gebhart/patrepeval huggingface dataset:
Aligning single-cell developmental and reprogramming trajectories identifies molecular determinants of reprogramming outcome (2017)

Abstract Cellular reprogramming through manipulation of defined factors holds great promise for large-scale production of cell types needed for use in therapy, as well as for expanding our understanding of the general principles of gene regulation. MYOD-mediated myogenic reprogramming, which converts many cell types into contractile myotubes, remains one of the best characterized model system for direct conversion by defined factors. However, why MYOD can efficiently convert some cell types into myotubes but not others remains poorly understood. Here, we analyze MYOD-mediated reprogramming of human fibroblasts at pseudotemporal resolution using single-cell RNA-Seq. Successfully reprogrammed cells navigate a trajectory with two branches that correspond to two barriers to reprogramming, with cells that select incorrect branches terminating at aberrant or incomplete reprogramming outcomes. Differential analysis of the major branch points alongside alignment of the successful reprogramming path to a primary myoblast trajectory revealed Insulin and BMP signaling as crucial molecular determinants of an individual cell’s reprogramming outcome, that when appropriately modulated, increased efficiency more than five-fold. Our single-cell analysis reveals that MYOD is sufficient to reprogram cells only when the extracellular milieu is favorable, supporting MYOD with upstream signaling pathways that drive normal myogenesis in development.
Activity-Independent Discovery of Secondary Metabolites Using Chemical Elicitation and Cheminformatic Inference (2015)

Most existing antibiotics were discovered through screens of environmental microbes, particularly the streptomycetes, for the capacity to prevent the growth of pathogenic bacteria. This "activity-guided screening" method has been largely abandoned because it repeatedly rediscovers those compounds that are highly expressed during laboratory culture. Most of these metabolites have already been biochemically characterized. However, the sequencing of streptomycete genomes has revealed a large number of "cryptic" secondary metabolic genes that are either poorly expressed in the laboratory or that have biological activities that cannot be discovered through standard activity-guided screens. Methods that reveal these uncharacterized compounds, particularly methods that are not biased in favor of the highly expressed metabolites, would provide direct access to a large number of potentially useful biologically active small molecules. To address this need, we have devised a discovery method in which a chemical elicitor called Cl-ARC is used to elevate the expression of cryptic biosynthetic genes. We show that the resulting change in product yield permits the direct discovery of secondary metabolites without requiring knowledge of their biological activity. We used this approach to identify three rare secondary metabolites and find that two of them target eukaryotic cells and not bacterial cells. In parallel, we report the first paired use of cheminformatic inference and chemical genetic epistasis in yeast to identify the target. In this way, we demonstrate that oxohygrolidin, one of the eukaryote-active compounds we identified through activity-independent screening, targets the V1 ATPase in yeast and human cells and secondarily HSP90.
Thrombus Characterization with Intravascular Ultrasound: Potential to Predict Successful Thrombolysis (2003)

Purpose: To define analysis methods using radiofrequency (RF) data from intravascular ultrasound (IVUS) to characterize thrombus so that the success or failure of thrombolysis can be predicted. Methods: Experimentation was done in 2 phases: first, 40 clots created from platelet-rich (n = 20) and platelet-poor (n = 20) plasma were imaged with 20 and 30-MHz IVUS probes. The digitized RF signals were analyzed to determine the attenuation and slope of attenuation characteristics as a reference standard for the second part of the study. In this phase, 20 perfusion trials were performed with 10 platelet-rich and 10 platelet-poor samples in an in vitro arterial perfusion model; the composition of the samples was blinded during interrogation with IVUS. Alteplase (0.1 mg) was then infused directly into the thrombus for 1 hour; restoration of flow and amount of lysis were quantified. Results: Significant differences were detected for the integrated attenuation value (p&lt;0.001) between platelet-poor and platelet-rich clots interrogated with a 30-MHz probe, but no differences were noted using the 20-MHz catheter. However, both transducers were capable of differentiating platelet-rich and platelet-poor clots using a slope of attenuation analysis, which was successful in identifying all 20 (100%) of the blinded clots in the in vitro model. The speed and completeness of lysis were significantly higher (p&lt;0.05) for platelet-rich (78%) than platelet-poor (21%) clots. Conclusions: IVUS preprocessed imaging is capable of differentiating various types of thrombus. This information can be used to predict the success or failure of pharmacological lysis techniques.
TIL system with nonlinear phase conjugation (2007)

