gebhart/patrepeval huggingface dataset:
Predicting phenotype from patterns of annotation (2003)

We use decision trees to predict phenotypes associated with Saccharomyces cerevisiae genes on the basis of Gene Ontology (GO) functional annotations from the Saccharomyces Genome Database (SGD) and other phenotypic annotations from the Yeast Phenotype Catalog at the Munich Information Center for Protein Sequences (MIPS). We assess the methodology in three ways: (1) we use cross-validation on the phenotypic annotations listed in MIPS, and show ROC curves indicating the tradeoff between true-positive rate and false-positive rate; (2) we do a literature-search for 100 of the predicted gene-phenotype associations that are not listed in MIPS, and find evidence for 43 of them; (3) we use deletion strains to experimentally assess 61 predicted gene-phenotype associations not listed in MIPS; significantly more of these deletion strains show abnormal growth than would be expected by chance.
Virtual Thermocouple: A Non-Invasive Multipoint Product Temperature Measurement for Lyophilization (2021)

Abstract Monitoring product temperature during lyophilization is of critical importance, especially during the process development stage, as the final product may be jeopardized if its process temperature exceeds a threshold value. While conventional thermocouples can track product temperature, they are invasive and can significantly alter the freezing and drying behavior. In this work, a new methodology for non-invasive product temperature monitoring and drying behavior during the entire lyophilization process is proposed and experimentally validated. The method is based on a new flexible wireless multi-point temperature sensing probe that is attached to the outside of the vial. Combining the wirelessly-collected data with advanced multi-physics simulations allows the accurate extraction of the product temperature non-invasively.
Quantum limits for receiver sensitivity with coding (2004)

We connect the quantum limits for receiver sensitivity to the Shannon channel capacity and identify the corresponding quantum limits for direct-detection on-off keying modulation with forward error correction codes.
Pattern transfer of directed self-assembly patterns for CMOS device applications (2013)

A study on the optimization of etch transfer processes using 200-mm-scale production type plasma etch tools for circuit relevant patterning in the sub-30-nm pitch regime using directed self-assembly (DSA) line–space patterning is presented. This work focuses on etch stack selection and process tuning, such as plasma power, chuck temperature, and end point strategy, to improve critical dimension control, pattern fidelity, and process window. Results from DSA patterning of gate structures featuring a high-k dielectric, a metal nitride and poly Si gate electrode, and a SiN capping layer are also presented. These results further establish the viability of DSA pattern generation as a potential method for Complementary metal–oxide–semiconductor (CMOS) integrated circuit patterning beyond the 10-nm node.
Interlayer Exchange Coupling in Fe|MgO|Fe Magnetic Tunnel Junctions (2006)

Interlayer exchange coupling (IEC) in fully epitaxial Fe/MgO/Fe (001) tunnel junctions with wedge-shaped MgO layers is measured at room temperature from the unidirectional shift of the Kerr hysteresis loop. It is found that the IEC is antiferromagnetic for small MgO thickness but changes sign at 0.8 nm. Ab initio calculations of IEC show that this behavior can be explained by the presence of O vacancies in the MgO barrier which makes IEC antiferromagnetic for thin barriers. With increasing MgO thickness the resonance contribution to IEC from localized defect states is reduced resulting in the ferromagnetic coupling typical for perfect MgO barriers.
Ultra-compact high order ring resonator filters using submicron silicon photonic wires for on-chip optical interconnects (2007)

Ultra-compact 5(th) order ring resonator optical filters based on submicron silicon photonic wires are demonstrated. Out-of-band rejection ratio of 40dB, 1dB flat-top pass band of 310GHz with ripples smaller than 0.4dB, and insertion loss of only (1.8+/-0.5)dB at the center of the pass band are realized simultaneously, all within a footprint of 0.0007mm(2) on a silicon chip.
Practical Synthesis of a Highly Functionalized Thiazole Ketone. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Synthesis and Suzuki Reactions of N-Heterocyclic Carbene Difluoro(aryl)-boranes (2015)

