gebhart/patrepeval huggingface dataset:
The β-lactamase cycle: a tale of selective pressure and bacterial ingenuity (1999)

peer reviewed
Draft Genome Sequence of Pseudomonas mosselii Gil3, Isolated from Catfish and Antagonistic against Hypervirulent Aeromonas hydrophila (2016)

Pseudomonas mosselii Gil3 was isolated from a catfish that survived from lethal challenge with hypervirulent Aeromonas hydrophila (vAh). When assayed in vitro, the bacterium showed antagonism against vAh. Sequence analysis revealed that the genome of P. mosselii Gil3 encodes numerous aromatic metabolism pathways and proteins for biosynthesis of antimicrobial compounds.
Relationships between gene expression and behavior in mice in response to systemic modulation of the O‐GlcNAcylation pathway (2023)

Enhancing protein O-GlcNAcylation by pharmacological inhibition of the enzyme O-GlcNAcase (OGA), which removes the O-GlcNAc modification from proteins, has been explored in mouse models of amyloid-beta and tau pathology. However, the O-GlcNAcylation-dependent link between gene expression and neurological behavior remains to be explored. Using chronic administration of Thiamet G (TG, an OGA inhibitor) in vivo, we used a protocol designed to relate behavior with the transcriptome and selected biochemical parameters from the cortex of individual animals. TG-treated mice showed improved working memory as measured using a Y-maze test. RNA sequencing analysis revealed 151 top differentially expressed genes with a Log2fold change >0.33 and adjusted p-value <0.05. Top TG-dependent upregulated genes were related to learning, cognition and behavior, while top downregulated genes were related to IL-17 signaling, inflammatory response and chemotaxis. Additional pathway analysis uncovered 3 pathways, involving gene expression including 14 cytochrome c oxidase subunits/regulatory components, chaperones or assembly factors, and 5 mTOR (mechanistic target of rapamycin) signaling factors. Multivariate Kendall correlation analyses of behavioral tests and the top TG-dependent differentially expressed genes revealed 91 statistically significant correlations in saline-treated mice and 70 statistically significant correlations in TG-treated mice. These analyses provide a network regulation landscape that is important in relating the transcriptome to behavior and the potential impact of the O-GlcNAC pathway.
Refrigerant Leakage Detection and Diagnosis for a Distributed Refrigeration System (2006)

A new technique to detect and diagnose leakage in a distributed refrigeration system is proposed in this paper. Unlike a simple refrigeration system of an HVAC system, a distributed refrigeration system, such as the refrigeration system in a supermarket, consists of several racks of compressors and evaporators, large condenser systems on the roof, meters of refrigerant piping systems, and liquid receivers. There are several potential leak points all over the system, and the presence of liquid receivers alters the equilibrium of the system. Therefore, existing leakage instruments or existing thermodynamic-based measuring techniques for HVAC applications do not guarantee correct detection and diagnosis. The proposed technique is not only based on simple and inexpensive measurements of refrigerant thermodynamic states but also accounts for the complexity of the system and the presence of the liquid receiver. Key disciplines to develop the leakage detection and diagnosis include the belief network technique and the decision theory. The probabilistic approach embedded in these two principles makes the detection and diagnosis more effective and precise. Additionally, a neural network model is constructed to make the technique faster and more practical for field implementation with small microcomputers. By implementing the technique in a real supermarket store in Longmont, Colorado, it is shown that the technique is capable of distinguishing between leak and no-leak systems. The developed technique detected a leakage if the refrigeration system lost more than 1.0%, or 5.3 kg, of the initial charge and misclassified one data set from ten data sets.
Community Issues in American Metropolitan Cities (2014)

