gebhart/patrepeval huggingface dataset:
Atlas of dihydrotestosterone actions on the transcriptome of prostate in vivo (2008)

Our data support the idea that ARGs are essential for the normal development of the prostate and can also be responsible for the pathogenesis of the prostate cancer.
Atomic to Nanoscale Investigation of Functionalities of an Al2O3 Coating Layer on a Cathode for Enhanced Battery Performance (2016)

Surface coating has been identified as an effective approach for enhancing the capacity retention of layered structure cathode. However, the underlying operating mechanism of such a thin coating layer, in terms of surface chemical functionality and capacity retention, remains unclear. In this work, we use aberration-corrected scanning transmission electron microscopy and high-efficiency spectroscopy to probe the delicate functioning mechanism of an Al2O3 coating layer on a Li1.2Ni0.2Mn0.6O2 cathode. We discovered that in terms of surface chemical function, the Al2O3 coating suppresses the side reaction between the cathode and the electrolyte during battery cycling. At the same time, the Al2O3 coating layer also eliminates the chemical reduction of Mn from the cathode particle surface, therefore preventing the dissolution of the reduced Mn into the electrolyte. In terms of structural stability, we found that the Al2O3 coating layer can mitigate the layer to spinel phase transformation, which otherwise will be initiated from the particle surface and propagate toward the interior of the particle with the progression of battery cycling. The atomic to nanoscale effects of the coating layer observed here provide insight into the optimized design of a coating layer on a cathode to enhance the battery properties.
Voriconazole Inhibits Melanization in Cryptococcus neoformans (2007)

Voriconazole is a triazole antifungal drug that inhibits ergosterol synthesis and has broad activity against yeast and molds. While studying the interaction of voriconazole and Cryptococcus neoformans, we noted that cells grown in the presence of subinhibitory concentrations of voriconazole reduced melanin pigmentation. We investigated this effect systematically by assessing melanin production in the presence of voriconazole, amphotericin B, caspofungin, itraconazole, and fluconazole. Only voriconazole impeded the formation of melanin at subinhibitory concentrations. Voriconazole did not affect the autopolymerization of l-dopa, and 0.5 MIC of voriconazole did affect the gene expression of C. neoformans. However, voriconazole inhibited the capacity of laccase to catalyze the formation of melanin. Hence, voriconazole affects melanization in C. neoformans by interacting directly with laccase, which may increase the efficacy of this potent antifungal against certain pigmented fungi.
Spectral discrimination of breast pathologies in situusing spatial frequency domain imaging (2013)

SFDI is a new quantitative imaging technique that renders a specific tissue-type diagnosis. Its combination of planar sampling and frequency-dependent depth sensing is clinically pragmatic and appropriate for breast surgical-margin assessment. This study is the first to apply SFDI to pathology discrimination in surgical breast tissues. It represents an important step toward imaging surgical specimens immediately ex vivo to reduce the high rate of secondary excisions associated with breast lumpectomy procedures.
Multi-scale capture of facial geometry and motion (2007)

We present a novel multi-scale representation and acquisition method for the animation of high-resolution facial geometry and wrinkles. We first acquire a static scan of the face including reflectance data at the highest possible quality. We then augment a traditional marker-based facial motion-capture system by two synchronized video cameras to track expression wrinkles. The resulting model consists of high-resolution geometry, motion-capture data, and expression wrinkles in 2D parametric form. This combination represents the facial shape and its salient features at multiple scales. During motion synthesis the motion-capture data deforms the high-resolution geometry using a linear shell-based mesh-deformation method. The wrinkle geometry is added to the facial base mesh using nonlinear energy optimization. We present the results of our approach for performance replay as well as for wrinkle editing.
Integrated direct-coupled gyrator (1967)

An integrated gyrator is described. The device uses 1 diode, 12 resistors and 9 transistors, two of which are lateral p-n-p. Experimental results on gyration resistance, input impedance and resonant-circuit Q factor show excellent agreement with theory.
Synthesis of Mesoporous Silica Materials by Using Anionic Surfactants as Template (2007)

Mesoporous materials have attracted a great deal of attention because of their controllable structures and compositions, which make them suitable for a wide range of applications in catalysis, environmental clean-up, and development of advanced materials. Various mesoporous materials can be synthesized based on the self-assembly of surfactants and inorganic precursors. We previously demonstrated a novel templating route for preparing mesoporous silicas based on the self-assembly of anionic surfactants and inorganic precursors in the presence of aminosilane or quaternized aminosilane as a co-structure-directing agent (CSDA). We continue to investigate the resultant novel mesoporous materials called anionic surfactant mesoporous silica (AMS). The latest AMS series is a novel bicontinuous cubic Pn3m mesoporous silica (AMS-10). We have also found that the assynthesized AMS is transformed into amino-functionalized mesoporous silica, by removal of only the surfactant by extraction, with potential uses as high-performance catalysts and adsorbents. Furthermore, the use of a chiral anionic surfactant derived from the amino acid, N-myristoyl-L-alanine sodium salt, provides chiral mesoporous silica. Such anionic surfactant templating routes will provide a new family of mesoporous materials as well as information on the structural behavior of anionic surfactants. This review describes the preparation, properties, and potential applications of anionic surfactant templated mesoporous silicas.
A mathematical model of ctDNA shedding predicts tumor detection size (2020)