Readily available NHC-arylboranes (NHC-BH2Ar) are converted in high yield to stable NHC-difluoro(aryl)boranes (NHC-BF2Ar) by treatment with 2 equiv of 1-chloromethyl-4-fluoro-1,4-diazonia-bicyclo[2.2.2]octane bis(tetrafluoroborate) (Selectfluor). In turn, the NHC-difluoro(aryl)boranes participate directly in Suzuki reactions under conditions previously used for anionic trifluoroborate salts. Accordingly, NHC-difluoroboranes are a new class of stable precursors for Suzuki reactions.
PPARδ is a ligand-dependent negative regulator of vitamin D3-induced monocyte differentiation (2008)

A number of reports indicate that peroxisome proliferator-activated receptor (PPAR) delta is involved in the molecular control of monocyte-macrophage differentiation. In this regard, the recent demonstration that PPARdelta is a primary response gene of 1alpha,25-dihydroxyvitamin D3 (VD), i.e. a powerful inducer of such process, allowed us to hypothesize the existence of a cross talk between PPARdelta and VD receptor pathways. To address this issue, we analyzed the effects promoted by stimulation with PPARdelta ligands and by overexpression of this nuclear receptor in monoblastic cell lines undergoing exposure to VD. The results obtained evidenced that, although promoting a weak differentiation effect by themselves, PPARdelta ligands efficiently co-operated with VD treatment. In spite of this, PPARdelta overexpression exerted a remarkable inhibitory effect on monocyte-macrophage differentiation induced by VD that was, at least partly, reverted by stimulation with a highly specific PPARdelta ligand. These data indicate that, although acting through a ligand-dependent modality, PPARdelta is a negative regulator of VD-mediated monocyte differentiation, allowing us to hypothesize a role of the investigated nuclear receptor in the differentiation block of M5 type (monoblastic) acute myeloid leukemias (AMLs). Bioinformatic analysis of a microarray database, containing the expression profiles of 285 AML cases, further supported this hypothesis demonstrating the existence of a subset of M5 type (monoblastic) AMLs that overexpress PPARdelta gene.
Robust algorithm for real-time route planning (2000)

Route planning for intelligent guidance and navigation systems is an extremely complex problem with both military and commercial applications. Standard route planning algorithms usually generate a minimum cost route based on a predetermined cost function. Unfortunately, such a solution may not represent a desirable route for various mission scenarios. We present a novel route planning approach to generate mission-adaptable routes in an accurate and efficient manner. The routes are computed in real-time and are able to take into account various mission constraints including: minimum route leg length, maximum turning angle, route distance constraint, and fixed approach vector to goal position.
iGSE-CD—An Electric-/Displacement-Field Related Steinmetz Model for Class II Multilayer Ceramic Capacitors Under Low-Frequency Large-Signal Excitation (2023)

Multilayer Ceramic Capacitors (MLCCs) are of paramount importance in electronics and ferroelectric Class II dielectrics enable outstanding energy-density values. However, the non-linear dielectric constant and associated low-frequency large-signal excitation losses of Class II MLCCs may cause critical overheating. A peak-charge based Steinmetz loss model entitled iGSE-C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</sub> is known in literature and allows to accurately calculate MLCC low-frequency large-signal excitation losses under various operating conditions including biased and non-sinusoidal excitation voltage waveforms. Such a macroscopic iGSE-C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Q</sub> model, however, is inherently limited to a specific MLCC, and in contrast to Steinmetz loss modeling for ferromagnetic inductor cores, the losses of other devices employing the same dielectric material cannot be predicted. Recent literature therefore proposed a microscopic and/or material specific MLCC Steinmetz Model entitled iGSE-C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</sub> which allows to calculate the losses of any MLCC of the same dielectric material based upon just a single set of Steinmetz parameters. However, due to the lack of information on the internal device geometry, the iGSE-C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</sub> could be verified only indirectly so far by means of a loss normalization based on the device capacitance and rated voltage. In this paper, we demonstrate the feasibility of a microscopic iGSE-C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</sub> MLCC loss model enabled by manufacturer data on the internal capacitor structure. The iGSE-C <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</sub> is verified for two different MLCC series employing a conventional X7R dielectric and a novel Hiteca (with reduced non-linearity) Class II dielectric material with loss estimation error below 22%. This error results due to component tolerances and is acceptable, especially when compared to the loss calculation based on the datasheet information which can be off by up to a factor of ten. The analysis of the Hiteca dielectric reveals a frequency behavior different to the X7R material, and is discussed in the Appendix of this paper.
Non-volatile chirality switching by all-optical magnetization reversal in ferromagnetic Weyl semimetal Co3Sn2S2 (2022)