Efficient laser beam delivery on a distant target remains a key problem for practical implementation of tactical laser systems. Since the conventional target-in-the-loop (TIL) concept is generally not effective in such operational environments, new solutions are needed. In this report we discuss an innovative approach for effective compensation of laser beam aberrations in TIL systems. It is based on a recently devised technique that combines optical phase conjugation (OPC) with a TIL system for effective hot-spot formation. The proposed method should enable delivery of enhanced density laser energy to a target within a finite number of iteration cycles. Using the model based on an analogy between the TIL system and laser resonator, pointing of the laser beam on the target is performed at the image plane, resulting in reduced hot-spot formation time.
Power optimization of variable voltage core-based systems (2002)

The growing class of portable systems, such as personal computing and communication devices, has resulted in a new set of system design requirements, mainly characterized by dominant importance of power minimization and design reuse. We develop the design methodology for the low power core-based real-time system-on-chip based on dynamically variable voltage hardware. The key challenge is to develop effective scheduling techniques that treat voltage as a variable to be determined, in addition to the conventional task scheduling and allocation. Our synthesis technique also addresses the selection of the processor core and the determination of the instruction and data cache size and configuration so as to fully exploit dynamically variable voltage hardware, which result In significantly lower power consumption for a set of target applications than existing techniques. The highlight of the proposed approach is the non-preemptive scheduling heuristic which results in solutions very close to optimal ones for many test cases. The effectiveness of the approach is demonstrated on a variety of modem industrial-strength multimedia and communication applications.
1 Technologies for Cooling of Large Distributed Loads (2016)

In future space applications, large and distributed loads will require active thermal control if their lifetimes are to be extended beyond one or two years. Examples include Zero Boil-Off (ZBO) cryogenic systems for exploration missions, and cooling of widely distributed sensor arrays and large deployable structures, such as mirrors and sunshades, for space science missions. These applications will require efficient means of heat transfer from extended structures or from several discrete elements to one or more remotely located heat rejection packages consisting of active and passive components. More or less stringent temperature control will also be required. We have recently undertaken a program to develop a number of technologies relevant to the issues associated with distributed cooling. These include circulation networks that transfer heat via steady flows of cold pressurized gas; gas rectifiers for use with linear pressure wave generators; and MEMS-based throttling valves for precise temperature control. This paper describes the studies that are underway to establish the performance potential of each.
Layer thickness and draft angle selection for stereolithography injection mould tooling (2002)

This article has been published in the journal, International Journal of Production Research [© Taylor &amp; Francis]. The definitive version: HARRIS, R.A...et al., 2002. Layer thickness and draft angle selection for stereolithography injection mould tooling. International Journal of Production Research, 40(3), pp.719 - 729, is available at: http://dx.doi.org/10.1080/00207540110091875
Schottky behavior at InN–GaN interface (2005)

In this work, GaN Schottky diodes were fabricated by depositing InN on GaN surfaces. The junction between these two materials exhibits strong rectifying behavior. The barrier heights were determined to be 1.25 eV, 1.06 eV, and 1.41 eV by current-voltage, current-voltage-temperature, and capacitance-voltage methods, respectively. These values exceed those of any other metal∕GaN Schottky barriers. Therefore, the conduction-band offset between InN and GaN should not be smaller than the barrier heights obtained here.
Reassortment between avian H5N1 and human H3N2 influenza viruses creates hybrid viruses with substantial virulence (2010)