Early cancer detection aims to find tumors before they progress to an incurable stage. To determine the potential of circulating tumor DNA (ctDNA) for cancer detection, we developed a mathematical model of tumor evolution and ctDNA shedding to predict the size at which tumors become detectable. From 176 patients with stage I to III lung cancer, we inferred that, on average, 0.014% of a tumor cell's DNA is shed into the bloodstream per cell death. For annual screening, the model predicts median detection sizes of 2.0 to 2.3 cm representing a ~40% decrease from the current median detection size of 3.5 cm. For informed monthly cancer relapse testing, the model predicts a median detection size of 0.83 cm and suggests that treatment failure can be detected 140 days earlier than with imaging-based approaches. This mechanistic framework can help accelerate clinical trials by precomputing the most promising cancer early detection strategies.
Spatial transformation-enabled electromagnetic devices: from radio frequencies to optical wavelengths (2015)

Transformation optics provides scientists and engineers with a new powerful design paradigm to manipulate the flow of electromagnetic waves in a user-defined manner and with unprecedented flexibility, by controlling the spatial distribution of the electromagnetic properties of a medium. Using this approach, over the past decade, various previously undiscovered physical wave phenomena have been revealed and novel electromagnetic devices have been demonstrated throughout the electromagnetic spectrum. In this paper, we present versatile theoretical and experimental investigations on designing transformation optics-enabled devices for shaping electromagnetic wave radiation and guidance, at both radio frequencies and optical wavelengths. Different from conventional coordinate transformations, more advanced and versatile coordinate transformations are exploited here to benefit diverse applications, thereby providing expanded design flexibility, enhanced device performance, as well as reduced implementation complexity. These design examples demonstrate the comprehensive capability of transformation optics in controlling electromagnetic waves, while the associated novel devices will open up new paths towards future integrated electromagnetic component synthesis and design, from microwave to optical spectral regimes.
An in-line MOSFET process with photomask fabrication process in a minimal fab (2017)

This paper describes a cleanroom-less device fabrication process of a minimal fab including an in-line photomask fabrication process, where half-inch wafers and half-inch photomasks are transferred in airtight containers and loaded into fabrication tools to prevent invasion of air-borne particles, gases and UV light from outside. Photomasks are fabricated using a maskless exposure system in the minimal fab. We have fabricated two types of MOSFET using the photomasks or maskless exposure system, and found that the two types of MOSFET have the almost same electric performance with the density of interface states (D <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">it</inf> ) of the order of ID <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">10</sup> states/cm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Optimizing epitope conformational ensembles using α -synuclein cyclic peptide “glycindel” scaffolds: A customized immunogen method for generating oligomer-selective antibodies for Parkinson’s disease (2021)

Abstract Effectively presenting epitopes on immunogens, in order to raise conformationally selective antibodies through active immunization, is a central problem in treating protein misfolding diseases, particularly neurodegenerative diseases such as Alzheimer’s disease or Parkinson’s disease. We seek to selectively target conformations enriched in toxic, oligomeric propagating species while sparing the healthy forms of the protein that are often more abundant. To this end, we computationally modelled scaffolded epitopes in cyclic peptides by inserting/deleting a variable number of flanking glycines (“glycindels”), to best mimic a misfolding-specific conformation of an epitope of α -synuclein enriched in the oligomer ensemble, as characterized by a region most readily disordered and solvent-exposed in a stressed, partially denatured protofibril. We screen and rank the cyclic peptide scaffolds of α -synuclein in silico based on their ensemble overlap properties with the fibril, oligomer-model, and isolated monomer ensembles. We present experimental data of seeded aggregation that supports nucleation rates consistent with computationally predicted cyclic peptide conformational similarity. We also introduce a method for screening against structured off-pathway targets in the human proteome, by selecting scaffolds with minimal conformational similarity between their epitope and the same solvent-exposed primary sequence in structured human proteins. Different cyclic peptide scaffolds with variable numbers of glycines are predicted computationally to have markedly different conformational ensembles. Ensemble comparison and overlap was quantified by the Jensen-Shannon Divergence, and a new measure introduced here—the embedding depth, which determines the extent to which a given ensemble is subsumed by another ensemble, and which may be a more useful measure in developing immunogens that confer conformational-selectivity to an antibody. Graphical TOC Entry
Directed network topology inference via sparse joint diagonalization (2017)

