gebhart/patrepeval huggingface dataset:
Structure of the Al-GaAs(110) interface from an energy-minimization approach (1982)

The structure of the Al-GaAs(110) interface at the initial stages of Al deposition has been studied. In this system, the adatom-substrate and the adatom-adatom interactions are not necessarily weak, and the interface region may be strongly perturbed. The pseudopotential-energy minimization method is ideally suited for determining the stable structure of such systems involving significant energy change, and this method is successfully applied to the Al-GaAs system in the present study. By the calculation of the chemisorption energy of the Al atom at different sites on the entire GaAs surface, an energy contour map is obtained for the first time. Favorable channels of migration of Al atoms on this map are identified, which suggests preferential surface diffusion along the Ga---As bonding chain direction. The calculated surface hopping diffusion is sufficiently high even at room temperature so that Al atoms frequently encounter and interact with other Al atoms to form Al clusters. The Al clusters are found to have lower free energy than chemisorbed Al atoms. Al atoms eventually replace substrate Ga atoms and form Al---As bonds in the interface region to minimize the energy of the system.
Long‐term ingestion of ammonium increases acetylglutamate and urea levels without affecting the amount of carbamoyl‐phosphate synthase (1988)

Rats were fed the following diets: standard (20% protein), high-protein (80%), protein-free, standard plus ammonium and protein-free plus ammonium for six weeks. The standard plus ammonium diet was prepared to contain ammonia equivalent to that supplied by the high-protein diet. Addition of ammonium acetate (20% by mass) to the 20% protein or protein-free diets results in 2.3- and 10-fold increases of urea excretion respectively, without increase of carbamoyl-phosphate synthase. Supplementation of the standard diet with ammonium increases the mitochondrial content of acetylglutamate from 830 to 1590 pmol/mg protein, and of the protein-free diet from 130 to 1040 pmol/mg. However, ingestion of ammonium did not increase the activity of acetylglutamate synthase. Therefore the efflux of acetylglutamate from mitochondria was determined. After 30 min at 37 degrees C liver mitochondria from rats on standard diet released 61% of the initial acetylglutamate while mitochondria from animals on standard plus ammonium diet released only 20%. These results indicate that ingestion of ammonium increases the content of acetylglutamate in rat liver by decreasing its efflux from mitochondria. This effect is similar to that produced in mice by a high protein diet [Morita et al. (1982) J. Biochem. (Tokyo) 91, 563-569]. However, while the high-protein diet increases carbamoylphosphate synthase content, the ammonium diet does not.
Mismatch Analysis of DTCs With an Improved BIST-TDC in 28-nm CMOS (2021)

Nonlinearity of a digital-to-time converter (DTC) is pivotal to spur performance in DTC-based all-digital phase-locked-loops (ADPLL). In this paper, we characterize and analyze the mismatch of cascaded-delay-unit DTCs. Through an improved built-in-self-test (BIST) time-to-digital converter (TDC) assisted with phase-to-frequency detector (PFD), a measurement system of sub-half-ps accuracy is constructed to conduct the characterization. Fabricated in 28-nm CMOS, the DTC transfer functions are measured, and mismatches are compared against Monte-Carlo simulation results. The integral nonlinearity (INL) results are compared against each other and converted to the in-band fractional spur level when the DTC would be deployed in the ADPLL. The BIST-TDC system thus characterizes the on-chip delays without expensive equipment or complex setup. The effectiveness of adding a PFD into the <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$\Delta \!\Sigma $ </tex-math></inline-formula> loop is validated. The entire BIST system consumes 0.6mW with a system self-calibration algorithm to tackle the analog blocks’ nonlinearities.
Comparison of dendrimer‐based macromolecular contrast agents for dynamic micro‐magnetic resonance lymphangiography (2003)

