gebhart/patrepeval huggingface dataset:
Mutation spectrum of congenital heart disease in a consanguineous Turkish population (2022)

Our WES screen of a Turkish consanguineous population with structural CHD revealed its unique genetic architecture. Six of seven damaging homozygous variants in CHD causal genes occur in the setting of laterality defects implies a strong contribution from consanguinity to these defects specifically. Our study thus provided valuable information about the genetic landscape of CHD in consanguineous families in Turkey.
The role of the visual system's orientation mechanisms in the perception of spatial aliasing (2004)

While visual models have been used for several decades to improve the perceived image quality of image processing algorithms and display design, the complexity of these visual models has been steadily increasing as progress is made in basic visual science. Beginning in the early 1990's applied visual models began to use not only a multiband approach in radial spatial frequency (e.g., the Laplacian pyramid) but also in orientation. At this point, the ability to predict the important effects of masking became more accurate. This paper will provide a close look at the role of these orientation bands in the application image scaling, which must balance the tradeoffs between sharpness, aliasing, and ringing, all acting in concert with the masking caused by the signal itself.
Advances in the computational and molecular understanding of the prostate cancer cell nucleus (2018)

Nuclear alterations are a hallmark of many types of cancers, including prostate cancer (PCa). Recent evidence shows that subvisual changes, ones that may not be visually perceptible to a pathologist, to the nucleus and its ultrastructural components can precede visual histopathological recognition of cancer. Alterations to nuclear features, such as nuclear size and shape, texture, and spatial architecture, reflect the complex molecular-level changes that occur during oncogenesis. Quantitative nuclear morphometry, a field that uses computational approaches to identify and quantify malignancy-induced nuclear changes, can enable a detailed and objective analysis of the PCa cell nucleus. Recent advances in machine learning-based approaches can now automatically mine data related to these changes to aid in the diagnosis, decision making, and prediction of PCa prognoses. In this review, we use PCa as a case study to connect the molecular-level mechanisms that underlie these nuclear changes to the machine learning computational approaches, bridging the gap between the clinical and computational understanding of PCa. First, we will discuss recent developments to our understanding of the molecular events that drive nuclear alterations in the context of PCa: the role of the nuclear matrix and lamina in size and shape changes, the role of 3-dimensional chromatin organization and epigenetic modifications in textural changes, and the role of the tumor microenvironment in altering nuclear spatial topology. We will then discuss the advances in the applications of machine learning algorithms to automatically segment nuclei in prostate histopathological images, extract nuclear features to aid in diagnostic decision making, and predict potential outcomes, such as biochemical recurrence and survival. Finally, we will discuss the challenges and opportunities associated with translation of the quantitative nuclear morphometry methodology into the clinical space. Ultimately, accurate identification and quantification of nuclear alterations can contribute to the field of nucleomics and has applications for computationally driven precision oncologic patient care.
Nanoscale flexible organic thin-film transistors (2022)

Direct-write electron-beam lithography has been used to fabricate low-voltage p-channel and n-channel organic thin-film transistors with channel lengths as small as 200 nm and gate-to-contact overlaps as small as 100 nm on glass and on flexible transparent polymeric substrates. The p-channel transistors have on/off current ratios as large as 4 × 10<sup>9</sup> and subthreshold swings as small as 70 mV/decade, and the n-channel transistors have on/off ratios up to 10<sup>8</sup> and subthreshold swings as low as 80 mV/decade. These are the largest on/off current ratios reported to date for nanoscale organic transistors. Inverters based on two p-channel transistors with a channel length of 200 nm and gate-to-contact overlaps of 100 nm display characteristic switching-delay time constants between 80 and 40 ns at supply voltages between 1 and 2 V, corresponding to a supply voltage-normalized frequency of about 6 MHz/V. This is the highest voltage-normalized dynamic performance reported to date for organic transistors fabricated by maskless lithography.
Quasi-Molecular Ion (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Performance analysis of large scale MU-MIMO with optimal linear receivers (2012)

We consider the uplink of multicell multiuser MIMO (MU-MIMO) systems with very large antenna arrays at the base station (BS). We assume that the BS estimates the channel through uplink training, and then uses this channel estimate to detect the signals transmitted from a multiplicity of autonomous users in its cell. By taking the correlation between the channel estimate and the interference from other cells into account, we propose an optimal linear receiver (OLR) which maximizes the received signal-to-interference-plus-noise (SINR). Analytical approximations of the exact and lower bound on the achievable rate are then derived. The bound is very tight, especially at large number of BS antennas. We show that at low SINR, maximal ratio combing (MRC) receiver performs as well as OLR, however at high SINR, OLR outperforms MRC. Compared with the typical minimum mean-square error receiver, our proposed OLR improves systematically the system performance, especially when the interference is large.
Cross-linked human serum albumin dimer has the potential for use as a plasma-retaining agent for the fatty acid-conjugated antidiabetic drugs (2014)

