gebhart/patrepeval huggingface dataset:
Core/Shell Approach to Dopant Incorporation and Shape Control in Colloidal Zinc Oxide Nanorods (2016)

Tunable aliovalent doping is critical to controlling the optoelectronic properties of semiconductor nanocrystal systems. However, unintentional dopant-induced shape evolution and kinetically limited doping reactions in low-temperature nanocrystal syntheses make it difficult to independently control shape and incorporate dopants in colloidal metal oxide nanocrystals. Here, we demonstrate a synthetic strategy for achieving simultaneous control of both nanorod shape and dopant concentration in colloidal zinc oxide nanorods. We show that this approach succeeds in doping zinc oxide nanorods using Group III dopants (indium or aluminum) in varying concentrations, and we quantify the effects of dopant incorporation on the structural, optical, and plasmonic properties of the nanorods. The synthesis of undoped zinc oxide nanorod templates and subsequent addition of dopant salts to the ongoing reaction enables both shape retention and dopant incorporation. Subsequent growth of an undoped shell on the nanorods incorporates surface segregated dopants with high efficiency. This “core/shell” doping strategy presents a general route to achieving controlled dopant incorporation and morphological retention in anisotropic metal oxide nanocrystal systems.
Thermal Expansion Behavior of SiCP/Aluminum Alloy Composites Fabricated by a Low-Pressure Infiltration Process (2004)

Thermal cycling test was carried out for 20 vol% and 40 vol% SiC particle/Al-4 mass%Cu alloy composites to evaluate the bonding strength of the SiC particle/matrix interface in PRMMC fabricated by a low-pressure infiltration process (LPI process). The SiC particles were distributed homogenously in the specimens and a reaction layer of less than 1 μm thickness was observed at the SiC particle/matrix interface before thermal cycling test. This reaction layer was identified as Al4C3 formed by the reaction between the alloy melt and SiC particle during infiltration. The θ phase, which might form a coherent interface with Al4C3, crystallized around the SiC particles through the Al4C3 layer. The coefficient of thermal expansion was hardly changed during thermal cycling for both the 20 vol% and 40 vol% SiC particle/Al-Cu composites. No significant change in the microstructure and no detachment at the SiC particle/matrix interface were observed after thermal cycling test. The interfacial structure consisting of SiC, Al4C3, θ phase and α-Al in order was considered to exhibit a strong bonding of SiC particles to the matrix. The Vickers microhardness measured on the SiC particles in the specimens having a strongly bound interface show hardness values with a small scatter, while those for the specimens having a weakly bound interface exhibit a large scatter in the hardness values. It is suggested that the bonding strength of the reinforcement particle/matrix interface could be evaluated qualitatively from the Vickers microhardness test.
Suppression of Grain Growth in Sol–Gel‐Derived Tin Dioxide Ultrathin Films (1996)

Tin dioxide thin films of various thicknesses up to 150 nm were prepared on quartz glass substrates from a sol solution of SnO 2 (particle size 3 nm) by a spin‐coating method and subjected to calcination at different temperatures up to 800°C for 30 min. The grain size of SnO 2 was found to be far smaller than those obtained from the SnO 2 sol‐derived powder under the same calcination conditions. The suppression of grain growth of SnO 2 was more conspicuous as the film thickness decreased so that in the thinnest film (20 nm thick) the SnO 2 grain size remained as small as 6 nm after calcination at 800°C. It is suggested that the SnO 2 grains in the ultrathin film deposited on the substrate are restrained from moving and coalescing with each other, resulting in the suppression of grain growth.
Single-Cell Transcriptome Analysis Reveals Gene Signatures Associated with T-cell Persistence Following Adoptive Cell Therapy (2019)