The city of San Francisco in California has 826,000 residents and is growing slowly compared to other large cities in the western United States, facing concerns such as an aging population and flight of families to nearby suburbs. This case study investigates the social and demographic factors that are causing this phenomenon based on data that were collected by San Francisco's city controller's office in its annual survey to residents. By using data analytics, we can predict which residents are likely to move away, and this help us infer which factors of city life and city services contribute to a resident's decision to leave the city. Results of this research indicate that factors like public transportation services, public schools, and personal finances are significant in this regard, which can potentially help the city of San Francisco to prioritize its resources in order to better retain its locals.
Sitara: Spectrum Measurement Goes Mobile Through Crowd-Sourcing (2019)

Software-defined radios (SDRs) are often used in the experimental evaluation of next-generation wireless technologies. While crowd-sourced spectrum monitoring is an important component of future spectrum-agile technologies, there is no clear way to test it in the real world, i.e., with hundreds of users each carrying an SDR while uploading data to a cloud-based controller. Current fully functional SDRs are bulky, with components connected via wires, and last at most hours on a single battery charge. To address the needs of such experiments, we design and develop a compact, portable, untethered, and inexpensive SDR we call Sitara. Our SDR interfaces with a mobile device over Bluetooth 5 and can function standalone or as a client to a central command and control server. The Sitara offers true portability: it operates up to one week on battery power, requires no external wired connections and occupies a footprint smaller than a credit card. It transmits and receives common waveforms, uploads IQ samples or processed receiver data through a mobile device to a server for remote processing and performs spectrum sensing functions. Multiple Sitaras form a distributed system capable of conducting experiments in wireless networking and communication in addition to RF monitoring and sensing activities. In this paper, we describe our design, evaluate our solution, present experimental results from multi-sensor deployments and discuss the value of this system in future experimentation.
Reconstruction of attosecond pulses in the presence of interfering dressing fields using a 100 kHz laser system at ELI-ALPS (2019)

Attosecond Pulse Trains (APT) generated by high-harmonic generation (HHG) of high-intensity near-infrared (IR) laser pulses have proven valuable for studying the electronic dynamics of atomic and molecular species. However, the high intensities required for high-photon-energy, high-flux HHG usually limit the class of adequate laser systems to repetition rates below 10 kHz. Here, APT's generated from the 100 kHz, 160 W, 40 fs laser system (HR-1) currently under commissioning at the extreme light infrastructure attosecond light pulse source (ELI-ALPS) are reconstructed using the reconstruction of attosecond beating by interference of two-photon Transitions (RABBIT) technique. These experiments constitute the first attosecond time-resolved photoelectron spectroscopy measurements with attosecond pulses performed at 100 kHz repetition rate and one of the first experiments performed at ELI-ALPS in the framework of projects commissioning its newly installed technologies. These RABBIT measurements were taken with an additional IR field temporally locked to the extreme-ultraviolet APT, resulting in an atypical ω beating. We show that the phase of the 2ω beating recorded under these conditions is strictly identical to that observed in standard RABBIT measurements within second-order perturbation theory. This work highlights an experimental simplification for future experiments based on attosecond interferometry (or RABBIT), which is particularly useful when lasers with high average powers are used.
Abstract 2154: Expression of androgen receptor splice variant, AR-V7, in high grade serous ovarian cancer (2021)

