gebhart/patrepeval huggingface dataset:
Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance (2009)

This study illustrates the significance of using comparative genomics approaches to identify molecular elements unique to parasitic nematodes, which have adapted to a particular host organism and mode of existence during evolution. While the focus of this study was on nematodes, the approach has applicability to a wide range of other groups of organisms.
Data from Anti-CD30 diabody-drug conjugates with potent antitumor activity (2023)

&lt;div&gt;Abstract&lt;p&gt;Anti-CD30 diabodies were engineered with two cysteine mutations for site-specific drug conjugation in each chain of these homodimeric antibody fragments. Diabodies were conjugated with ∼4 equivalents of the anti-tubulin drugs, monomethyl auristatin E or F, via a protease-cleavable dipeptide linker, to create the conjugates, diabody-vcE4 and diabody-vcF4, respectively. Diabody conjugation had only minor (&lt;3-fold) effects on antigen binding. Diabody-vcF4 was potently cytotoxic against the antigen-positive cell lines, Karpas-299 (34 pmol/L IC&lt;sub&gt;50&lt;/sub&gt;) and L540cy (22 pmol/L IC&lt;sub&gt;50&lt;/sub&gt;), and was 8- and 21-fold more active than diabody-vcE4 against these cell lines, respectively. Clearance of diabody-vcF4 (99-134 mL/d/kg) was 5-fold slower than for the nonconjugated diabody in naive severe combined immunodeficient mice. Diabody-vcF4 had potent and dose-dependent antitumor activity against established Karpas-299 xenografts and gave durable complete responses at well-tolerated doses. Biodistribution experiments with diabody-[&lt;sup&gt;3&lt;/sup&gt;H]-vcF4 (0.72-7.2 mg/kg) in tumor-bearing mice showed a dose-dependent &lt;i&gt;increase&lt;/i&gt; in total auristatin accumulation in tumors (≤520 nmol/L) and &lt;i&gt;decrease&lt;/i&gt; in relative auristatin accumulation (≤8.1 %ID/g), with peak localization at 4 to 24 h after dosing. Diabody-vcF4 had ∼4-fold lower cytotoxic activity than the corresponding IgG1-vcF4 conjugate &lt;i&gt;in vitro&lt;/i&gt;. A similar potency difference was observed &lt;i&gt;in vivo&lt;/i&gt; despite 25- to 34-fold faster clearance of diabody-vcF4 than IgG1-vcF4. This may reflect that dose-escalated diabody-vcF4 can surpass IgG1-vcF4 in auristatin delivery to tumors, albeit with higher auristatin exposure to some organs including kidney and liver. Diabody-drug conjugates can have potent antitumor activity at well-tolerated doses and warrant further optimization for cancer therapy. [Mol Cancer Ther 2008;7(8):2486–97]&lt;/p&gt;&lt;/div&gt;
Characterizing advanced breast cancer heterogeneity and treatment resistance through serial biopsies and comprehensive analytics (2021)

Molecular heterogeneity in metastatic breast cancer presents multiple clinical challenges in accurately characterizing and treating the disease. Current diagnostic approaches offer limited ability to assess heterogeneity that exists among multiple metastatic lesions throughout the treatment course. We developed a precision oncology platform that combines serial biopsies, multi-omic analysis, longitudinal patient monitoring, and molecular tumor boards, with the goal of improving cancer management through enhanced understanding of the entire cancer ecosystem within each patient. We describe this integrative approach using comprehensive analytics generated from serial-biopsied lesions in a metastatic breast cancer patient. The serial biopsies identified remarkable heterogeneity among metastatic lesions that presented clinically as discordance in receptor status and genomic alterations with mixed treatment response. Based on our study, we highlight clinical scenarios, such as rapid progression or mixed response, that indicate consideration for repeat biopsies to evaluate intermetastatic heterogeneity (IMH), with the objective of refining targeted therapy. We present a framework for understanding the clinical significance of heterogeneity in breast cancer between metastatic lesions utilizing multi-omic analyses of serial biopsies and its implication for effective personalized treatment.
Effects of the diurnal distribution of carbohydrates and fat on the adipose tissue transcriptome in humans (2018)