Adoptive cell therapy (ACT) using tumor-infiltrating lymphocytes (TIL) can mediate responses in some patients with metastatic epithelial cancer. Identifying gene signatures associated with successful ACT might enable the development of improved therapeutic approaches. The persistence of transferred T cells in the peripheral blood is one indication of clinical effectiveness, but many T-cell and host factors may influence T-cell persistence. To limit these variables, we previously studied a patient with metastatic colorectal cancer treated with polyclonal TILs targeting the <i>KRAS</i>(G12D) hotspot mutation, who experienced a partial response for 9 months. Three dominant clonotypes specifically recognizing KRAS(G12D) epitopes were identified, but we found that only two clonotypes persisted 40 days after ACT. Because of these findings, in this study, we performed the single-cell transcriptome analysis of the infused TILs. The analysis revealed a total of 472 genes that were differentially expressed between clonotypes 9.1-NP and 9.2-P single cells, and 528 genes between 9.1-NP and 10-P. Following these clonotypes in the peripheral blood after ACT, the gene expression patterns changed, but <i>IL7R, ITGB1, KLF2</i>, and <i>ZNF683</i> remained expressed in the persistent 9.2-P and 10-P cells, compared with the nonpersistent 9.1-NP cells. In addition, four autologous TILs, which were used for treatment but persisted poorly 1 month after ACT, did not express the gene profiles associated with persistence. These results suggest that certain TIL populations possess a unique gene expression profile that can lead to the persistence of T cells. Thus, this single-patient study provides insight into how to improve ACT for solid cancer.
Tmix (2006)

In order to perform realistic network simulations, one needs a traffic generator that is capable of generating realistic synthetic traffic in a closed-loop fashion that "looks like" traffic found on an actual network. We describe such a traffic generation system for the widely used ns-2 simulator. The system takes as input a packet header trace taken from a network link of interest. The trace is "reverse compiled" into a source-level characterization of each TCP connection present in the trace. The characterization, called a connection vector, is then used as input to an ns module called tmix that emulates the socket-level behavior of the source application that created the corresponding connection in the trace. This emulation faithfully reproduces the essential pattern of socket reads and writes that the original application performed without knowledge of what the original application actually was. When combined with a network path emulation component we have constructed called DelayBox , the resulting traffic generated in the simulation is statistically representative of the traffic measured on the real link. This approach to synthetic traffic generation allows one to automatically repro-duce in ns the full range of TCP connections found on an arbitrary link. Thus with our tools, researchers no longer need make arbitrary decisions on how traffic is generated in simulations and can instead easily generate TCP traffic that represents the use of a net-work by the full mix of applications measured on actual network links of interest. The method is evaluated by applying it to packet header traces taken from campus and wide-area networks and comparing the statistical properties of traffic on the measured links with traffic generated by tmix in ns .
The Pair Approach Applied to Kinetics in Restricted Geometries:  Strengths and Weaknesses of the Method (2003)

In the rapidly emerging field of nanotechnology, as well as in biology, where chemical reaction phenomena take place in systems with characteristic length scales ranging from micrometer to the nanometer range, understanding of chemical kinetics in restricted geometries is of increasing interest. In particular, there is a need to develop more accurate theoretical methods. We used a many-particle-density-function formalism (originally developed to study infinite systems) in its simplest form (pair approach) to study a two-species A + B → 0 reaction−diffusion model in a finite volume. For simplicity reasons, it is assumed that the geometry of the system is one-dimensional (1d) and closed into a ring to avoid boundary effects. The two types of initial conditions are studied with (i) equal initial number of A and B particles, N0,A = N0,B, and (ii) initial number of particles equal on average, 〈N0,A〉 = 〈N0,B〉. In both cases, it was assumed that the particles are well mixed in the initial state. It is found that the particle concentration decays exponentially for both types of initial conditions. In the case of the type ii initial condition, the results of the pair-like analytical model agrees qualitatively with computer experiments (Monte Carlo simulation), while less agreement was obtained for the type i initial condition, and the reasons for such behavior are discussed.
White X‐ray microdiffraction analysis of defects, strain and tilts in a free standing GaN film (2008)