Abstract Objective: Androgen receptors (AR) are expressed in up to 55% of ERα-negative breast cancers overall and up to 35% of those classified as TNBC. Similarly, AR is expressed in approximately 40% of high grade serous ovarian cancer (HGSOC). The development of AR splice variants (AR-SV), particularly AR-V7, has been shown to be a poor prognostic feature, and mechanism of androgen resistance in breast and prostate cancers. We sought to determine if AR-V7 was present in HGSOC and if there was a correlation with platinum sensitivity and/or treatment outcomes. Methods: Pair-matched chemo-naïve and platinum-treated HGSOC specimens were identified from our tissue repository. Formalin-fixed paraffin-embedded tumor (FFPE) blocks were collected and tested for expression of AR-V7. Gene fusion detection and variant detection were performed on mRNA isolated from a formalin-fixed paraffin-embedded tumor sample using the Illumina NovaSeq platform (Illumina, Inc., San Diego, CA) and Agilent SureSelect Human All Exon V7 bait panel (Agilent Technologies, Santa Clara, CA). FFPE specimens underwent pathology review to diagnose percent tumor content and tumor size; a minimum of 10% of tumor content in the area for microdissection was required. Results: Twelve chemo-naïve specimens collected at time of diagnosis by initial biopsy (n=8) or primary debulking surgery (n=4) were pair-matched with the patients' subsequent platinum-treated specimens from either interval debulking surgery (n=6) or biopsy of recurrence (n=6). Following penultimate platinum, 50% were platinum resistant and 50% were platinum sensitive at time of second pathology. Only 19 of the 24 specimens submitted had sufficient RNA for testing, 8 chemo-naïve and 11 platinum-treated. AR-V7 variant transcript was not detected in any of the specimens submitted. Conclusions: AR-V7 was not expressed in any specimen before or after platinum based chemotherapy suggesting it may not be a useful prognostic marker in the management of HGSOC. Further investigation into gynecologic malignancies with high AR expression and treated with androgen deprivation therapy may elucidate different results. Citation Format: Benjamin Wilson, Joanne Xiu, Michael Ulm, Tiffany Redfern, Ramesh Narayanan, Adam ElNaggar. Expression of androgen receptor splice variant, AR-V7, in high grade serous ovarian cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2154.
Immunohistochemical Analysis of Human Mesenchymal Stem Cells Differentiating into Chondrogenic, Osteogenic, and Adipogenic Lineages (2011)

Mesenchymal stem cells (MSCs) are multipotent cells that have the potential to differentiate into various mesenchymal lineages in vitro and in vivo. Due to their availability from tissues such as bone marrow, synovium, fat, and muscle, and their highly proliferative capacity, MSCs have evoked interest as a potential cell source for repair and regeneration of various types of tissues. Characterization by the expression of a panel of surface markers and the ability of MSCs to undergo multilineage differentiation is the benchmark for identifying this stem cell population. In this chapter, the protocols for the differentiation of MSC to chondrogenic, osteogenic, and adipogenic lineages and histological and immunostaining protocols for confirming trilineage differentiation of the MSC cells are described.
CCDC 282086: Experimental Crystal Structure Determination (2006)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
Flexible query processor on FPGAs (2013)

In this work, we demonstrate Flexible Query Processor (FQP), an online reconfigurable event stream query processor. FQP is an FPGA-based query processor that supports select, project and join queries over event streams at line rate. While processing incoming events, FQP can accept new query expressions, a key distinguishing characteristic from related approaches employing FPGAs for acceleration. Our solution aims to address performance limitations experienced with general purpose processors needing to operate at line rate and lack of on the fly reconfigurability with custom designed hardware solutions on FPGAs.
GOTHIC ARCHITECTURE (2014)

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Inhibition of mTOR by Rapamycin Aggravates Corneal Epithelial Stem Cell Deficiency by Upregulating Inflammatory Response (2019)

The mammalian target of rapamycin (mTOR) signaling is critical to the regulation of stem cell maintenance and function in a cell-type and context-dependent manner. However, the effects of mTOR signaling on corneal epithelial stem cells (CESCs) under inflammatory conditions are not clear. Here, we demonstrate that mTOR inhibition with rapamycin promotes apoptosis of CESCs in a mouse model of sterile inflammation-induced CESC deficiency, and thereby aggravates the disease. Apoptosis induction in CESCs by rapamycin is not due to direct effect of rapamycin on the cells, but mediated by increase in neutrophilic inflammation. The interleukin (IL)-10/signal transducer and activator of transcription 3 anti-inflammatory pathway was downregulated in a Toll-like receptor 2-independent manner after rapamycin treatment and IL-10 replenishment abrogated the effects of rapamycin on inflammation and CESC apoptosis. Hence, our data reveal that the mTOR signaling is implicated in the control of the pro-inflammatory and anti-inflammatory balance in the cornea and that mTOR inhibition with rapamycin is detrimental to CESCs by accelerating inflammation-induced collateral damage to the cells. Stem Cells 2019;37:1212-1222.
Determination of the Molecular Weight of Ovine Luteinizing Hormone (LH) and of its Two Subunits by Sodium Dodecyl Sulfate (SDS) Polyacrylamide Gel Electrophoresis (1972)