Discovering the connectivity patterns of directed networks is a crucial step towards understanding complex systems such as human brains and financial markets. Network inference approaches aim at estimating the hidden topology given nodal observations. Existing approaches relying on structural equation models (SEMs) require full knowledge of exogenous inputs, which may be unrealistic in certain applications. Recent tensor-based alternatives advocate reformulation of SEMs as a three-way tensor decomposition task that only requires second-order statistics of exogenous inputs for identifying the hidden topology. However, the tensor-based methods are computationally expensive, and is hard to incorporate prior information of the network structure (e.g., sparsity and local smoothness), but prior information is often important for enhancing performance. The present work puts forth a joint diagonalizaition (JD)-based formulation for directed network inference. JD can be viewed as a variant of tensor decomposition, but features more efficient algorithms and can readily incorporate prior information of network topology. New topology identification guarantees that do not rely on knowledge of exogenous inputs are established. Judiciously designed simulations are presented to showcase the effectiveness of the proposed approach.
Discriminating endogenous vaccine‐elicited anti‐Spike antibody responses from exogenous anti‐Spike monoclonal antibodies: The case of Evusheld (2022)

immunocompromised patients represent the most problematic cohort of COVID19 management nowadays, given the inability of most to mount a protective antibody response after vaccination. This article is protected by copyright. All rights reserved.
Dissolution characteristics optimization for chemically amplified positive resist (1994)

Dissolution kinetics of a 3-component chemically amplified positive resist, which consists of t-BOC protected phenolic resin, benzenesulfonic acid derivative as a PAG and an additional dissolution inhibitor, have been investigated under various conditions. Especially, the effects of t-BOC protection ratio and molecular weight of the base resin have been studied. In a previous paper, we reported that the dissolution rate R of a 2- component positive resist was determined by one rate determining step, i.e., developer penetration into hydrophobic t-BOC protected phenolic resin. Rapid formation of surface insoluble layer which induced T-toping profiles deteriorated its original resist performance. In this paper, we evaluated both t-BOC protection ratio and the molecular weight dependencies of the dissolution characteristics. The 3-component resist evaluated did not produce distinct T-topping profile when time duration between exposure and PEB was within 30 minutes.
Molecular Dynamics Simulation of β-Lactoglobulin at Different Oil/Water Interfaces (2016)

Controlling and manipulating protein behavior at an interface is of immense relevance to a broad range of physicochemical and biological phenomena and technological processes. Although many experimental studies have contributed to rapid progress in the fundamental knowledge of protein behavior at interfaces, detailed molecular-level understanding of the mechanism of protein adsorption at an interface is still remarkably lacking. In this study, atomistic molecular dynamics simulations were used to characterize the adsorption of β-lactoglobulin at two different oil/water (O/W) interfaces, where the oil was either the marginally hydrophilic octanol or the more hydrophilic triolein, and the results were compared to those of a previous study utilizing the hydrophobic oil decane. Both the approach to the surface and the mechanism of adsorption depend upon the hydrophilicity of the oil and the interfacial tension of the O/W interface, with the nature of the adsorption, the accompanying structural changes, and the energetic driving force differing markedly between the different oils. Intriguingly, the behavior of the protein resembles that predicted for a soft spherical particle at an O/W interface. The results are also in agreement with key experimental findings, particularly the observation that proteins undergo more conformational change upon adsorption to hydrophobic surfaces, flattening out to expose hydrophobic interior residues to the surface, and that a thicker layer of native-like adsorbed protein forms at hydrophilic surfaces, and reveal structural and mechanistic detail behind each mechanism of adsorption.
Emulation Techniques for Small Scale Fading Aspects by Using Reverberation Chamber (2018)

Reverberation chambers (RVCs) are used to provide an efficient and reliable testbed for emulating the wireless channel effects in the laboratory environment. In the literature, various techniques have been studied to enrich the channel emulation capabilities of RVCs. However, insufficient control of some of the emulated channel characteristics (such as time and frequency dispersions) still leaves an open problem for RVC-based channel emulators. In this paper, novel channel emulation techniques by using RVC are introduced to enhance the flexibility in controlling the emulated time and frequency dispersions of the channels. Surface acoustic wave delay lines and power controllers (i.e., amplifiers and attenuators) are used to add degrees of freedom for manipulating the power delay profile during delay spread emulation. This technique also overcomes the challenge of achieving higher delay spread values with benchtop-sized RVC. The second technique is aimed to control the Doppler spectrum shape emulated in the chamber by judiciously placing radio frequency absorbers around the mechanical stirrer. Experimental and mathematical analyses are conducted to evaluate the proposed techniques, and the results show that the proposed methods can improve the channel emulation in the RVCs.
Molecular doping of MoS2 transistors by self-assembled oleylamine networks (2016)