The HSA dimer shows potential for use as a plasma-retaining agent for antidiabetic drugs due to its favourable pharmacokinetic properties.
Excitations in amorphous pyramidally bonded solids. II. Phonons (1978)

Phonon state densities are calculated for crystalline and amorphous As. The results indicate a strong analogy between the electronic $p$ states and the vibrational states. This isomorphism is used to derive relationships between the electronic and phonon coupling constants. The effects of topology upon the vibrational excitations in pyramidal solids are studied. A new model for infrared absorption is presented. The resulting spectra agree well with experimental measurements. Finally, inelastic neutron-structure factors are calculated and are used to interpret recent experimental results.
Metallorganic Chemical Vapor Deposition of Hafnium Silicate Thin Films Using a Dual Source Dimethyl-alkylamido Approach (2006)

A low-temperature metallorganic chemical vapor deposition process has been developed for the growth of hafnium silicate thin films for advanced gate dielectric applications. In this process, a metallorganic hafnium precursor, tetrakis(dimethylamino)hafnium, and a metallorganic silicon precursor, tris(dimethylamino)silicon, were employed, using as a co-reactant. Films were deposited at a substrate temperature in the range of . The films were subsequently annealed in oxygen and forming gas ambients to assess thermal stability. The resulting films were characterized by Auger electron spectroscopy to determine composition and X-ray diffraction to determine microstructure. Electrical test structures were fabricated with as-deposited and annealed hafnium silicate films, and C-V and J-V measurements were performed. As-deposited dielectric constant values ranging from 6.9 to 12.9 were achieved depending on processing conditions and resulting film composition. Leakage current density at flatband voltage minus for a thick as-deposited film was measured to be and was shown to decrease following an anneal. The performance of these hafnium silicate films was also compared to hafnium oxide films deposited using the same Hf precursor and oxidizer approach.
Abstract LB-174: A DNA hypermethylation module for the stem/progenitor cell signature of cancer (2011)

Abstract It has been firmly established that cancer gene expression partly mimics the gene expression signature in embryonic stem cells (ESC). Since most cancers arise in adult stem or progenitor cells, rather than ESC, we now compare cancer chromatin to both embryonic and adult cell renewal systems to understand the relationships between DNA hypermethylation, gene expression, and chromatin states. DNA hypermethylation at CpG island promoters of hundreds of genes, including classic tumor suppressors, is a major modulator of gene expression in human cancers. Past studies suggest ∼ 50% of these are frequently marked by polycomb complex (PcG) transcriptional repressors, but not DNA methylation, in embryonic stem cells (ESC). In ESC, PcG occupancy is predominantly in the context of “bivalent chromatin”, wherein the active transcription mark H3K4me3 and the repressive PcG mark H3K27me3 are simultaneously present. Genes so marked are in a low, but poised, transcription state important for stemness and self-renewal, characteristics shared with tumor cells. Using whole genome ChIP-seq and DNA methylation arrays, we find between 70 to 80% of genes with DNA hypermethylation in cancer have bivalent chromatin not only in ESC, but also in adult stem cells. For these genes, there appears to be an epigenetic switch in cancer wherein bivalent chromatin is replaced by DNA hypermethylation resulting in tighter repression of gene expression. Many of these DNA methylated cancer genes are constituents of the recently proposed “PRC module” of the “ESC cancer signature.” Our data suggest a “DNA methylation module” that recapitulates the “stem cell signature” and that DNA hypermethylation may be a key mechanism that confers cell-renewal and stemness to tumor cells. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr LB-174. doi:10.1158/1538-7445.AM2011-LB-174
Room temperature laser action from multiple bands in photoexcited GaN grown on a silicon substrate (2007)

Room temperature stimulated emission and laser action with well developed longitudinal optical modes from high-quality GaN films grown on silicon substrates by metal-organic chemical-vapor deposition are presented. Laser action with well developed Fabry-Pérot modes involving the A, B, and C bands was observed. Stimulated emission one exciton below the A band and the B band and one longitudinal optical phonon below the B band was also observed. The effective index of refraction during laser operation was measured to be 2.9.
Dichloromethane transformation over bifunctional PtFAU catalysts. Influence of the acidobasicity of the zeolite (2005)