Abstract A novel white‐beam microdiffraction analysis of defects, strains and tilts in a free standing m ‐plane GaN film grown via hydride vapor phase epitaxy is presented. It is shown that misfit dislocations are grouped within cell boundaries creating local lattice rotations (tilts) between the growing cells. Distribution of lattice rotations in the film is not homogeneous. Regions of large rotations are separated by low rotations regions. The dominating rotation axis is parallel [11 $ \bar 2 $ 0] direction. High in plane shear stress component is observed along [0001]. (© 2008 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Quantifying the thermal conductivity enhancement of percolating thermal underfills (2015)

A major limitation in high-power three-dimensional chip stacks is the heat removal of dissipated power. To this end, highly thermally conductive intra-stack bondlines are required. Percolating thermal underfills (PTUs), where densely packed micron-sized dielectric particles fill the open space resulting from the electrical interconnects between individual chips, are expected to improve the effective thermal conductivity within the chip stack. Even more so, the thermal performance of the layer is additionally enhanced by areal contacts between micron-sized features created by the self-assembly of nanoparticles. Accurate and precise thermal characterization of these underfill layers is required for appropriate electronic packaging design. In this paper, a technique is introduced to allow the thermal characterization on non-dense thin material layers, such as particles only. The effects of different material combinations are investigated, as well as processing influences. Ultimately the effects of dielectric nanoparticle neck contributions are determined, showing a 2.4-fold thermal conductivity increase for an appropriate mixture of large and small nanoparticles, compared to microparticles only. This constitutes a very significant improvement to state-of-the-art thermal underfill systems, which will enable more efficient electronic packaging designs and ultimately contribute to energy savings.
Self-limiting Deposition of N-(3-Trimethoxysilylpropyl)ethylenediaminetriacetic Acid for the Production of Aqueous-stable Iron Oxide Nanoparticles (2011)

Abstract This paper presents a novel self-limiting deposition of a carboxysilane functional group to the surface of maghemite iron oxide nanoparticles (IOP). Self-limited deposition of N-(3-trimethoxysilylpropyl)ethylenediaminetriacetic acid on iron oxide is achieved by rapid injection of the basic silane into acid-stabilized iron oxide. The instant pH shift from 2.3 to 11 through neutral promotes silane deposition on the iron oxide surface but is rapid enough to prevent aggregation and free condensation. Carboxysilane iron oxide particles (CSIOP) are rendered aqueous stable in all pH &amp;gt;5.95. Silane coating is characterized by FTIR, TEM, and DLS.
Toward correcting drift in target position during radiotherapy via computer‐controlled couch adjustments on a programmable Linac (2013)

This work illustrates the potential for reduction in baseline respiratory drift with periodic adjustments in couch position during treatment. Future treatment machine capabilities will enable the use of "on-the-fly" couch adjustments during treatment.
Stable cavitation in ultrasound image-guided high intensity focused ultrasound therapy (2007)

Microbubble activity is significantly involved in both diagnostic and therapeutic aspects of ultrasound image-guided HIFU therapy. Ultrasound interrogation techniques (A-, B-, M-mode, Doppler, harmonic and contrast imaging, and passive and active cavitation detection) were integrated with HIFU. Our results using HIFU devices of 1–5 MHz, and focal, derated intensities of 1,000–10,000 W/cm2, show the formation of microbubbles (about 100 bubbles/mm3, 5–100 microns in size) at the HIFU focus. Boiling, stable, and inertial acoustic cavitation activities were detected during therapy. The presence of bubbles allows the observation of the treatment spot as bright hyperechoic regions in ultrasound images, providing an effective method for guidance and monitoring of therapy. The stable cavitation of microbubbles may provide a mechanism for enhanced HIFU energy delivery, as well as induction of biological responses for stimulation and regulation of specific physiological events such as coagulum and thrombus formation for hemostasis applications, apoptotic activity in treating tumor margins, and stimulation of immune response. Stable cavitation of extrinsic bubbles (contrast agents) is used in detection and localization of internal occult bleeding, using harmonic imaging. There appears to be benefits in utilizing stable cavitation in both diagnostic and therapeutic objectives of ultrasound image-guided HIFU. Funding: DoD, NIH, NSBRI.
To Update or Not To Update?: Bandwidth-Efficient Intelligent Replacement\n Policies for DRAM Caches (2019)