Thin MoS2 films continue to be of key interest for numerous applications; however, effective doping and high metal to MoS2 contact resistance are challenges for future applications. We report on the self-assembly of oleylamine on top of MoS2 thin-films and the effective doping of MoS2 thin-film field effect transistors by oleylamine. Atomic force microscopy revealed that oleylamine organizes in lamellae domains on MoS2 thin films with similar characteristics of those previously observed on highly ordered pyrolytic graphite. A carrier concentration increase from 7.1 × 1011 cm−2 up to 1.9 × 1013 cm−2 at 0 V gate voltage is achieved together with a reduction of the contact resistance by a factor of 5 when using gold as metal contact. Furthermore, this non-covalent doping proves to be removable and reproducible among different flakes and does not degrade the electron mobility. Thus, this work opens the path for future works on controlling the doping of MoS2 by proper selection of the self-assembled species.
Simple model of the high frequency permeability of narrow thin-film structures with eddy currents, walls, and saturation (1992)

The authors report the derivation and experimental verification of a simple model of the high-frequency permeability of narrow soft-magnetic thin-film structures which includes eddy currents and magnetization rotation, wall motion, and saturation. Data are presented for long narrow magnetic rectangles with the idea that common thin-film magnetic structures, such as recording heads, can be modeled as connected stripes of different widths. The easy magnetic axis is aligned perpendicular to the applied field and to the long axis of the stripes. The model has two terms: from the easy-axis aligned domains, the bulk permeability (magnetization rotation) reduced by eddy currents and and constriction due to closure domains, and from the hard axis regions, domain wall motion described by the standard damping limited theory of wall motion solved for an oscillatory field. Saturation is handled by clipping the total moment change of 4 pi M, and replacing the wall phase delay with the transit time for a wall to cross the film.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Examination ofSerpulina pilosicolifor attachment and invasion determinants of Enterobacteria (1998)

The spirochaete, Serpulina pilosicoli, is the agent of intestinal spirochaetosis, a diarrhoeal disease of humans and other species. By mechanisms as yet unknown, large numbers of these spirochaetes intimately attach to the colonic mucosa by one cell end. In some infected individuals, the spirochaetes may invade the lamina propria and adjacent tissues, and they may cause spirochaetaemia. To examine S. pilosicoli for pathogenic determinants homologous with Enterobacteria, DNA was extracted from six strains of S. pilosicoli and hybridised at low stringency with DNA probes derived from the inv, ail and yadA genes of Yersinia enterocolitica, the eae gene from enteropathogenic Escherichia coli and a probe derived from the virulence plasmid of Shigella flexneri. No hybridisation of the enterobacterial probes to S. pilosicoli DNA was detected, indicating that these gene sequences, which are known to be involved in the attachment and invasion processes of the other intestinal pathogens, were not present in the spirochaetes.
Exerting Fine-Grained Path Control over Legacy Switches in Hybrid Networks (2016)

Software-defined networking (SDN) provides fine-grained network control and monitoring that simplifies network management. Unfortunately, upgrading existing enterprise networks, comprised of numerous “legacy” switches, to SDN is often cost-prohibitive. We argue that it is possible to achieve most of the benefits of a fully deployed SDN at a fraction of the cost by strategically replacing only few legacy switches with – or introducing a few – new SDN-capable switches in a legacy network, thus creating a hybrid network. We present Magneto, a unified network controller that exerts SDN-like, fine-grained path control over both OpenFlow and legacy switches in hybrid networks. Magneto i) introduces magnet MAC addresses and dynamically updates IP-to-magnet MAC mappings at hosts via gratuitous ARP messages for visibility and routing control; and ii) uses the ability of SDN switches to send “custom” packets into the data plane to manipulate legacy switches into updating forwarding entries with magnet MAC addresses for enhanced routing flexibility. Our evaluations on a lab testbed and through extensive simulations on large enterprise network topologies show that Magneto is able to achieve full control over routing when only 20% of network switches are programmable, with negligible computation and latency overhead.
Characterization of silica xerogel films by variable-angle spectroscopic ellipsometry and infrared spectroscopy (2001)

Silica xerogel films with low dielectric constants were prepared using a sol-gel spin coating method. The as-prepared films were further treated by hexamethyldisilazane to achieve the hydrophobization of the pore surfaces, by replacing hydrophilic silanol groups with hydrophobic trimethylsilyl (TMS) groups. The thickness and optical constants of the films were derived from variable-angle spectroscopic ellipsometry measurements. The determined refractive index decreases from 1.271±0.008 to 1.188±0.003 (values at 632.8 nm) while the porosity increases from 40.4 to 58.6% with the process parameters used. The Maxwell-Garnet approximation was used to relate the ellipsometric data to porosity. The IR absorption bands of CH species in TMS groups reveal that the surface area of the pores is larger in the samples with lower porosity.