We investigated effects of the diurnal distribution of carbohydrates and fat consumption on the subcutaneous adipose tissue (SAT) transcriptome in humans.
In situ verification of single-domain III-V on Si(100) growth via metal-organic vapor phase epitaxy (2008)

Reflectance anisotropy spectroscopy (RAS) was used in situ for the quantification of antiphase domains on surfaces of thin GaP films deposited onto Si(100) by metal-organic vapor phase epitaxy (MOVPE). The preparation of a single-domain GaP∕Si(100) surface was determined via the analysis of RAS peak intensities in reference to the well-known P-rich surface reconstruction of homoepitaxially grown GaP(100). Both preprocessed Si(100) substrates and MOVPE as-grown GaP∕Si(100) films were also characterized ex situ by atomic force microscopy to identify the formation of mono- and diatomic surface steps and to analyze of the domain distribution, respectively.
Sub 100-fs, 5.2-micron ZGP Parametric Amplifier Driven by a ps Ho:YAG Chirped Pulse Amplifier and its application to high harmonic generation (2016)

We demonstrate a sub-100-fs, 5.2-micrometer parametric amplifier driven by a ps 2.1-micrometer Ho:YAG chirped-pulse amplifier and its application to high harmonic generation. We also present a novel approach for further pulse compression.
Guidelines for Treatment of Hypertension in the Elderly. 2002 Revised Version. (2003)

(Hypertens Res 2003; 26: 1-36)
Glycogen depletion patterns during ice hockey performance. (1978)

Eight male varsity ice hockey players were studied during 4 hockey games to investigate the alteration in blood substrates and the depletion pattern of glycogen in the fibers of the vastus lateralis muscle. Venous blood was sampled before and after each period and biopsies were taken prior to and immediately following each game. Significant elevations (p less than 0.05) in blood glucose, lactate and plasma FFA occurred following each period with little difference shown between the periods. Muscle glycogen declined an average of 60%. The histochemically determined glycogen depletion pattern indicated utilization of Type I, IIA and IIB fibers, with the greatest depletion occurring in the Type I fibers. In spite of the differences between forwards and defensemen in the length and number of shifts, the blood substrate profile, amount and pattern of glycogen depletion were similar.
Solder Ball Joint Reliability with Electroless NI/PD/AU Plating-Influence of Electroless PD Deposition Reaction Process and Electroless PD Film Thickness (2017)

ABSTRACT On the solder ball joint reliability, the influence of electroless Pd deposition reaction process and Pd film thickness in electroless Ni/Pd/Au plating was examined. The solder ball joint reliability was evaluated by a high-speed solder ball shear test. Sn-3.0Ag-0.5Cu (SAC305) was used as the solder ball in this study. In the electroless Pd deposition on the electroless Ni film, deposition reaction processes involve replacement reaction and following reduction reaction. We considered that the solder joint reliability was influenced by Pd replacement reaction time and was excellent when replacement reaction time was short. On the basis of the solder joint reliability obtained after multiple reflow cycles and thermal aging, the optimum thickness of the Pd film was found to be 0.05–0.2 μm. The covering property of electroless Pd plating film on the electroless Ni plating film was also investigated. We found that an electroless Pd plating film with a thickness of 0.02 μm or more covered the electroless Ni plating film adequately, and the solder ball joint reliability in this case was better than that with electroless Ni/Au plating. We consider that the shape of the intermetallic compounds (IMCs) is one of the factors that influence the solder joint reliability after multiple reflow cycles. Consequently, we inferred that the high adhesion at the dendrite layers of IMCs/solder interface resulted in excellent solder ball joint reliability after the reflow cycles. We consider that the thickness of the IMCs is one of the factors that influence the solder joint reliability after thermal aging. In (Cu, Ni, Pd) 6 Sn 5 IMCs that contained trace amounts of Pd, the growth of the IMCs is prevented by Pd, resulting in excellent solder ball joint reliability after thermal aging.
Source-Based Nomenclature for Single-Strand Homopolymers and Copolymers (IUPAC Recommendations 2016) (2017)