Few methods are currently available to visualize the entire lymphatic system. A method known as micro-magnetic resonance lymphangiography (MRL), which employs a dendrimer-based MRI contrast agent (PAMAM-G8) and a clinical-grade 1.5T MRI instrument, was recently developed for use in mice. In the present study, three dendrimer-based MRI contrast agents (PAMAM-G8, DAB-G5, and PAMAM-G4) with different pharmacokinetic characteristics were compared to determine the best reagent to visualize the lymphatic system under physiological or pathological conditions. In addition, two established MRI contrast agents (Gadomer-17 and Gd-[DTPA]-dimeglumine (Magnevist)) were used as control agents. In experiments with mice, most of the deep lymphatic system was visualized by micro-MRL with all agents except Gd-[DTPA]-dimeglumine. PAMAM-G8 was best for visualizing lymphatic vessels, whereas DAB-G5 was better for visualizing lymph nodes. PAMAM-G4 was intermediate in character between PAMAM-G8 and DAB-G5, except in exhibiting a low background signal (especially in the liver). The lymphatic system was not clearly visualized with Gd-[DTPA]-dimeglumine; however, the lymph nodes were visualized with Gadomer-17, although not as well as with dendrimer-based agents. In conclusion, DAB-G5 and PAMAM-G4 can be used to identify lymph nodes and lymphatic vessels, respectively. Their rapid excretion makes these compounds potentially attractive for human use.
Inhibition of thrombosis in melanoma allografts in mice by endogenous mast cell heparin (2003)

An unexplained paradox of malignant melanoma is the apparent failure of the blood within the tumor to clot despite the presence of multiple factors that should promote blood clotting. Here we present histochemical evidence that human and murine melanomas are extensively infiltrated by abundant mast cells. Because mast cells contain the natural anticoagulant heparin, the present studies were aimed at defining the role of mast cell heparin in preventing the blood from clotting within B16 melanoma grafts in C57BL/6 J mice. Mice bearing B16 melanoma grafts were treated with non-specific or specific inhibitors of mast cell heparin (protamine or heparinase, respectively). After the drug treatment there was histologic and functional evidence of selective thrombosis of the blood vessels within the protamine and heparinase treated melanoma grafts. A similar, high degree of thrombosis was also observed in B16 tumors grown in transgenic NDST-2 knockout mice bearing a targeted disruption in the gene coding for mast cell heparin synthesis. The tumors grown in the protamine-treated animals were significantly smaller than the tumors from control (untreated mice). By contrast, the tumors treated with heparinase or grown in the NDST-2 knockout mice were significantly larger than the tumors from control (untreated) mice. We conclude that the intrinsic procoagulant properties of malignant melanoma are neutralized in vivo by the anticoagulant properties of endogenous heparin produced by mast cells that naturally infiltrate the tumor. Our results also suggest that thrombosis and hemostasis within melanoma may play a complex role in modulating the growth of the tumor.
What works and what does not work in Alzheimer’s disease? From interventions on risk factors to anti‐amyloid trials (2020)

Alzheimer's disease (AD) is a progressive neurodegenerative disorder with no approved disease-modifying therapy (DMT). In this review, we summarize the various past approaches taken in an attempt to find treatments capable of altering the long-term course for individuals with AD, including: translating epidemiological observations into potential treatment options; seeking a single-treatment approach across the continuum of AD severity; utilizing biomarkers for assessing target engagement; using biomarkers as early surrogates of clinical efficacy; and enriching study populations to demonstrate adequate placebo decline during the limited duration of clinical trials. Although targeting the amyloid-β (Aβ) pathway has been central to the search for an effective DMT, to date, trials of anti-Aβ monoclonal antibodies have failed to consistently demonstrate significant clinical efficacy. Key learnings from these anti-Aβ trials, as well as the trials that came before them, have shifted the focus within clinical development programs to identifying target populations thought most likely to benefit from treatments (i.e., individuals at an earlier stage of disease). Other learnings include strategies to increase the likelihood of showing measurable improvements within the clinical trial setting by better predicting decline in placebo participants, as well as developing measures to quantify the needed treatment exposure (e.g., higher doses). Given the complexity associated with AD pathology and progression, treatments targeting non-amyloid AD pathologies in combination with anti-amyloid therapies may offer an alternative for the successful development of DMTs.
Personalized Federated Learning via Convex Clustering (2022)