The molecular weight of ovine luteinizing hormone and of its 2 subunits has been determined by SDS polyacrylamide gel electrophoresis. In this system, the apparent molecular weight of LH is 34,350. When LH is reduced and alkylated, the apparent molecular weight of LHa is 18,750 and that of LHP 16,000. (Endocrinology90: 1101, 1972)
Potential of large diameter MgF 2 single crystal grown by Czochralski method (2011)

Magnesium fluoride (MgF<sub>2</sub>) single crystal is expected as the alternative of Quartz for polarizing materials in high power lithography system. MgF<sub>2</sub> is anisotropic crystal and its physical properties are different along each crystal axes. Therefore it is difficult to make large diameter single crystal by using Bridgman method which is mainly used for growth of fluoride crystals. We have been studying on making large diameter and high quality single crystal by using Czochralski (CZ) method [1,2]. Previously we reported the stable growth of it with 150mm diameter. This time we succeeded to grow the crystal with over 200mm diameter. Additionally, by improving the purification process and growth process, we succeeded to reduce 75 percent of the amount of color center induced by irradiation of ArF laser.
Nitrided Ferroalloy Production By Metallurgical SHS Process: Scientific Foundations and Technology (2019)

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Energy availability in athletes (2011)

This review updates and complements the review of energy balance and body composition in the Proceedings of the 2003 IOC Consensus Conference on Sports Nutrition. It argues that the concept of energy availability is more useful than the concept of energy balance for managing the diets of athletes. It then summarizes recent reports of the existence, aetiologies, and clinical consequences of low energy availability in athletes. This is followed by a review of recent research on the failure of appetite to increase ad libitum energy intake in compensation for exercise energy expenditure. The review closes by summarizing the implications of this research for managing the diets of athletes.
Protein threading using context-specific alignment potential (2013)

http://raptorx.uchicago.edu/download/.
64% efficiency enhancement-mode power heterojunction FET for 3.5 V Li-ion battery operated personal digital cellular phones (2002)

This paper describes 950 MHz power performance of an enhancement-mode double-doped AlGaAs/InGaAs/AlGaAs heterojunction FET operated at 3.5 V for personal digital cellular phones. The developed 0.5 /spl mu/m gate length FET exhibited an on-resistance of 1.5 /spl Omega/.mm and a threshold voltage of +0.09 V. Under single 3.5 V operation, a 19.2 mm gate width FET exhibited an output power of 1.03 W (30.1 dBm) and a power-added efficiency of 64.0% with an adjacent channel leakage power of -48.7 dBc at 50 kHz off-center frequency.
Triage Framework for Resource Conservation in a Speaker Identification System (2007)

We present a novel framework for triaging (prioritizing and discarding) data to conserve resources for a speaker identification (SID) system. Our work is motivated by applications that require a SID system to process an overwhelming volume of audio data. We design a triage filter whose goal is to conserve recognizer resources while preserving relevant content. We propose triage methods that use signal quality assessment tools, a scaled-down version of the main recognizer itself, and a fusion of these measures. We define a new precision-based measure of effectiveness for our triage framework. Our experimental results with the 35-speaker tactical SID corpus bear out the validity of our approach.
C04 Optimization of a Thermoacoustic Engine using Particle Swarm Optimization Method (2014)

This paper presents the application of The Particle Swarm Optimization (PSO) for the design of a thermoacoustic device. As a thermoacoustic device, a traveling wave thermoacoustic refrigerator with a branched tube is employed and the three parameters, regenerator's radius, position, and length, were optimized. The obtained results are compared with the results obtained without PSO method.
An assessment of visualization tools for patient monitoring and medical decision making (2015)