IUPAC recommendations on source-based nomenclature for single-strand polymers have so far addressed its application mainly to copolymers, non-linear polymers and polymer assemblies, and within generic source-based nomenclature of polymers. In this document, rules are formulated for devising a satisfactory source-based name for a polymer, whether homopolymer or copolymer, which are as clear and rigorous as possible. Thus, the source-based system for naming polymers is presented in a totality that serves as a user-friendly alternative to the structure-based system of polymer nomenclature. In addition, because of their widespread and established use, recommendations for the use of traditional names of polymers are also elaborated.
Recent developments in solid-state dye-sensitized photovoltaic devices based on spiro-MeOTAD (2003)

The photovoltaic performance of solid-state dye-sensitized solar cells based on spiro-MeOTAD (2,2'7,7'-tetrakis(N,N-di-p-methoxyphenyl-amine)-9,9'-spirobifluorene) has been improved to 3.2% overall conversion efficiency under air mass AM 1.5 illumination by performing the dye adsorption in the presence of silver ions in the dye solution. Different spectroscopic methods, such as X-ray photoelectron, Fourier-transform infrared and UV-visible spectroscopy have been employed to scrutinize the impact of the silver on the dye-sensitized device. From spectroscopic evidence it is inferred that the silver binds to the sensitizer mainly via the amphidentate thiocyanate, allowing the formation of ligand-bridged dye complexes. The enhancement in overall device efficiency is a result of increased open circuit potential and short circuit current. The increased open circuit voltage was explained by the blocking of the dark current as a result of a closer packed dye layer and/or the partial formation of a dye double layer upon silver coordination. The increased short circuit current corresponds to the higher amount of ruthenium dye units adsorbed to the TiO 2 surface.
Effect of atrial natriuretic peptide on catecholamine release from human pheochromocytoma (1989)

The effect of synthetic alpha human atrial natriuretic peptide on catecholamine release from human pheochromocytomas was studied both in vivo and in vitro. Iv infusion of atrial natriuretic peptide at a rate of 0.1 microgram.kg-1.min-1 for 60 min into two normotensive patients with pheochromocytoma caused a small decrease in the mean blood pressure, increase in the heart rate, and marked increase in the plasma level of norepinephrine (2.08 to 6.83 nmol/l, and 1.15 to 2.83 nmol/l, respectively) compared with 0.60 +/- 0.10 to 1.19 +/- 0.20 nmol/l in normal subjects. Treatment with atrial natriuretic peptide also increased the plasma epinephrine level from 0.34 to 1.27 nmol/l, and from 0.67 to 0.79 nmol/l in the patients with pheochromocytoma, but not in the normal subjects (0.05 +/- 0.01 to 0.05 +/- 0.01 nmol/l). After removal of the tumour, the responses of the plasma norepinephrine and epinephrine to atrial natriuretic peptide infusion were normalized. There was no significant effect of 10(-8) to 10(-5) mol/l atrial natriuretic peptide on the basal release of catecholamines from isolated superfused pheochromocytoma tissue. Atrial natriuretic peptide (10(-7) mol/l) did not affect the increase in catecholamine release induced by glucagon (10(-5) mol/l). These results suggest that the exaggerated responses of plasma catecholamines to atrial natriuretic peptide in patients with pheochromocytoma may be due to a washout effect resulting from change in blood flow in the vessels feeding the tumour rather than increased sympathetic nerve activity induced by hypotension and hypovolemia. The results also suggest that atrial natriuretic peptide dose not have any direct action on pheochromocytoma tissue causing catecholamine release.
MoodLens (2016)

Using an outward-facing display mounted on eyeglasses, MoodLens seeks to help individuals express emotion who have lost the ability to speak or use facial muscles. MoodLens looks like normal eyeglasses when not in use and allows the wearer to experience eye contact normally. We collected data from non-disabled participants (i.e., potential conversation partners for the wearer) who viewed smiling, neutral and frowning emoticons on MoodLens accompanied by computerized speech. The emoticons were recognizable at conversational distances and altered the perceived emotional content of the speech significantly.
Mechanical properties of polymers containing fillers (1999)