This paper investigates intelligent replacement policies for improving the\nhit-rate of gigascale DRAM caches. Cache replacement policies are commonly used\nto improve the hit-rate of on-chip caches. The most effective replacement\npolicies often require the cache to track per-line reuse state to inform their\ndecision. A fundamental challenge on DRAM caches, however, is that stateful\npolicies would require significant bandwidth to maintain per-line DRAM cache\nstate. As such, DRAM cache replacement policies have primarily been stateless\npolicies, such as always-install or probabilistic bypass. Unfortunately, we\nfind that stateless policies are often too coarse-grain and become ineffective\nat the size and associativity of DRAM caches. Ideally, we want a replacement\npolicy that can obtain the hit-rate benefits of stateful replacement policies,\nbut keep the bandwidth-efficiency of stateless policies.\n In our study, we find that tracking per-line reuse state can enable an\neffective replacement policy that can mitigate common thrashing patterns seen\nin gigascale caches. We propose a stateful replacement/bypass policy called\nRRIP Age-On-Bypass (RRIP-AOB), that tracks reuse state for high-reuse lines,\nprotects such lines by bypassing other lines, and Ages the state On cache\nBypass. Unfortunately, such a stateful technique requires significant bandwidth\nto update state. To this end, we propose Efficient Tracking of Reuse (ETR). ETR\nmakes state tracking efficient by accurately tracking the state of only one\nline from a region, and using the state of that line to guide the replacement\ndecisions for other lines in that region. ETR reduces the bandwidth for\ntracking replacement state by 70%, and makes stateful policies practical for\nDRAM caches. Our evaluations with a 2GB DRAM cache, show that our RRIP-AOB and\nETR techniques provide 18% speedup while needing less than 1KB of SRAM.\n
Synchronous Vector TAG for Syntax and Semantics: Control Verbs, Relative Clauses, and Inverse Linking (2008)

Recent work has used the synchronous tree-adjoining grammar (STAG) formalism to demonstrate that many of the cases in which syntactic and semantic derivations appeared to be divergent could be handled elegantly through synchronization. This research has provided syntax and semantics for diverse and complex linguistic phenomena. However, certain hard cases push the STAG formalism to its limits, requiring awkward analyses or leaving no clear solution at all. In this paper a new variant of STAG, synchronous vector TAG (SV-TAG), and demonstrate that it has the potential to handle hard cases such as control verbs, relative clauses, and inverse linking, while maintaining the simplicity of previous STAG syntax-semantics analyses.
Eight-Week Vibration Training of the Elbow Flexors by Force Modulation (2015)

Vibration exercise (VE) has been suggested as an effective method to improve strength and power capabilities. However, the underlying mechanisms in response to VE are still unclear. A pulley-like VE system, characterized by sinusoidal force applications has been developed and tested for proof of concept in a previous study. The aim of this study was to evaluate the effects of such force modulation on elbow flexors strength and compare it with conventional methods. Forty subjects were randomly divided into 4 groups of 10: the vibration group (VG), the no-vibration group (NVG), the dumbbell group (DG), and the control group (CG). Biceps curl exercises were used to train the elbow flexors 2 times a week for 8 weeks. Subjects in the VG were trained using a ramp-up baseline with superimposed 30 Hz sinusoidal vibration whereas the subjects in the NVG were trained using the same baseline but without vibration. Subjects in the DG were trained using dumbbells, and the subjects in the CG were not trained. The isometric break force (IBF) and 1 repetition maximum (1RM) of the subject's dominant arm were assessed before and after the 8-week training period. The VG achieved 1RM improvement (22.7%) larger than the NVG (10.8%) and comparable with the DG (22.3%). Differences in IBF gains following the training period among the training groups were found to be not significant. Our results support the inclusion of the proposed VE in strength training programs aimed at improving dynamic strength on the elbow flexors.
Genomic analysis of a synthetic reversed sequence reveals default chromatin states in yeast and mammalian cells (2022)