The spread of avian H5N1 influenza viruses around the globe has become a worldwide public health concern. To evaluate the pathogenic potential of reassortant viruses between currently cocirculating avian H5N1 and human H3N2 influenza viruses, we generated all the 254 combinations of reassortant viruses between A/chicken/South Kalimantan/UT6028/06 (SK06, H5N1) and A/Tokyo/Ut-Sk-1/07 (Tok07, H3N2) influenza viruses by reverse genetics. We found that the presence of Tok07 PB2 protein in the ribonucleoprotein (RNP) complex allowed efficient viral RNA transcription in a minigenome assay and that RNP activity played an essential role in the viability and replicative ability of the reassortant viruses. When the pathogenicity of 75 reassortant H5 viruses was tested in mice, 22 were more pathogenic than the parental SK06 virus, and three were extremely virulent. Strikingly, all 22 of these viruses obtained their PB2 segment from Tok07 virus. Further analysis showed that Tok07 PB1 alone lacked the ability to enhance the pathogenicity of the reassortant viruses but could do so by cooperating with Tok07 PB2. Our data demonstrate that reassortment between an avian H5N1 virus with low pathogenicity in mice and a human virus could result in highly pathogenic viruses and that the human virus PB2 segment functions in the background of an avian H5N1 virus, enhancing its virulence. Our findings highlight the importance of surveillance programs to monitor the emergence of human H5 reassortant viruses, especially those containing a PB2 segment of human origin.
ChemInform Abstract: Native Oxides Formed on Single‐Crystal Germanium by Wet Chemical Reactions. (1988)

Abstract Stable oxide films are prepared on n‐Ge wafers ((111), (110), and (100) surfaces) by oxidation in aqueous HF/H2O2 solution.
P‐6: A Poly‐Si TFT Fabricated by a Novel Laser‐Crystallization Technique Using Blu‐Ray Disc Technology (2009)

Abstract Using Blu‐ray disc technology in which the focus servo‐system and the energy servo‐system are mounted on one head, we can precisely control the scanning beam and thus the location of the grain boundaries generated by the scanning beam.
Infrared Imaging for Human Thermography and Breast Tumor Classification using Thermal Images (2020)

Human thermography is considered to be an integral medical diagnostic tool for detecting heat patterns and measuring quantitative temperature data of the human body. It can be used in conjunction with other medical diagnostic procedures for getting comprehensive medication results. In the proposed study we have highlighted the significance of Infrared Thermography (IRT) and the role of machine learning in thermal medical image analysis for human health monitoring and various disease diagnosis in preliminary stages. The first part of the proposed study provides comprehensive information about the application of IRT in the diagnosis of various diseases such as skin and breast cancer detection in preliminary stages, dry eye syndromes, and ocular issues, liver disease, diabetes diagnosis and last but not least the novel COVID-19 virus. Whereas in the second phase we have proposed an autonomous breast tumor classification system using thermal breast images by employing state of the art Convolution Neural Network (CNN). The system achieves the overall accuracy of 80% and recall rate of 83.33%.
Mass-Analyzed Ion Kinetic Energy Spectrometry (MIKES) (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
Natural-photosynthesis-inspired photovoltaic cells using carotenoid aggregates as electron donors and chlorophyll derivatives as electron acceptors (2015)

In this study, we describe photosynthetic active layers-based photovoltaic cells employing a linear carotenoid as the donor and chlorophyll derivatives as the acceptors.
Carbon Protonation of 2,4,6-Triaminopyrimidines:  Synthesis, NMR Studies, and Theoretical Calculations (2006)

Several C5-substituted 2,4,6-triaminopyrimidine derivatives and their HBF4 salts were synthesized to study the carbon protonation of the pyrimidine ring. NMR investigations in DMSO-d6 prove experimentally that, in addition to the usual protonation at N1, the compounds can be protonated at C5 as well. We present several new stable cationic sigma-complexes in the pyrimidine series, where C5 protonation predominates over N1 protonation. Quantum chemical calculations using the B3LYP/cc-pVDZ method were utilized in the gas phase and also in DMSO solvent with the polarized continuum model (PCM) method to rationalize the observed protonation behavior. Results of the calculations accord with the experimental observations and prove that combined steric and electronic effects are responsible for the observed C5 protonation and for sigma-complex stability. We demonstrate that C5 protonation is a general feature of the 2,4,6-triaminopyrimidine system.
High-Efficiency Zinc-Metal Anode Enabled by Liquefied Gas Electrolytes (2021)

