gebhart/patrepeval huggingface dataset:
Abstract 1883: Large scale viability screening with PRISM underscores non-inhibitory properties of small molecules (2022)

Abstract Oncology drug discovery has been dependent on phenotypic screening that lead to discovery of many drugs that remain essential cancer treatments to this day. Historically, logistical and technological limitations have hampered the scale of phenotypic small molecule screening across genomic diverse models. Until recently, large scale phenotypic screening across many cell lines, reflecting the somatic diversity in cancer, has not been possible. The PRISM technology does allow for a high-throughput approach to phenotypic viability screening by pooling cell lines and deconvoluting their response to small molecules using unique integrated DNA-barcodes. Here, we report on the results of a large phenotypic screening effort to identify novel small molecules and targets that can expand our knowledge on cancer vulnerabilities and can spur development of phenotypic drug discovery. A library of 18.000 compounds was assembled based on structural diversity and ability to induce gene-expression changes. Of these 18.000 compounds, around 3.500 were found to reduce cell viability of at least 5 cell lines in the PRISM assay. Of the cytotoxic compounds, we did not identify many small molecules that correlated strongly with CRISPR KO dependency data from project Achilles, and instead found that gene-expression correlations hold much more predictive value. By using additional approaches, we were able to identify the target of select novel cytotoxic small molecules and their respective mechanism-of-action. To our surprise, we have identified few compounds that act as canonical inhibitors of cancer drivers, and instead found compounds that act as molecular glues, prodrugs or inhibitors of more general cellular processes. These findings make a strong case for large scale phenotypic viability screening across genomically diverse models as a complementary approach to target identification next to target based drug discovery. Citation Format: Lucian de Waal, Kevin Larpenteur, Li Wang, Cong Zhu, Jordan Bryan, Mustafa Kocak, Corrie Aghia, Joshua Bittker, Victor Jones, Anita Vrcic, Edward McBride, Samantha Bender, Kalea Gore, Frank Li, Zhenghao Chen, Aviad Tsherniak, Aravind Subramanian, Daphne Koller, Jeffery Settleman, Chris C. Mader, David Stokoe, Ari Firestone, Jennifer A. Roth, Todd R. Golub. Large scale viability screening with PRISM underscores non-inhibitory properties of small molecules [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1883.
A study of document-context models in information retrieval (2011)

In this thesis we study new retrieval models which simulate the relevance decision-making for every term location in a document, these local relevance decisions are then combined as the document-wide relevance decision for the document. Local relevance decision for a term t occurred at the k-th location in a document is made by considering the document-context which is the window of terms centred at the term t at the k-th location. Therefore, different relevance scores (preferences) are obtained for the same term t at different locations in a document depending on its document-contexts. This differs from traditional models which term t receives the same score disregard of its locations in a document.
A hybrid document-context model is studied which is the combination of various existing effective models and techniques. It estimates the relevance decision preference of document-contexts as the log-odds and combines the estimated preferences using different types of aggregation operators that comply with the relevance decision principles. The model is evaluated using retrospective experiments to reveal the potential of the model. Besides retrospective experiments, we also use top 20 documents from the initial ranked list to perform relevance feedback experiments with a probabilistic document-context model and the results are promising. 
We also show that when the size of the document-contexts is shrunk to unity, the document-context model is simplified to a basic ranking formula that directly corresponds to the TF-IDF term weights. Thus TF-IDF term weights can be interpreted as making relevance decisions. This helps to establish a unifying perspective about information retrieval as relevance decision-making and to develop advance TF-IDF-related term weights for future elaborate retrieval models.
Lastly, we develop a new relevance feedback algorithm by splitting the ranked document list into multiple lists of document-contexts. The judgement of relevance of the documents is not done sequentially. This is called active feedback and we show that our new relevance feedback algorithm obtained better results than the conventional relevance feedback algorithm and this is done more reliably than a maximal marginal relevance (MMR) method which does not use document-contexts.
End-to-end Procedural Material Capture with Proxy-Free Mixed-Integer Optimization (2023)