Abstract Weyl semimetals show unique physical properties exemplified by the colossal anomalous Hall effect, arising from exotic quasiparticles called Weyl fermions emerging around the Weyl nodes. Manipulating these topologically protected Weyl nodes is anticipated to play a leading role towards the on-demand control of quantum properties in Weyl semimetals. We demonstrate non-volatile chirality switching in a ferromagnetic Weyl semimetal Co 3 Sn 2 S 2 via all-optical magnetization reversal. When excited by circularly polarized mid-infrared light pulses, the sign reversal of the anomalous Hall conductivity stemming from the Berry curvature is observed, manifesting the switching of the chirality of the Weyl nodes accompanying with the magnetization reversal. Magneto-optical imaging measurements reveal that the mechanism of the magnetization/chirality switching is attributed to the helicity-dependent deterministic magnetization associated with the magnetic circular dichroism.
Contribution of domain 30 of tropoelastin to elastic fiber formation and material elasticity (2016)

Elastin is a fibrous structural protein of the extracellular matrix that provides reversible elastic recoil to vertebrate tissues such as arterial vessels, lung, and skin. The elastin monomer, tropoelastin, contains a large proportion of intrinsically disordered and flexible hydrophobic sequences that collectively are responsible for the initial phase separation of monomers during assembly, and are essential for driving elastic recoil. While structural disorder of hydrophobic sequences is controlled by a high proline and glycine residue composition, hydrophobic domain 30 of human tropoelastin is atypically proline-poor, and forms β-sheet amyloid-like fibrils as an individual peptide. We explored the contribution of confined regions of secondary structure at the location of domain 30 in human tropoelastin to fiber assembly and mechanical properties using a set of mutations designed to inhibit or enhance the propensity of β-sheet formation at this location. Our data support a dual role for confined β-sheet secondary structure in domain 30 of tropoelastin in guiding the formation of fibers, and as a determinant of stiffness and viscoelastic properties of cross-linked materials. Together, these results suggest a mechanism for specificity in fiber assembly, and elucidate structure-function relationships for the rational design of elastomeric biomaterials with defined mechanical properties.
Diagnostics of a glow discharge used to produce hydrogenated amorphous-silicon films. Quarterly progress report, July 15, 1982-October 14, 1982 (1982)

A high resolution, magnetically confined electron gun ionizer has been constructed for use in conjunction with a mass spectrometer in order to detect neutral radicals produced in the a-Si:H deposition discharge. Measurements have been completed of electron collisional ionization of silane while the new ionizer and mass spectrometer system were evaluated to obtain cross sections in the threshold region for the dissociative ionization processes. (LEW)
Vanity fair (2008)