The addition of fillers can significantly change the mechanical characteristics of a material. In this paper, a general, mechanistic model is established to determine the moduli, relaxation moduli, break strengths, and break strains for polymer films containing liquid and solid micro fillers. Based on rigorous continuum mechanics principles, this model considers the filler/filler interactions, incorporates the nonlinear synergistic effects of fillers, and provides accurate predictions in comparison with experimental data. The analytical model developed provides information that is not available or extremely difficult to obtain experimentally. The model can be applied to determine the filler/matrix adhesion and filler modulus using measured modulus of a filled polymer film (a filled polymer is a polymer containing fillers). It is found that the compression moduli of polymer films containing liquid fillers differ significantly from the tension moduli, especially when the volume fraction of the filler is high. The difference in compression and tension Young's moduli normalized by the tension Young's modulus is as high as 35%. The relative error in maximum pressure calculation during Hertzian contact caused by using the tension moduli is as high as 48%. The relaxation modulus of a filled polymer film is determined through inverse Laplace transforms of its composite modulus in the s-space. For a filled polymer film containing liquid phase fillers, a closed form solution for its relaxation modulus has been obtained. It is found that the composite relaxation modulus of the filled polymer is proportional to the relaxation modulus of the matrix polymer multiplied by a factor related to the volume fraction of the liquid filler. The break strength of the filled polymer is found to be proportional to the break strength of the polymer matrix material multiplied by a power function of the modulus ratio of filled polymer to polymer matrix, R. The break strain of the filled polymer is proportional to the break strain of the polymer matrix multiplied by a power function of 1/R. © 1999 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 37: 155–172, 1999
On the Cutting Edge: Simplified O(n) Planarity by Edge Addition (2004)

We present new O(n)-time methods for planar embedding and Kuratowski subgraph isolation that were inspired by the Booth-Lueker PQ-tree implementation of the Lempel-Even-Cederbaum vertex addition method. In this paper, we improve upon our conference proceedings formulation and upon the Shih-Hsu PC-tree, both of which perform comprehensive tests of planarity conditions embedding the edges from a vertex to its descendants in a ‘batch’ vertex addition operation. These tests are simpler than but analogous to the templating scheme of the PQ-tree. Instead, we take the edge to be the fundamental unit of addition to the partial embedding while preserving planarity. This eliminates the batch planarity condition testing in favor of a few localized decisions of a path traversal process, and it exploits the fact that subgraphs can become biconnected by adding a single edge. Our method is presented using only graph constructs, but our definition of external activity, path traversal process and theoretical analysis of correctness can be applied to optimize the PC-tree
Sweat chloride quantification using capillary electrophoresis (2018)

WynSep-CE is an accurate, fast, easy-to-use and an appropriate method for CF diagnosis.
Delamination mechanisms of thermal interface materials in organic packages during reflow and moisture soaking (2009)

A thermal interface material (TIM) is typically a compliant material with high thermal conductivity that is applied between a heat-generating chip and a heat spreader in an electronic package. For a high-conductivity polymeric TIM, the adhesion strength between the TIM and its mating interfaces is typically weak, making the TIM susceptible to degradation when subjected to environmental stresses. At typical chip operating temperatures which are below the curing temperature of the TIM, a compressive force acts on the TIM at the chip center due to the CTE mismatch between the die and the organic chip carrier. Conversely at high BGA(Ball Grid Array) or card-attach reflow temperatures, the TIM center is under tension and the TIM tends to either cohesively separate or adhesively separate from the interfaces. Also, during moisture soaking, such as 85C/85%RH, the organic chip carrier absorbs moisture and expands. The hygroscopic expansion of the organic chip carrier is of the same order of magnitude as the thermal expansion. This expansion reduces the compressive force acting on the TIM, and for certain package constructions, this can lead to degradation of thermal performance. In this paper, the delamination mechanism of a polymer-based thermal interface material in an organic package during reflow and moisture soaking is investigated. The in-situ deformation of the TIM bondline was measured by a digital image correlation (DIC) method on a cross-sectioned part. The TIM bondline deformation was also captured by a digital camera. The coefficients of thermal expansion and hygroscopic expansion for different organic materials were measured, and a finite element analysis of the hygroscopic expansion and TIM bondline deformation was conducted. The affect of T&H stress was analyzed using an equivalent CTE concept.
Task-aware Warping Factors in Mask-based Speech Enhancement (2021)