Abstract Up to 93% of the human genome may show evidence of transcription, yet annotated transcripts account for less than 5%. It is unclear what makes up this major discrepancy, and to what extent the excess transcription has a definable biological function, or is just a pervasive byproduct of non-specific RNA polymerase binding and transcription initiation. Understanding the default state of the genome would be informative in determining whether the observed pervasive activity has a definable function. The genome of any modern organism has undergone billions of years of evolution, making it unclear whether any observed genomic activity, or lack thereof, has been selected for. We sought to address this question by introducing a completely novel 100-kb locus into the genomes of two eukaryotic organisms, S. cerevisiae and M. musculus , and characterizing its genomic activity based on chromatin accessibility and transcription. The locus was designed by reversing (but not complementing) the sequence of the human HPRT1 locus, including ∼30-kb of both upstream and downstream regulatory regions, allowing retention of sequence features like repeat frequency and GC content but ablating coding information and transcription factor binding sites. We also compared this reversed locus with a synthetic version of the normal human HPRT1 locus in both organismal contexts. Despite neither the synthetic HPRT1 locus nor its reverse version coding for any promoters evolved for gene expression in yeast, we observed widespread transcriptional activity of both loci. This activity was observed both when the loci were present as episomes and when chromosomally integrated, although it did not correspond to any of the known HPRT1 functional regulatory elements. In contrast, when integrated in the mouse genome, the synthetic HPRT1 locus showed transcriptional activity corresponding precisely to the HPRT1 coding sequence, while the reverse locus displayed no activity at all. Together, these results show that genomic sequences with no coding information are active in yeast, but relatively inactive in mouse, indicating a potentially major difference in “default genomic states” between these two divergent eukaryotes.
Abstract B17: Identification of Druggable Targets through Functional Multi-Omics in Renal Medullary Carcinoma (2017)

Abstract Renal medullary carcinoma is a rare kidney cancer that is primarily seen in adolescent and young adult African American patients with sickle cell trait. Prognosis is poor and treatment options are limited. We have developed several cell line models that recapitulate the primary and relapsed metastatic samples from a patient who succumbed to this disease. We have confirmed by whole exome sequencing that our models have sickle cell trait and loss of heterozygosity of the SMARCB1 loci, both hallmarks of this disease. By RNA-sequencing, we see a lack of SMARCB1 transcription. We have further shown dependency of our models to SMARCB1 re-expression thus suggesting that this cancer is indeed driven by loss of SMARCB1 at a functional level. We performed pooled CRISPR-Cas9 and RNAi loss of function screens and a small molecule screen focused on druggable cancer targets based on our previous work in parallel to a genome-wide pooled CRISPR-Cas9 loss of function screen. Integrating these complementary and orthogonal methods, we identified a number of targets for further validation. These targets, when combined may provide a rational approach to therapeutic targeting for this rare kidney cancer. Citation Format: Andrew L. Hong, Yuen-Yi Tseng, Bryan D. Kynnap, Mihir B. Doshi, Gabriel Sandoval, Coyin Oh, Abeer Sayeed, Gill Shubhroz, Alanna J. Church, Paula Keskula, Anson Peng, Paul A. Clemons, Aviad Tsherniak, Francisca Vazquez, Carlos Rodriguez-Galindo, Katherine A. Janeway, Levi A. Garraway, Stuart L. Schreiber, David E. Root, Elizabeth Mullen, Kimberly Stegmaier, Cigall Kadoch, Charles W.M. Roberts, Jesse S. Boehm, William C. Hahn. Identification of Druggable Targets through Functional Multi-Omics in Renal Medullary Carcinoma [abstract]. In: Proceedings of the AACR Precision Medicine Series: Opportunities and Challenges of Exploiting Synthetic Lethality in Cancer; Jan 4-7, 2017; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Ther 2017;16(10 Suppl):Abstract nr B17.