, we find substantial statistical agreement between our results and the human-perceived small group structure of the crowd. Results from our automated crowd analysis also reveal interesting patterns governing the shape of pedestrian groups. These discoveries complement current research in crowd dynamics, and may provide insights to improve evacuation planning and real-time situation awareness during public disturbances.
Mirror-terminated Mach-Zehnder interferometer based on SiNOI slot and strip waveguides for sensing applications using visible light (2023)

In this work, a highly sensitive sensor based on silicon nitride (SiN) waveguide is proposed that can be used for gas sensing using visible light. The whole sensor waveguide uses a silicon dioxide (SiO 2 ) cladding while the sensing arm uses a fluidic cladding such as water. The proposed device is based on loop-mirror terminated (LMT) Mach-Zehnder interferometer (MZI), where the reference arm is exposed to the reference SiO 2 medium, while the sensing arm is exposed to the sensing medium leading to a change in the refractive index of the waveguide cladding. The sensor performance is overall optimized by optimizing the design performance of all the components of the structure one by one. The waveguide sensitivity of both strip and slot types is analyzed for gaseous medium in order to compare their sensitivities and select the dimensions of the waveguide that results in the highest device sensitivity. Transverse-electric (TE) polarization is considered in this study for strip waveguide, where a higher sensitivity is founded with respect to the transverse-magnetic (TM) polarization. The field confinement in the slot waveguide in the sensing region is investigated and verified with a mode solver, where the optimum dimensions are obtained using finite difference eigenmode and finite difference time domain solvers. With a sensing arm length of 150 μm only, the proposed sensor achieves a device sensitivity of about 1,320 nm/RIU and a figure-of-merit (FOM) as high as 641 RIU −1 at the wavelength of 650 nm, which is the highest reported FOM up to the author’s knowledge. Higher values of the FOM are possible by employing a longer sensing arm.
A potassium channel in the apical membrane of rabbit thick ascending limb of Henle's loop (1990)

We used the patch-clamp technique to study the activity of single potassium channels in the apical membrane of isolated thick ascending limbs of Henle's loop (TAL) of rabbit kidneys. In cell-attached patches with NaCl Ringer or high-K+ solution in the bath and 140 mM K+ in the pipette, an inwardly rectifying K+ channel was observed with an inward slope conductance of 22.0 +/- 0.5 pS and outward slope conductance of 10.2 +/- 0.3 pS at 22 degrees C (n = 15). The channel was highly selective for K+, with a calculated permeability ratio for K(+)-to-Na+ of 20:1 (n = 4). The open probability (Po) of the channel was 0.89 +/- 0.03 (n = 15) and was not voltage dependent. In inside-out patches with 140 mM K+ in both the bath and the pipette solutions, both Po and conductance of the channel were similar to that in cell-attached patches. Addition of 0.1 mM Ba2+ to the pipette solution reduced Po of the channel in a voltage-dependent manner. Lowering the pH of the bath solution from 7.4 to 6.9 or increasing Ca2+ concentration from 0 to 0.5 mM in inside-out patches did not alter either Po or conductance of the channel. Addition of 2 mM ATP to the bath solution completely inhibited channel activity. This ATP-induced inhibition was fully reversible and was found to be dependent on the ratio of ATP to ADP, since adding 1 mM ADP to the bath solution relieved the ATP-induced blockade. The property of this small-conductance K+ channel make it a likely candidate for recycling of K+ across the apical membrane of TAL of the rabbit kidney. ATP and ADP are possible intracellular regulators of the channel's activity.
Nucleotide Pyrophosphatase/Phosphodiesterase 1 Is Responsible for Degradation of Antisense Phosphorothioate Oligonucleotides (2007)

The rapid degradation of unmodified phosphodiester oligodeoxynucleotides (PO-oligos) by exo -and endonucleases limits their application as antisense constructs and requires the synthesis and use of modified oligonucleotides. Phosphorothioate analogs of oligonucleotides (PS-oligos) are much more stable against nucleolytic degradation than their unmodified counterparts, and this is one of the reasons for which they are a promising class of antisense oligonucleotides. However, PS-oligos also undergo slow hydrolysis by enzymes present in plasma. The oligonucleotide degradation proceeds mainly from the 3' -end, resulting in the formation of a typical ladder of shorter products and the release of the mononucleoside 5' -phosphorothioates. So far, little has been known concerning the molecular identity of the enzymes involved in the degradation of PS-oligos. We now identify the human plasma 3' -exonuclease responsible for their degradation as a soluble form of nucleotide pyrophosphatase/phosphodiesterase 1 (NPP1) (EC 3.1.4.1/EC 3.6.1.9), also known as the plasma cell differentiation antigen PC-1. We also show that adenosine or deoxyadenosine (alpha-thio)triphosphates can act as potent inhibitors of NPPs.
ChemInform Abstract: Semi‐Synthetic Squalestatins: Squalene Synthase Inhibition and Antifungal Activity. The SAR of C6 and C7 Modifications. (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Ellipsometric analysis of built-in electric fields in semiconductor heterostructures (1993)

Measurements of Franz–Keldysh (FK) effects in GaAs‐AlxGa1−xAs heterostructures by variable angle of incidence spectroscopic ellipsometry are reported. The measured FK effects are due to the built‐in band bending at the surface and heterointerfaces, with no externally applied bias or modulating voltage. The polarity of the FK line shape indicates whether the field is uniform or nonuniform (inhomogeneous) in the direction along the growth axis, while the linewidth is determined by the peak field strength. This information can be used to characterize the doping concentration in the AlxGa1−xAs layer.
<title>Statistical analysis of Terfenol-D material properties</title> (1997)

Modeling of magnetostrictive Terfenol-D transducer performance requires reliable data on functional trends of the magnetostrictive element's material properties under various operating conditions. A statistical study was designed to experimentally evaluate material properties of 50 Terfenol-D samples under varied mechanical loads, varied ac drive levels, magnetic bias and mechanical prestress typical of transducer applications. This approach is based on a low-signal, linear- magnetomechanical model of the test transducer, and electroacoustics theory. Statistical analysis is provided for the material properties: Young's modulus at constant applied magnetic field, linear coupling coefficient (or axial strain coefficient), magnetomechanical coupling factor, and magnetic permeability at constant strain. Functional relations between material properties and ac drive levels and loads are developed, and corresponding confidence intervals are assessed. The trends show the sensitivity of Terfenol-D material properties to the operating variables and highlight the importance of properly understanding the effects of operating conditions on transducer performance.