Visualization of health data can increase situational awareness, maximize utility of patient data, and improve the clinical decision-making processes in critical care settings. Many hospitals are burdened by vast quantities and varieties of data and are struggling to manage, analyze, interpret, and present it in a meaningful way. Graphical visualization and predictive modeling are effective mechanisms to aid clinicians in assessing patient status and recognizing critical changes over time. In an analysis of the UVa Hospital's Surgical Trauma Burn Intensive Care Unit (STBICU), we examined the impacts that technology and data have on workflow and the value added to various stakeholders. An online survey was distributed to Attending Physicians, Residents, Nurse Practitioners, and Nurses. The goal of this survey was to better understand the ways that various clinical positions interact with data visualization technology regarding patient diagnosis and general workflow. The survey results indicated that graphical representations are under-utilized compared to spreadsheets and progress notes. Additionally, clinicians consider current information technology to be sufficient for evaluating patients' past and current health data, but not for future health status. Data visualization technology and predictive models provide an alternative monitoring solution to overcome existing system limitations.
From X- to O-shaped spatiotemporal spectra of light filaments in water (2005)

We show that the angle-wavelength spectra of light filaments excited by ultrashort pulses experience a transition from X- to O-like structures when their carrier wavelengths are switched from normal to anomalous dispersion. Calculations confirm that the O-shaped conical emission follows the elliptic geometry of the nonlinear Schrödinger equation with anomalous dispersion.
VML 3.0 Reactive Sequencing Objects and Matrix Math Operations for Attitude Profiling (2012)

VML (Virtual Machine Language) has been used as the sequencing flight software on over a dozen JPL deep-space missions, most recently flying on GRAIL and JUNO. In conjunction with the NASA SBIR entitled Reactive Rendezvous and Docking Sequencer, VML version 3.0 has been enhanced to include object-oriented element organization, built-in queuing operations, and sophisticated matrix / vector operations. These improvements allow VML scripts to easily perform much of the work that formerly would have required a great deal of expensive flight software development to realize. Autonomous turning and tracking makes considerable use of new VML features. Profiles generated by flight software are managed using object-oriented VML data constructs executed in discrete time by the VML flight software. VML vector and matrix operations provide the ability to calculate and supply quaternions to the attitude controller flight software which produces torque requests. Using VML-based attitude planning components eliminates flight software development effort, and reduces corresponding costs. In addition, the direct management of the quaternions allows turning and tracking to be tied in with sophisticated high-level VML state machines. These state machines provide autonomous management of spacecraft operations during critical tasks like a hypothetic Mars sample return rendezvous and docking. State machines created for autonomous science observations can also use this sort of attitude planning system, allowing heightened autonomy levels to reduce operations costs. VML state machines cannot be considered merely sequences - they are reactive logic constructs capable of autonomous decision making within a well-defined domain. The state machine approach enabled by VML 3.0 is progressing toward flight capability with a wide array of applicable mission activities.
EOS AM Capillary Pumped Heat Transport System Development Testing Using TDM (1993)

&lt;div class="htmlview paragraph"&gt;NASA's Earth Observing System (EOS) Program will place large unmanned polar-orbiting spacecraft in low-earth orbit to support a variety of earth-observation missions. The EOS AM instrument set has two instruments requiring Capillary Pumped Heat Transport Systems (CPHTS) using Capillary Pumped Loop (CPL) technology for thermal accommodation. Significant development testing is required to retire CPHTS design risks early in the EOS program. The first phase of CPHTS development testing has been completed using a modified version of an existing Martin Marietta test bed, the Technology Demonstration Model (TDM). The EOS/TDM testing provided additional proof-of-concept testing for CPL operations and pushed the performance envelope of the TDM system in order to determine the limits of CPL system performance. In addition, the testing provides a database from which analysis methods can be validated. This paper summarizes the EOS/TDM test results.&lt;/div&gt;