A recently proposed approach to address privacy concerns in storing web search querylogs is bundling logs of multiple users together. In this work we investigate privacy leaks that are possible even when querylogs from multiple users are bundled together, without any user or session identifiers. We begin by quantifying users' propensity to issue own-name vanity queries and geographically revealing queries. We show that these propensities interact badly with two forms of vulnerabilities in the bundling scheme. First, structural vulnerabilities arise due to properties of the heavy tail of the user search frequency distribution, or the distribution of locations that appear within a user's queries. These heavy tails may cause a user to appear visibly different from other users in the same bundle. Second, we demonstrate analytical vulnerabilities based on the ability to separate the queries in a bundle into threads corresponding to individual users. These vulnerabilities raise privacy issues suggesting that bundling must be handled with great care.
Personal microdevices for wide-area location via mobile gateways (2005)

Diverse social applications rely on remote location of personal devices: house arrest tracker systems, remote monitoring of alcoholic persons, child locator devices and remote protection of victims of domestic abuse are some examples. However, existing personal location devices either depend on a fixed station (a domestic gateway) -thus limiting user mobility-, or include a full cell phone -thus increasing weight, cost and power consumption-. In this demonstration, we present a new system we have developed for the Galician regional government (Spain) to track domestic abusers and their victims. It consists of two units, namely a personal low-cost light microdevice (bracelet in the sequel) and a commercial cell phone. The latter acts as a mobile gateway, which the bracelet accesses via a PAN. By doing so, we benefit from the advantages of the two previous approaches: the small size of bracelets for fixed gateways and the full mobility of those including a full cell phone. Wide-area location capability may reside either in the bracelet (as a GPS modem) or in the mobile gateway (either as a GPS modem or via core network-assisted location). If the bracelet leaves mobile gateway PAN range, the latter alerts the user and/or sends an alarm to a remote monitoring station.
A novel bandpass filter based on substrate integrated waveguide (2015)

Substrate integrated waveguides (SIWs) have been preferred over conventional micro-strip and coplanar transmission lines owing to their minimal conductor losses especially at millimeter-wave frequencies. These have been extensively used in different active and passive circuits (M. Bozzi, A. Georgiadis, IET, 5, 909–920, 2011). Different configurations of SIW-based filters have also been presented, including LTCC-based multilayered structures, and half-mode and ridged SIW filters. These typical SIW designs can suffer from size constraints or require complex fabrication procedures.
ALSUntangled #70: caffeine (2023)

ALSUntangled reviews alternative and off-label treatments for people living with amyotrophic lateral sclerosis (PALS). Here, we review caffeine which has plausible mechanisms for slowing ALS progression. However, pre-clinical studies are contradictory, and a large case series showed no relationship between caffeine intake and ALS progression rate. While low doses of caffeine are safe and inexpensive, higher doses can cause serious side effects. At this time, we cannot endorse caffeine as a treatment to slow ALS progression.
Conformal barriers by interfacial polymerization in contact with cells and tissue (1993)

Interfacial polymn. of photopolymerizable macromers for phys. barriers between cells, clusters of cells, and/or tissues is described. The process of interfacial polymn. on islets of Langerhans is presented. [on SciFinder (R)]
Molecular Design for Organic Nonlinear Optics:  Polarizability and Hyperpolarizabilities of Furan Homologues Investigated by Ab Initio Molecular Orbital Method (2000)

Static polarizabilities and hyperpolarizabilities have been calculated for the furan homologues including furan (C4H4O), thiophene (C4H4S), selenophene (C4H4Se), and tellurophene (C4H4Te), at the Hartree−Fock and various correlation levels by ab initio molecular orbital methods. The influence of substitution with heavy atoms on the molecular properties of the homologues was examined theoretically. In the calculations for molecules with Se and Te atoms, the contribution of core electrons in the atoms was estimated using effective core potential (ECP) methods. With the calculation for the thiophene molecule, effectiveness of the use of the ECP method was examined, and the ECP method was found to give the (hyper)polarizability values similar to those obtained considering all electrons for the molecule. The calculated results show that substitution of the heteroatom with heavy atoms systematically increases the individual components of the polarizability, α, and second hyperpolarizability, γ. On the other hand, this does not give systematic variations on the first hyperpolarizability, β. The variation of these values depending on the homologues was examined in terms of the perturbation expansion formula and was explained by the energy levels of the electronic excited states in the valence states. The second hyperpolarizability values calculated, including electron correlation effect, are well correlated with the observed electronic components of nonlinear optical susceptibilities, χ(3), obtained using optical Kerr effect experiments, which have been done in our laboratory. However, some discrepancy is observed between the theoretical and the experimental values for the homologues with heavier heteroatoms. Possible causes for the discrepancy are discussed in detail.
Thermodynamic Analysis of Hydride Vapor Phase Epitaxy of GaN (1998)