We propose a parametric family of algorithms for personalized federated learning with locally convex user costs. The proposed framework is based on a generalization of convex clustering in which the differences between different users’ models are penalized via a sum-of-norms penalty, weighted by a penalty parameter λ. The proposed approach enables “automatic” model clustering, without prior knowledge of the hidden cluster structure, nor the number of clusters. Analytical bounds on the weight parameter, that lead to simultaneous personalization, generalization and automatic model clustering are provided. The solution to the formulated problem enables personalization, by providing different models across different clusters, and generalization, by providing models different than the per-user models computed in isolation. We then provide an efficient algorithm based on the Parallel Direction Method of Multipliers (PDMM) to solve the proposed formulation in a fed- erated server-users setting. Numerical experiments corroborate our findings. As an interesting byproduct, our results provide several generalizations to convex clustering.
Formulation of Percolating Thermal Underfill by Sequential Convective Gap Filling (2011)

In 3D chip stacks, heat dissipation through wiring layers and the bonding interface contributes to the total temperature gradient. The effective thermal impedance of micro solder-ball arrays filled with a poorly-conducting silica underfill can be as high as 30 K*mm2/W, three times the value of a thermal grease interface. Efforts to improve the underfill conductivity to 5 W/(m*K) are underway, which would translate into in a significant interface-resistance reduction. To achieve thermal conductivities &amp;gt;1 W/(m*K), alumina particles were introduced in capillary underfills at particle loadings above the percolation threshold, but at these loading levels the high viscosity of the resulting underfill no longer permits capillary filling. We propose a novel sequential gap-filling method. Particles are suspended in a carrier fluid at a low concentration (0.1 vol%). Using forced convection, the suspension is injected into the cavity formed between the IC dies by the C4 array. A filter element at the cavity outlet triggers particle accumulation in the cavity. The particles form a percolation network with an effective thermal conductivity of &amp;gt;1 W/(m*K). Next an evaporation step removes the carrier fluid, and the exposed pores between the particles are refilled with a particle-free adhesive using capillary forces. Finally, the matrix is cured at 65 °C. 10x10 mm2 standard and micro-C4 cavities (&amp;gt;30 μm) can be completely filled in 2 min at 0.2 bar, resulting in a homogeneous volumetric fill of 36%. Percolation was identified by SEM inspection. For the micro-C4 arrays filler particles of &amp;lt; 10 μm were used. Uniform particle filling is precluded because of the longer filling time due to the small pore sizes. Particle trapping sites are introduced to form local stacks that provide an additional drainage network to guarantee acceptable filling times. Effective thermal-conductivity values of the percolating thermal underfill method proposed here are reported.
Medical Treatment of Acromegaly (1978)

ade­ noma of the pituitary gland, causes morbidity and mortality in affected patients by both local and peripheral physical changes (1-7). First, GR-secreting ade­ nomas, like other tumors of the pituitary, cause compression of surrounding neural and bony structures, among which are the normal pituitary tissues, the sphenoid and cavernous sinuses, optic nerves, and third ventricle. Second, the excess secretion of GR in acromegaly can lead to changes in the peripheral tissues, which result in gross disfigurement of the face, hands, and other parts of the body; crippling arthritis; carpal tunnel syndromes; heart disease; hyper­ tension; lung disease; a number of dermal changes; and carbohydrate and lipid abnormalities. Obviously, patients with acromegaly require therapeutic
Storage and separation of methane and carbon dioxide using platinum- decorated activated carbons treated with ammonia (2021)

Abstract Activated carbon (AC) was treated with ammonia for nitrogen doping and then was further anchored with platinum nanoparticles through ultrasound-assisted impregnation method. Methane (CH 4 ) and carbon dioxide (CO 2 ) storage of the pristine and modified activated carbon were determined at ambient temperature. All the samples showed high storage capacities with preference towards carbon dioxide storage, which would be favorable for both energy and environmental applications. Ammonia treatment slightly improved the storage of both CH 4 and CO 2 for all the samples, which could be attributed to the little improvement in the micropore properties upon nitrogen doping. Platinum decoration had an opposite influence on both CH 4 and CO 2 storage, which might be due to the absence of metal encouraging storage mechanism such as gas dissociation or reconstruction on platinum’s surface in addition to the harmful effect of metal pore-blocking and higher density of metal particles.
Exploiting Adaptive Laboratory Evolution of Streptomyces clavuligerus for Antibiotic Discovery and Overproduction (2012)