The catalytic oxidation of dichloromethane (DCM) was investigated over PtNaX and PtNaY catalysts with different amounts and dispersions of Pt under the following conditions: fixed bed reactor, 1000 ppm of DCM in wet air, space velocity of 20,000 h –1 , temperature between 220 and 450 °C. It is shown that Pt has only a limited effect on DCM conversion but causes a significant change in the product composition; the only role of Pt is to oxidise formaldehyde resulting from DCM hydrolysis on the zeolite support. DCM hydrolysis was carried out over a series of FAU zeolites: NaX, LiY, NaY, KY, CsY and USHY. The hydrolysis rate was shown to increase significantly with the zeolite basicity. A general reaction mechanism is proposed involving mainly the transformation of DCM species adsorbed on acido (H + , alcaline cation) basic (zeolite, framework oxygens) sites into chloromethoxy then hydroxymethoxy species.
Chirp Monitoring and Fine Tuning System for Optical Pulses Based on Variable Dispersion Compensator and Peak Power Monitor (2012)

We developed a chirp monitoring and fine tuning system for chirp-free pulse generation by using a variable dispersion compensator and a peak power monitor. A correlation between the pulsewidth and the peak power was confirmed.
Optical phased array on silicon photonic platform (2013)

Large-scale optical phased arrays containing up to 64×64 nanoantennas are demonstrated on silicon photonic platform, representing the largest scale demonstrated to date. Active phase tuning is also realized for dynamic pattern generation.
Sex-Specific Cardiovascular Structure and Function in Heart Failure with Preserved Ejection Fraction (2014)

More pronounced diastolic dysfunction may contribute to the greater predisposition for HFpEF in women compared with men.
Efficient Few-Shot Fine-Tuning for Opinion Summarization (2022)

Abstractive summarization models are typically pre-trained on large amounts of generic texts, then fine-tuned on tens or hundreds of thousands of annotated samples. However, in opinion summarization, large annotated datasets of reviews paired with reference summaries are not available and would be expensive to create. This calls for fine-tuning methods robust to overfitting on small datasets. In addition, generically pre-trained models are often not accustomed to the specifics of customer reviews and, after fine-tuning, yield summaries with disfluencies and semantic mistakes. To address these problems, we utilize an efficient few-shot method based on adapters which, as we show, can easily store in-domain knowledge. Instead of fine-tuning the entire model, we add adapters and pretrain them in a task-specific way on a large corpus of unannotated customer reviews, using held-out reviews as pseudo summaries. Then, fine-tune the adapters on the small available human-annotated dataset. We show that this self-supervised adapter pre-training improves summary quality over standard fine-tuning by 2.0 and 1.3 ROUGE-L points on the Amazon and Yelp datasets, respectively. Finally, for summary personalization, we condition on aspect keyword queries, automatically created from generic datasets. In the same vein, we pre-train the adapters in a query-based manner on customer reviews and then fine-tune them on annotated datasets. This results in better-organized summary content reflected in improved coherence and fewer redundancies.
Effect of alumina incorporation on restricting grain growth of nanocrystalline tin(IV) oxide (2010)

Abstract In this project, nanocrystalline SnO2 powders were successfully prepared by (a) citrate sol-gel and (b) direct precipitation methods. Powders were characterized using thermal analysis techniques (DTA-TG-DSC), X-ray powder Diffraction (XRD), surface area (BET) and electrical conductivity measurements. XRD patterns showed the presence of the cassiterite structure. SnO2 particles, prepared through sol-gel method exhibit crystallite sizes in the range from 3.1 to 22.3 nm when the gel is heat treated at different temperatures up to 900°C. SnO2 nanocrystallites prepared by the precipitation method are comparatively larger in size. The higher specific surface area was obtained for the powder prepared using sol-gel method and the obtained average grain size (d) is relatively large compared with that of the average crystallite size. The powders show a semiconducting behavior with increasing temperature. The higher conductivity obtained for SnO2 prepared by sol-gel method can be attributed to their smaller average crystallite size. XRD of alumina doped powder exhibits finer particles than pure SnO2. TEM images showed that the particles are spherical in shape and consist of a core of SnO2 surrounded by a coating of alumina. The calculated surface area was found to decrease with temperature increases. Due to the effective role of Al2O3 additive as a grain growth inhibitor for the matrix grains, the observed surface area for the coated materials are predominantly higher than for the uncoated materials.
Description and characterization of the complex modes in a linear chain of gold nanospheres (2011)