A thermodynamic analysis of hydride vapor phase epitaxy (HVPE) is described for GaN. The partial pressures of gaseous species in equilibrium with GaN are calculated for temperatures, input GaCl partial pressures, input V/III ratios and mole fractions of hydrogen relative to the inert gas atoms. It is shown that the deposition of GaN is significantly influenced by the hydrogen mole fraction in the carrier gas. The growth rate is discussed in comparison with the experimental data reported in the literature. It is shown that the growth rate of GaN grown using HVPE is thermodynamically controlled.
Obesity and Insulin Resistance According to Age in Newly Diagnosed Type 2 Diabetes Patients in Korea (2016)

Objectives With the rapid increase in the prevalence of diabetes, the age groups of diabetic patients are becoming diversified. This study will examine the degree of obesity, insulin resistance, and insulin secretion ability among patients first diagnosed with diabetes according to age and gender. Methods The subjects of this study included 616 patients who were first diagnosed with diabetes during a routine physical examination. This sample was obtained from a total of 28,075 adults aged 19 years and older who received the examination among 33,829 participants in the Korea National Health &amp;amp; Nutrition Examination Survey (KNHANES) from 2007–2010. The subjects were categorized by age into young age (age: 19 – 39 years), middle age (age: 40 – 59 years), and old age (age: 60 years and older). The degree of obesity was categorized according to body mass index (BMI) into normal weight (BMI: 18.5 ∼ 22.9), overweight (BMI: 23 ∼ 24.9), and obesity (BMI: 25 or above). Insulin resistance was evaluated by homeostatic model assessment of insulin resistance (HOMA-IR). Results It was found that 14.1% (n = 87) of a total of 616 subjects (324 men, 292 women) were in the young age group, 43.8% (n = 270) were in the middle age group, and 42.1% (n = 259) were in the old age group. In addition, 83.3% of men that were overweight or obesity were in the young age group, while 79.2% and 60.5% were in the middle age and old age groups, respectively. A total of 82.2% of women that were overweight or obesity were in the young age group, while 79.5% and 77% were in the middle age and old age groups, respectively. For men, the more obesity they were in all age groups, the higher their HOMA-IR. For women, the more obesity they were in the young age and middle age groups, the higher their HOMA-IR; however, women in the old age group showed the highest HOMA-IR when they were of normal weight. Conclusion Among diabetic patients first diagnosed with the disease in Korea, the youth population had the highest obesity rate. Insulin resistance increases as an individual's weight increases among those patients who are first diagnosed with diabetes; the only exception noted is for elderly women.
Development and validation of a high‐sensitivity assay for measuring p217+tau in plasma (2021)

The assay described here exhibits good technical performance and shows potential as a highly accurate peripheral biomarker for A or T status in AD and cognitively normal subjects.
Benchmarking Methodology for EVPN Multicasting (1998)

This document defines methodologies for benchmarking IGMP proxy
performance over EVPN-VXLAN. IGMP proxy over EVPN is defined in draft-
ietf-bess-evpn-igmp-mld-proxy-02, and is being deployed in data center
networks. Specifically this document defines the methodologies for
benchmarking IGMP proxy convergence, leave latency Scale,Core
isolation, high availability and longevity.