Node-graph-based procedural materials are vital to 3D content creation within the computer graphics industry. Leveraging the expressive representation of procedural materials, artists can effortlessly generate diverse appearances by altering the graph structure or node parameters. However, manually reproducing a specific appearance is a challenging task that demands extensive domain knowledge and labor. Previous research has sought to automate this process by converting artist-created material graphs into differentiable programs and optimizing node parameters against a photographed material appearance using gradient descent. These methods involve implementing differentiable filter nodes [Shi et al. 2020] and training differentiable neural proxies for generator nodes to optimize continuous and discrete node parameters [Hu et al. 2022a] jointly. Nevertheless, Neural Proxies exhibits critical limitations, such as long training times, inaccuracies, fixed resolutions, and confined parameter ranges, which hinder their scalability towards the broad spectrum of production-grade material graphs. These constraints fundamentally stem from the absence of faithful and efficient implementations of generic noise and pattern generator nodes, both differentiable and non-differentiable. Such deficiency prevents the direct optimization of continuous and discrete generator node parameters without relying on surrogate models. We present Diffmat v2 , an improved differentiable procedural material library, along with a fully-automated, end-to-end procedural material capture framework that combines gradient-based optimization and gradient-free parameter search to match existing production-grade procedural materials against user-taken flash photos. Diffmat v2 expands the range of differentiable material graph nodes in Diffmat [Shi et al. 2020] by adding generic noise/pattern generator nodes and user-customizable per-pixel filter nodes. This allows for the complete translation and optimization of procedural materials across various categories without the need for external proprietary tools or pre-cached noise patterns. Consequently, our method can capture a considerably broader array of materials, encompassing those with highly regular or stochastic geometries. We demonstrate that our end-to-end approach yields a closer match to the target than MATch [Shi et al. 2020] and Neural Proxies [Hu et al. 2022a] when starting from initially unmatched continuous and discrete parameters.
Chemiresistors: Transistor‐Like Modulation of Gold Nanoparticle Film Conductivity Using Hydrophobic Ions (Adv. Mater. Interfaces 5/2014) (2014)

Functionalized gold nanoparticle films are wellknown to act as chemically-sensitive resistors (i.e., passive electrical components). B. Raguse, E. Chow, and co-workers report in article 1400062 that such nanoparticle films are also capable of being used as chemically-sensitive, active (transistor-like) components by applying an external gate potential in the presence of hydrophobic ions. An immediate application is the development of highly sensitive sensors where the sensitivity towards charged molecules is improved by several orders of magnitude.
Design of leaky bucket access control schemes in ATM networks (2002)

Depending on what enforcement action is taken and whether or not there is a 'shaping' buffer, four versions of the leaky bucket scheme are considered, and their cell loss performance is compared in conjunction with a statistical multiplexer. Based on the best-performing version, three architectures are proposed. Among them, a novel algorithm and its implementation method are proposed to accommodate a large number of virtual channel connections on each incoming STS-3c channel. A VLSI chip (called a sequencer), containing about 200 K CMOS transistors, has been designed to implement the architecture.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Low-loss splicing of microstructured fibers with conventional electric-arc splicers (2004)

We present experimental results demonstrating the possibility of obtaining low-loss splices of microstructured optical fibers (MOFs) by using conventional electric-arc splicers. We show evidence of the effectiveness of the method by splicing two MOFs together as well as a MOF with a standard single mode fiber (SMF). The results are presented in terms of fusion losses and tensile strength. Theoretical calculations of the losses attributable to mode mismatch between the MOF and the SMF suggest that the splicing losses could be further reduced by optimizing the MOF design parameters. For the case of a MOF-MOF splicing, the loss that could be due to a possible rotational misalignment that comes with the non-cylindrical symmetry of the modal distribution is also evaluated.
Energy Management System for an Electric Vehicle With a Rental Range Extender: A Least Costly Approach (2016)