The practical applications of rechargeable zinc metal batteries are prevented by poor Zn reversibility, which induces both inferior Coulombic efficiency (CE) and zinc dendrite growth that worsens at low temperatures because of deteriorated kinetics in both charge and mass transfer. Herein, a liquefied gas electrolyte based on a mixture of fluoromethane and difluoromethane is demonstrated, which displays an excellent conductivity (>3.4 mS cm–1) across a broad temperature range (−60 to +20 °C) and enables highly reversible Zn cycling with no evidence of shorting behavior at both room temperature and −20 °C for over 200 cycles (>400 h) with an average CE of >99.3% and 20% Zn utilization per cycle. Density functional theory calculations showed that such improvements benefited from a ZnF2-enriched interphase formed on the anode because of decomposition of the liquefied gas electrolyte. This electrolyte was verified in a Zn||Na2V6O16·1.63H2O cell with stable performance, where a similar ZnF2-rich interphase was also confirmed.
Development of 99mTc-EC-tyrosine as an amino acid transporter-targeting imaging agent for breast cancer (2011)

1602 Objectives 99mTc-labled α-methyltyrosine (AMT) using ethylenedicysteine (EC) as a chelator has been investigated as a potential breast tumor imaging agent. The aim of this study was to develop a 99mTc-labeled tyrosine using EC as the chelator, evaluate its imaging potential by comparing with that of 99mTc-EC-AMT in breast tumor-bearing rats. Methods The precursor EC-tyrosine was synthesized and its structure was confirmed by NMR, HPLC and mass spectra. The lipophilicity of 99mTc-EC-tyrosine was determined by measuring its partition coefficient value (log P). To assess the cellular uptake kinetics, the % uptake of 99mTc-EC-tyrosine was measured in rat breast cancer cell line 13762 at 0-2 h. To investigate the transport mechanism of 99mTc-EC-tyrosine, the competitive inhibition study using L-tyrosine as an inhibitor was performed in the 13762 cell line. Tissue distribution of 99mTc-EC-tyrosine was determined in normal rats up to 4 h after injection. Planar imaging of 99mTc-EC-tyrosine in breast tumor-bearing rats was performed at 0.5-4 h after injection. To investigate whether 99mTc-EC-tyrosine can differentiate tumor from inflammation, tumor-to-inflammation ratios (T/Is) were determined in the rats carrying both tumor and inflammation at 0.5-4 h. In all these studies, the previously developed 99mTc-EC-AMT was used as a reference. Results 99mTc-EC-AMT had higher lipophilicity than 99mTc-EC-tyrosine. The cellular uptake of 99mTc-EC-AMT was higher than that of 99mTc-EC-tyrosine in vitro. The cellular uptake of 99mTc-EC-tyrosine was inhibited by L-tyrosine. 99mTc-EC-tyrosine showed high in vivo stability in normal rats. Planar scintigraphy revealed that both radiotracers could clearly visualize tumors; and yet, 99mTc-EC-tyrosine had higher tumor-to-muscle ratios (T/Ms) and T/Is than 99mTc-EC-AMT. Conclusions In comparison to 99mTc-EC-AMT, 99mTc-EC-tyrosine showed greater potential in breast tumor imaging due to its higher sensitivity and specificity
Machine-Learning Based Active Measurement Proxy for IoT Systems (2019)

Network operators are accustomed to using IP-layer active measurements for assessing end-to-end network performance and expect that new technology, such as IoT, provides similar means. Unfortunately, active measurements in IoT systems are associated with both energy and network overhead.This paper presents and evaluates a novel active-measurement proxy approach, based on machine learning, that enables reduction of active measurement overhead in IoT systems. The paper describes the approach and its implementation. Further, the approach is evaluated in a IEEE 802.15.4 testbed, and the results show high-performing and accurate modeling.
Effects of Tebuthiuron on Characteristic Green Algae Found in Playa Lakes (1989)