Adaptation is normally viewed as the enemy of the antibiotic discovery and development process because adaptation among pathogens to antibiotic exposure leads to resistance. We present a method here that, in contrast, exploits the power of adaptation among antibiotic producers to accelerate the discovery of antibiotics. A competition‐based adaptive laboratory evolution scheme is presented whereby an antibiotic‐producing microorganism is competed against a target pathogen and serially passed over time until the producer evolves the ability to synthesize a chemical entity that inhibits growth of the pathogen. When multiple Streptomyces clavuligerus replicates were adaptively evolved against methicillin‐resistant Staphylococcus aureus N315 in this manner, a strain emerged that acquired the ability to constitutively produce holomycin. In contrast, no holomycin could be detected from the wild‐type strain. Moreover, genome re‐sequencing revealed that the evolved strain had lost pSCL4, a large 1.8 Mbp plasmid. This and other strains also acquired numerous single nucleotide polymorphisms, some of which are located within genes that have been shown to affect secondary metabolite biosynthesis. These results demonstrate that competition‐based adaptive laboratory evolution can constitute a platform to create mutants that overproduce known antibiotics and possibly to discover new compounds as well.
Disruption of Ini1 Leads to Peri-Implantation Lethality and Tumorigenesis in Mice (2001)

SNF5/INI1 is a component of the ATP-dependent chromatin remodeling enzyme family SWI/SNF. Germ line mutations of INI1 have been identified in children with brain and renal rhabdoid tumors, indicating that INI1 is a tumor suppressor. Here we report that disruption of Ini1 expression in mice results in early embryonic lethality. Ini1-null embryos die between 3.5 and 5.5 days postcoitum, and Ini1-null blastocysts fail to hatch, form the trophectoderm, or expand the inner cell mass when cultured in vitro. Furthermore, we report that approximately 15% of Ini1-heterozygous mice present with tumors, mostly undifferentiated or poorly differentiated sarcomas. Tumor formation is associated with a loss of heterozygocity at the Ini1 locus, characterizing Ini1 as a tumor suppressor in mice. Thus, Ini1 is essential for embryo viability and for repression of oncogenesis in the adult organism.
Improving Event Causality Recognition with Multiple Background Knowledge Sources Using Multi-Column Convolutional Neural Networks (2017)

We propose a method for recognizing such event causalities as "smoke cigarettes" → "die of lung cancer" using background knowledge taken from web texts as well as original sentences from which candidates for the causalities were extracted. We retrieve texts related to our event causality candidates from four billion web pages by three distinct methods, including a why-question answering system, and feed them to our multi-column convolutional neural networks. This allows us to identify the useful background knowledge scattered in web texts and effectively exploit the identified knowledge to recognize event causalities. We empirically show that the combination of our neural network architecture and background knowledge significantly improves average precision, while the previous state-of-the-art method gains just a small benefit from such background knowledge.
Electric field distribution in AlGaN/GaN high electron mobility transistors investigated by electroluminescence (2010)

Electric field distributions in AlGaN/GaN high electron mobility transistors have been assessed by studying electroluminescence and its spatial intensity distribution. Three gate architectures were compared: (i) standard gate, (ii) slant gate, and (iii) recessed slant gate with fluorination. It was found that differences in peak electric field strengths between devices, determined using electroluminescence, agreed well with simulations. However, recessed slant gate devices with fluorination exhibited a spread of electroluminescence intensity and therefore electric field distribution toward the drain contact by 0.2–0.3 μm which was not predicted by simulation. Implication of the disagreement between measured and simulated electric field distribution are discussed.
Tapped delay-line matched filtering using a high-contrast grating hollow-core waveguide (2011)

A tapped delay-line matched filter is designed using high-contrast grating hollow-core waveguides. Simulation results indicate a SNR gain of 18.24dB, which is ~83% of an idea matched filter, and a fabrication tolerance of ~ 75-nm.
Measurements of Blowdown Thrust Loading in Natural Gas Facilities (2019)