Range extenders (REs) increase the driving range of electric vehicles (EVs) at the price of additional weight and encumbrance, which are unnecessary in normal urban usage. An innovative concept of an extended range EV is studied here, i.e., an EV that can exploit a rental RE only when necessary to complete a mission. The energy management system not only dispatches power between a battery and an RE but also decides whether or not and when to rent the RE. This paper investigates the optimal control policy that minimizes the monetary cost attained by the user. A simulation analysis carried out in a representative set of scenarios demonstrates the interest of this formulation and shows that mixed-integer convex programming (MI-CP) attains high accuracy in a fraction of the time required by dynamic programming, with a negligible loss of performance. In a real-time framework, the MI-CP core is fed by a forecast of the mission and integrated with a power dispatch strategy that optimizes local performance. The simulation study shows that the resulting policy approaches the global optimum.
Expression of a Zeatin-O-Glucoside-Degrading [beta]-Glucosidase in Brassica napus (1995)

A beta-glucosidase was purified from seeds of Brassica napus L. (oilseed rape). The 130-kD native enzyme consisted of a disulfide-linked dimer of 64-kD monomers. Internal amino acid sequences were used to construct degenerate primers for polymerase chain reaction-mediated cloning of cDNA for the enzyme. One nearly full-length and one partial beta-glucosidase-encoding cDNA clone were isolated and sequenced. Southern hybridization showed that beta-glucosidase is encoded by a small gene family in B. napus. Northern hybridization showed that the genes are expressed in the seed, with a low degree of expression in other tissues. In the seed, the expression started at 30 days after pollination (DAP), with the highest expression at 40 DAP. The size of the transcript was approximately 1900 nucleotides. In situ hybridization to developing seeds of B. napus showed that the beta-glucosidase expression started at 30 DAP around the provascular tissue in the embryo axis. In the cotyledons, mRNA initially accumulated around the provascular tissues but was detected first at 35 DAP. At 40 DAP, expression occurred in most parts of the seed. In situ hybridization also detected beta-glucosidase mRNA in shoots, young roots, and the basal part of the hypocotyls. Zeatin-O-glucoside was identified as a natural substrate for B. napus beta-glucosidase.
IR GRIN optics: design and fabrication (2017)

Infrared (IR) transmitting gradient index (GRIN) materials have been developed for broad-band IR imaging. This material is derived from the diffusion of homogeneous chalcogenide glasses has good transmission for all IR wavebands. The optical properties of the IR-GRIN materials are presented and the fabrication and design methodologies are discussed. Modeling and optimization of the diffusion process is exploited to minimize the deviation of the index profile from the design profile. Fully diffused IR-GRIN blanks with &Delta;n of ~0.2 are demonstrated with deviation errors of &plusmn;0.01 refractive index units.
Relationship between carbon nanotube density and hysteresis characteristics of carbon nanotube random network-channel field effect transistors (2010)

We have investigated the hysteresis in the transfer characteristics of carbon nanotube (CNT) field effect transistors (FETs). The relationship between the hysteresis width and channel CNT density was studied for FETs of spun-on random network CNTs. The hysteresis width in the transfer characteristics decreases with an increase in the channel CNT density. To explain this relationship, we carried out simulations combining two models such as: the hysteresis model and the gate electric field model. Considering the finite channel thickness and trap-assisted tunneling current, the simulation described the experiments well. The simulation implies the possibility of reducing hysteresis by relaxing the strong gate electric field at the CNT surface. We also discuss other possibilities of hysteresis reduction on FETs whose channels are of nanoscale cylindrical material.
Fat suppression in combination with multiple overlapping thin-slab 3-D acquisition MR angiography: proposed technique for improved vessel visualization. (1992)

Implementation of fat saturation into carotid MR angiography markedly improves visualization of vascular anatomy without increasing imaging time.
Tedizolid for the Management of Human Infections: In Vitro Characteristics (2013)