This paper proposes the use of two task-aware warping factors in mask-based speech enhancement (SE). One controls the balance between speech-maintenance and noise-removal in training phases, while the other controls the degree of enhancement applied to specific downstream tasks in testing phases. Our proposal is based on the observation that SE systems trained to improve speech quality often fail to improve other downstream tasks, such as automatic speaker verification (ASV) and automatic speech recognition (ASR), because they do not share the same objectives. It is easy to apply the proposed dual-warping factors approach to any mask-based SE method, and it allows a single SE base module to handle multiple tasks without task-dependent training. The effectiveness of our proposed approach has been confirmed on the SITW dataset for ASV evaluation and the LibriSpeech test-clean set for ASR and speech quality evaluations of 0-20dB. We show that different warping values are necessary in the testing phases for a single SE base module to achieve optimal performance w.r.t. the three tasks. With the use of task-aware warping factors, speech quality was improved by an 84.7&#x0025; PESQ increase, while ASV had a 22.4&#x0025; EER reduction, and ASR had a 52.2&#x0025; WER reduction, on 0dB speech. The effectiveness of the task-aware warping factors were also cross-validated on VoxCeleb-1 test set for ASV and LibriSpeech dev-clean set for ASR and quality evaluations. The proposed method is highly effective and easy to apply in practice.
Visualization of Thermal Flows in an Automotive Cabin with Volume Rendering Method (2001)

A predictive system of thermal flow with quick turnaround time in a passenger compartment has been developed. An efficient method based on the Cartesian mesh system was used to reduce the period of analysis. The computed temperature in an automotive cabin was visualized by volume rendering techniques using an RVSLIB software library developed by NEC. Consecutive images of the flow were converted into MPEG1 movies, which gave us an overall understanding of the flow. The visualization results indicate that the present system is capable to sufficiently predict the thermal environment in a vehicle cabin at early stage of vehicle development.
Supplemental Figure Legends from <i>KRAS</i> Genomic Status Predicts the Sensitivity of Ovarian Cancer Cells to Decitabine (2023)

&lt;p&gt;Supplemental Figure Legends&lt;/p&gt;
Hyperpolarization of amino acid precursors to neurotransmitters with parahydrogen induced polarization (2013)

Several important neurotransmitter precursors were hyperpolarized via homogeneous hydrogenation with parahydrogen. Polarization enhancement was achieved for (1)H and (13)C spins by several orders of magnitude compared to thermal spectra. Such large signal enhancements of these molecules could facilitate neurotransmitter studies.
Modeling of the terahertz response of metal-semiconductor-metal photodetectors (1999)

In this paper a two-dimensional ensemble Monte Carlo particle method is used to simulate the metal-semiconductor-metal (MSM) photodetector response in the terahertz range of signal frequencies. We consider planar MSM photodetectors consisting of a GaAs absorbing layer with a system of Schottky contacts made 'back-to-back' on the above layer. The model takes into account the features of the carrier energy spectra, mechanisms of their scattering and a self-consistent electric field. The intrinsic transient response triggered by an ultra-short light pulse is calculated. The MSM frequency response is calculated using the Fourier transform of the obtained temporal dependences. It is shown that due to velocity overshoot effect exhibited by the photoelectrons, the MSM photodetector reveals rather high response to terahertz signals even if the contact spacing is relatively large. The frequency response of the MSM photodetectors utilizing the photoelectron velocity overshoot effect is compared with that of the MSM photodetectors with ultra-short carrier lifetime.
Towards a lazier symbolic pathfinder (2014)

To explore the state space of programs with complex user-defined data structures, most symbolic execution engines use the lazy initialization algorithm. Symbolic Pathfinder (SPF) is the symbolic execution engine for the Java PathFinder (JPF) model checker; SPF too contains an implementation of the lazy initialization algorithm. A number of extensions to the original lazy initialization algorithm have since been published. One such extension is the lazier# algorithm which demonstrated dramatic performance gains over the other algorithms. There is, however, no open-source implementation of the lazier# algorithm available. This work is an implementation of the the lazier# algorithm within the Symbolic PathFinder framework. In addition, this work describes the implementation of two heap bounding techniques in SPF, namely k-bounding and n-bounding. The purpose of this paper is to discuss the nature of the improvements, implementation details, usage and performance test results.