Abstract The thrust loading on a vertical blowdown stack during a natural gas blowdown was investigated using a combined experimental and modeling approach. A gravimetric vessel initially at 4000 kPa-g was blown down through two geometrically different stack assemblies. Thrust loads were measured using a dynamic weigh scale typically used for gravimetric calibration of gas flow meters. A one-dimensional (1D) compressible flow model, calibrated using the experimental data, revealed stagnation pressure losses at the entrance to the riser, resulting in lower thrust loads. A comparison between thrust loading obtained from the measurements and the 1D compressible flow model is presented. This work shows that the analytical flow model predicts the blowdown thrust loads within ±30%.
An exploration of sensorless manipulation (1988)

The use of motion strategies to eliminate uncertainty, without the use of sensors, is considered. The approach is demonstrated within the context of a simple method to orient planar objects. A randomly oriented object is dropped into a tray. When the tray is tilted, the object can slide into walls, along walls, and into corners, sometimes with the effect of reducing the number of possible orientations. For some objects a sequence of tilting operations exists that leaves the object's orientation completely determined. An automatic planner is described that constructs such a tilting program, using a simple model of the mechanics of sliding. The planner has been implemented, the resulting programs have been executed using a tray attached to an industrial manipulator, and sometimes the programs work. The authors explore the issue of sensorless manipulation, tray tilting in particular, within the context of a formal framework described by T. Lozano-Perez, M.T. Mason, and Rolf Taylor (1984). It is observed that sensorless motion strategies perform conditional actions using mechanical decisions in place of environmental inquiries.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Heterogeneously integrated 20 μm CW hybrid silicon lasers at room temperature (2015)

Here we experimentally demonstrate room temperature, continuous-wave (CW), 2.0 μm wavelength lasers heterogeneously integrated on silicon. Molecular wafer bonding of InP to Si is employed. These hybrid silicon lasers operate CW up to 35°C and emit up to 4.2 mW of single-facet CW power at room temperature. III-V tapers transfer light from a hybrid III-V/silicon optical mode into a Si waveguide mode. These lasers enable the realization of a number of sensing and detection applications in compact silicon photonic systems.
Inside Front Cover: Nanoscale Surface Morphology and Rectifying Behavior of a Bulk Single‐Crystal Organic Semiconductor (Adv. Mater. 12/2006) (2006)

Abstract Local surface measurements of rubrene single crystals reveal interesting insights on carrier‐transport mechanisms at the active interface of high‐performance field‐effect “air‐gap stamp” transistors, as reported by Fichou, Rogers, and co‐workers on p. 1552. Scanning tunneling microscopy (STM, tip shown schematically) images, combined with atomic force microscopy and X‐ray diffraction, reveal directly the position and orientation of individual molecules in the a–b plane. Local current–voltage curves recorded using STM in the dark and under illumination indicate a rectifying p‐type behavior.
T cell response to intact SARS-CoV-2 includes coronavirus cross-reactive and variant-specific components (2022)

SARS-CoV-2 provokes a brisk T cell response. Peptide-based studies exclude antigen processing and presentation biology and may influence T cell detection studies. To focus on responses to whole virus and complex antigens, we used intact SARS-CoV-2 and full-length proteins with DC to activate CD8 and CD4 T cells from convalescent persons. T cell receptor (TCR) sequencing showed partial repertoire preservation after expansion. Resultant CD8 T cells recognize SARS-CoV-2-infected respiratory cells, and CD4 T cells detect inactivated whole viral antigen. Specificity scans with proteome-covering protein/peptide arrays show that CD8 T cells are oligospecific per subject and that CD4 T cell breadth is higher. Some CD4 T cell lines enriched using SARS-CoV-2 cross-recognize whole seasonal coronavirus (sCoV) antigens, with protein, peptide, and HLA restriction validation. Conversely, recognition of some epitopes is eliminated for SARS-CoV-2 variants, including spike (S) epitopes in the alpha, beta, gamma, and delta variant lineages.