In this paper, complex modes in a linear chain of gold nanospheres are analyzed, accounting for metal losses. Dispersion diagrams are computed for travelling modes with both longitudinal and transverse (with respect to the array axis) polarization states. The procedure outlined in this work allows for the description of single mode evolution varying frequency, thus the modal dispersion diagrams are composed by the superposition of all the different modes in the one dimensional array. Each nanoparticle is modeled as an electric dipole, by adopting the single dipole approximation, and the complex zeroes of the homogeneous equation characterizing the field in the periodic structure are computed. The Ewald method is employed to analytically continue the periodic Green's function into the complex spectral domain and to achieve rapid convergence. Full characterization of the modes is provided in terms of their direction of propagation (forward/backward), their guidance and radiation properties (bound/leaky), the position of their wavenumber on the Riemann sheet (proper/improper), and also in terms of their possible physical excitation in the structure by a source in proximity of the array or a defect (physical/nonphysical modes). Understanding the modes excitable in this kind of structures is essential for possible applications in which the linear chain can be employed, from near-field enhancement to SERS, and innovative sensors.
Photodynamic therapy using intra‐articular photofrin for murine MRSA arthritis: Biphasic light dose response for neutrophil‐mediated antibacterial effect (2011)

PDT for murine MRSA arthritis requires appropriate light dosimetry to simultaneously maximize bacterial killing and neutrophil accumulation into the infected site, while too little light does not kill sufficient bacteria and too much light kills neutrophils and damages host tissue as well as bacteria and allows bacteria to grow unimpeded by host defense.
A chiral organocatalytic polymer-based monolithic reactor (2014)

Radical copolymerisation of divinylbenzene and a properly modified enantiomerically pure imidazolidinone inside a stainless steel column in the presence of dodecanol and toluene as porogens afforded the first example of a chiral organocatalyst immobilized onto a monolithic reactor. Organocatalyzed cycloadditions between cyclopentadiene and cinnamic aldehyde were performed under continuous-flow conditions; by optimizing the experimental set up, excellent enantioselectivities (90% ee at 25 °C) and high productivities (higher than 330) were obtained, thus showing that a catalytic reactor may work efficiently to continuously produce enantiomerically enriched compounds. The same catalytic reactor was also employed to carry out three different stereoselective transformations in continuo, sequentially, inside the chiral column (Diels–Alder, 1,3-dipolar nitrone-olefin cycloaddition, and Friedel–Crafts alkylation); excellent results were obtained in the case of the former two reactions (up to 99% yield, 93% ee and 71% yield, 90% ee, at 25 °C, respectively). In addition to simplify the product recovery, the monolithic reactor performed better than the same supported organocatalyst in a stirred flask and could be kept working continuously for more than 8 days.
Two-Way Acoustic Telemetry for Completion Installation, Control, and Monitoring (2018)

Abstract Technological advances are enabling the completion phase of well construction to evolve from interpreting surface-measured pressure and load charts to more direct communication for determining downhole activity and wellbore conditions. Bi-directional acoustic telemetry provides a method for communicating with downhole tools in real-time, where commands can be given to trigger an operational activity in lieu of traditional mechanical means, such as dropping a ball and building pressure, and in addition receive feedback that the activity has occurred. While current completion methods have been successful using pressure and applied mechanical loads to actuate tools, there are certain scenarios where operations are difficult to execute and it can be challenging to confirm that a piece of equipment has functioned as desired. There are environmental conditions, such as high deviations and s-shaped wellbore geometry, which can be prohibitive to tasks such as getting an activating ball to gravitate to bottom and land on its seat. Using bi-directional acoustic telemetry can eliminate the need for these manual manipulations. The aforementioned scenario has long been an issue for wells requiring sand control where the completion design might dictate deploying screens into an openhole horizontal wellbore section, performing a gravel pack for wellbore stability, and reducing the production of fines. With the growth of Extended Reach Drilling (ERD), this problem has become more common. This paper discusses adoption of proven bi-directional acoustic telemetry as a method to reduce completion time and remove some of the uncertainty in completing a well. The signal can be transmitted through the drillpipe by use of repeaters that allow for communication to extended depths. When setting a packer, receipt of the command at the hydrostatically operated setting tool triggers the setting tool to function. As a result, the packer at the top of the lower completion sets and the screens become anchored at the desired location. Bi-directional communication allows for confirmation at the surface that the signal was received and the tool properly triggered. This telemetry can further be used during the gravel packing operations to get near real-time temperature and pressure readings from washpipe gauges housed within the screen assembly. The example documented in this paper is a novel method of deploying a gravel pack system with a bi-directional, acoustic through pipe telemetry within completion tools now in development. This method provides a platform for real-time control and monitoring in the completion environment.
Building voiceXML browsers with openVXI (2002)

The OpenVXI is a portable open source based toolkit that interprets the VoiceXML dialog markup language. It is designed to serve as a framework for system integrators and platform vendors who want to incorporate VoiceXML into their platform. A first version of the toolkit was released in the winter of 2001, with a second version released in September of 2001. A number of companies and individuals have adopted the toolkit for their platforms. In this paper we discuss the architecture of the toolkit, the architectural issues involved with implementing a framework for VoiceXML, performance results with the OpenVXI, and future directions for the toolkit.