The emerging antibiotic resistance of Gram-positive pathogens represents a significant challenge to the management of human infections. The novel oxazolidinone tedizolid demonstrates antimicrobial activity across a broad range of Gram-positive pathogens and greater potency than linezolid against wild-type and drug-resistant pathogens, including linezolid-resistant Staphylococcus aureus strains possessing mutations in chromosomal genes encoding 23S rRNA or ribosomal proteins L3 or L4. Strains harboring such mutations are also selected for much less frequently with tedizolid than with linezolid. In addition, tedizolid has a significant potency advantage over linezolid-resistant strains carrying the horizontally transferable cfr gene. Methylation of A2503 of 23S rRNA by the Cfr methyltransferase confers resistance to linezolid (and a variety of other 50S ribosomal subunit-targeted antibiotics) but not to tedizolid because of structural differences in A-ring C5 substituents between the 2 drugs. The greater potency and improved resistance profile of tedizolid provides the microbiologic basis for considering this molecule as an alternative to linezolid for the treatment of serious infections caused by Gram-positive pathogens.
QuasiCW laser diode pumped master-oscillator power-amplifier system in single frequency operation (2004)

In this paper, nonlinear conversion in a wide optical region, from VUV to THz-wave is investigated. Many techniques of generating such special wavelengths have been developed. To achieve efficient frequency conversion high power laser with good beam quality is required. Narrow linewidth is often needed. The master-oscillator power-amplifier (MOPA) is significant technique to achieve good beam quality and high power at the same time. In this study, a quasiCW laser diode (QCW-LD) pumped Nd:YAG MOPA system is developed to obtain single frequency pulses with high energy and high averaged power. The laser operated in single frequency, single transversal mode with the energy and the repetition rate of 22 mJ/pulse and 400 Hz, respectively.
Tumor Burden Assessment In Lymphoma Patients: Hierarchical Analysis Of Whole Body CT (2019)

Detecting and characterizing lymph nodes in Computed Tomography (CT) scans is a necessary task for the diagnosis and staging of multiple types of cancers. The task is tedious and difficult due to the lymph nodes distribution in the body, their varying size, and low contrast appearance relative to surrounding vessels or other anatomical structures. Recent developments in machine learning enable hierarchical information extraction from medical scans, from specific landmark positions to 3D delineation of regions and organs, and identification and characterization of abnormalities. We exemplify the application of hierarchical parsing to the task of lymph node identification by automatically indexing the data according to 120+ anatomical landmarks, performing segmentation of main organs, and automatically determine the lymph nodes of interest given their context. Landmarks are robustly detected using deep reinforcement learning, organs delineated using generative adversarial networks, and lymph nodes detected using context-based deep dense neural networks. We evaluated the system on a database having more than 3000 lymph nodes from abdominal, mediastinal and axillary locations from 390 CT volumes. The performance of the system compares favorably to the previously reported methods and attains a True Positive Rate (TPR) of 85% with 1.5 False Positives (FP) per volume, 98% TPR with 0.2 FP for axillary nodes, 85% TPR with 3 FP for mediastinal nodes and 80% TPR with 4.8 FP for abdominal nodes. When these results are combined with the segmentation of the enlarged lymph nodes, the system has the potential to become the first automatic total tumor burden estimator for cancer patients.
Rapid Identification of Methicillin-Resistant Staphylococci by Biosensor Assay Consisting of Nanoscale Films on Optical Fiber Long-Period Gratings (2016)

Methicillin-resistance among Staphylococcus species is a major health problem in hospitals, communities, and animals. There is a need for culture-free diagnostic assays that can be carried out rapidly, and maintain a high degree of sensitivity and specificity. To address this need an ionic self-assembled multilayer (ISAM) film was deposited on the surface of a long-period grating (LPG) optical fiber with the terminal carboxyl groups covalently conjugated to monoclonal antibodies (MAb) specific to penicillin-binding-protein 2a of methicillin resistant (MR) staphylococci. After exposure of the LPG-ISAM to 102 colony forming units (CFU)/ml of MR S. aureus (MRSA) for 50 min., light transmission was reduced by 19.7%. In contrast, after exposure to 106 CFU/ml of methicillin-sensitive S. aureus (MSSA) attenuation of light transmission was less than 1.8%. When the sensor was tested with 36 strains of MR staphylococci, 15 strains of methicillin-sensitive staphylococci, 10 strains of heterologous genera (all at 104 CFU/ml), there was complete agreement between MR and non-MR bacteria determined by antibiotic susceptibility testing and the biosensor assay when the cutoff value for attenuation of light transmission was 6.3%. Thus, the biosensor described has the potential to detect MR staphylococci in clinical samples with a high degree of sensitivity and specificity.
Degradation analysis of datapath logic subblocks under NBTI aging in FinFET technology (2014)