Abstract There are many studies on the effects of tebuthiuron ( N ‐(5‐(1,1‐dimethylethyl)‐1,3,4‐thiadiazol‐2‐yl)‐ N,N′ ‐dimethylurea) on organisms, but only limited information regarding the impact that the herbicide has on green algae. Eleven species of green algae common to playa lakes were exposed tebuthiuron in 400‐mL microcosm cultures. The cultures were treated with 0.18 µ g/mL tebuthiuron, simulating the highest concentration of the herbicide found in natural runoff from agricultural areas treated with &gt; 2.24 kg/ha tebuthiuron. Sixty‐six cultures were treated before active growth (first treatment) and 45 separate cultures were treated after maximum growth (second treatment). The first treatment was used to simulate the exposure of algal communities to tebuthiuron from runoff during the wet months of May and June. The second treatment simulated exposure to the herbicide once the community was established. Production and nutrient uptake by treated algal cultures was decreased by the first treatment with tebuthiuron. Of the eleven algal species selected, only Bracteacoccus minor was significantly inhibited by tebuthiuron in the first treatment. Photosynthetic pigments, total cell counts, and packed cell volumes for cultures exposed to tebuthiuron in the first treatment were lower than controls ( P &lt; 0.05). Effects caused by the herbicide on the cultures were also evidenced by decreased water quality variables in cultures treated before active growth, with the exceptions of orthophosphates and chloride. No differences were detected between controls and treated samples 210 d after initial treatment with tebuthiuron. Once the algae reached stable cell numbers (second treatment), tebuthiuron demonstrated no significant ( P &lt; 0.05) effects on the cultures. This study indicated that runoff from agricultural fields treated with concentrations &gt; 2.24 kg/ha tebuthiuron may adversely affect the green algal communities of playa lakes.
Cognitive State Estimation in Mobile Environments (2008)

ork in the field of augmented cognition began by classifying aspects of cognitive processing (attention, working memory, executive function, and sensory processing) with well-defined, well-understood laboratory tasks (often referred to informally as “Psych 101” tasks). As researchers have moved from the laboratory environment to the field environment, they have introduced the artifacts (motion, electrical, networking traffic, and disconnect) and stressors (information overload, physical load, competition, and threat of pain) inherent in some operational environments to which augmented cognition systems would be transitioned. The move from the laboratory to mobile field environments brings a number of unique challenges that must be addressed if cognitive state assessment is to be used successfully in task domains that require the operator to be mobile. Tough sacrifices need to be made, with limitations on the sensors to be used, processing power, and knowledge of the task environment. Therefore, unique techniques must be developed to enable this technology to move beyond sedentary operator domains. W
Water-Immersible MEMS Scanning Mirror Enhanced Optical-Resolution Photoacoustic Microscopy (2012)

A fast scanning optical-resolution photoacoustic microscopy has been developed using a water-immersible MEMS mirror. A B-scan rate of 400 Hz over a 3 mm scanning range has been demonstrated in phantom studies.
HIGHLY RELIABLE InGaAsP/InP LASERS WITH NEWLY COMPOSED HBr-BASED SOLUTIONS DEFECT-FREE REGROWTH INTERFACES FORMED BY (2001)

The reliability of buried heterostructure laser diodes (BHLDs) that have a dry-etched mesa structure has been improved by about ten times by using optimized HBr-based wet chemical etchants. This improved reliability was achieved by reducing the amount of defects at the regrowth interfaces by using a newly optimized HBr-Br2-H20 solution with a composition range from 0.30 M HBd0.022 M Br2 to 0.50 M HBd0.020 M Br2. Solutions in this range produce the same etching rates of the (710) InP cladding layers and the (110) InGaAsP multi-quantum-well active layer. The etching mechanism of the InGaAsP/InP material system in the HBr-Br2-H20 solutions was found to be an oxide-dissolution reaction.