Reliability of advanced deeply scaled CMOS technologies is being threatened by time-dependent degradation mechanisms such as Negative Bias Temperature Instability (NBTI) phenomenon that cause workload-dependent shifts on a transistor's threshold voltage (V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> ), and performance during its lifetime. In this study, NBTI related performance degradation of datapath logic subblocks (i.e. adder, multiplier, shifter, mux-demux) are investigated in relation to workload dependency, and architectural topology at 10nm FinFET technology. A workload-dependent, NBTI aging-aware digital design flow was developed within the industry standard EDA tool chain. NBTI model is based on the measured Capture and Emission Time (CET) maps, and scaled to 10nm node. Static Timing Analysis (STA) is performed to evaluate the performance degradation at 3σ corner. Results on datapath subblocks under NBTI aging after 3 years show a performance loss up to 16.7%. NBTI aging results in the replacement of the time-zero critical path by a non-critical path during a circuit's lifetime, and it can be significantly high as 91%. Finally, the correlation between aging sensitivity to workload variations, and architectural parameters are shown, and it can vary 12×, and 9×, respectively.
Optical Density Dependence of Write/Read Characteristics in Photon-Mode Photochromic Memory (1996)

When photobleaching reactions are used for writing in a photochromic optical memory, the initial optical density in the recording layer plays an important role in the various write/read characteristics; i.e., secondary harmonics, repeatedly readout characteristics, and crosstalks in a multi-wavelength recording. Better characteristics, that is, lower secondary harmonics, higher readout repeatability and lower nonlinear component of crosstalks, were obtained for media with higher optical density.
Prospects for 100% wall-plug efficient III-nitride LEDs (2018)

The possibility of a III-nitride LED with 100% or greater wall-plug efficiency is examined considering recent observations of the phenomenon for smaller bandgap mid-IR LEDs under extremely low-bias operation [Phys. Rev. Lett. 108, 1 (2012)]. Thermoelectric pumping of carriers by lattice heat enables ≥ 100% WPE, but this effect is relatively weaker for the wider band gap III-nitrides. This work assesses the electrical and optical performance of several state-of-the-art nitride devices and summarizes the requirements and prospects for approaching ≥ 100% WPE for III-nitride LEDs operating at technologically relevant current densities (> 1 A/cm<sup>2</sup>).
Respirometry and Cell Viability Studies for Sustainable Polyesters and Their Hydrolysis Products (2021)

Significant research effort has been directed toward the development of sustainable plastics that are high-performance, bioderived, and/or degrade into nontoxic byproducts in natural or engineered environments (i.e., industrial composting facilities). We report the low cytotoxicity of poly(γ-methyl-ε-caprolactone) (PMCL)-based materials and the hydrolysis product of PMCL, sodium 6-hydroxy-4-methylcaproate. The concentration of sodium 6-hydroxy-4-methylcaproate that leads to 50% cell death (TD50) is 179 mM, a value that is similar to that of the hydrolysis product of polycaprolactone and higher than that of the hydrolysis product of polylactide. We also report the degradability of two PMCL materials with different architectures (cross-linked and linear triblock polymers) under simulated industrial composting conditions. These materials reached high degrees of carbon mineralization (>85%) over the course of 120 days as monitored by CO2 evolution. Finally, we examined the industrial compostability of a new aromatic polyester, poly(salicylic methyl glycolide). This material reached 89% carbon mineralization after 120 days, an important finding given the recalcitrance toward degradation of ubiquitous aromatic polyesters.