gebhart/patrepeval huggingface dataset:
Gamma Interferon Triggers Interaction between ICSBP (IRF-8) and TEL, Recruiting the Histone Deacetylase HDAC3 to the Interferon-Responsive Element (2002)

ICSBP (IRF-8) is a transcription factor of the IRF family expressed only in the immune system. It is induced in macrophages by gamma interferon (IFN-gamma) and contributes to macrophage functions. By interacting with Ets family protein PU.1, ICSBP binds to the IRF/Ets composite element and stimulates transcription. ICSBP binds to another DNA element, the IFN-stimulated response element (ISRE), a common target of the IRF family. Limited knowledge as to how ICSBP and other IRF proteins regulate ISRE-dependent transcription in IFN-gamma-activated macrophages is available. By mass-spectrometric analysis of ISRE-bound proteins in macrophages, we identified TEL, another Ets member, as a factor recruited to the element in an IFN-gamma-dependent manner. In vitro analysis with recombinant proteins indicated that this recruitment is due to a direct interaction between ICSBP and TEL, which is enhanced by the presence of ISRE. Significantly, the interaction with TEL in turn resulted in the recruitment of the histone deacetytase HDAC3 to the ISRE, causing increased repression of IFN-gamma-mediated reporter activity through the ISRE. This repression may provide a negative-feedback mechanism operating after the initial transcriptional activation by IFN-gamma. By associating with two different Ets family proteins, ICSBP exerts a dual function in IFN-gamma-dependent gene regulation in an immune system-specific manner.
145. Harnessing the Inoculum Effect to Diagnose Molecular Mechanisms of Carbapenem Resistance (2022)

Abstract Background The global spread of carbapenem-resistant Enterobacterales (CRE) presents a major threat to public health. CRE employ two molecular mechanisms to evade carbapenems: 1) expression carbapenemases (CPases), which efficiently hydrolyze carbapenems or 2) disruption of porins, which reduces carbapenem influx to levels that can be hydrolyzed by certain beta-lactamases. Diagnosing mechanisms underlying carbapenem resistance is important for infection control and to administer appropriate treatments. Methods We measured Meropenem and Ertapenem minimum inhibitory concentrations (MICs) for 103 clinical Enterobacterales isolated from hospitals in Massachusetts and California using broth microdilution assays at 14 inocula spanning four orders of magnitude. They represented 30 isolates encoding CPases and intact porins, 46 isolates with disruptions in one or both of the porins responsible for carbapenem influx (OmpC and OmpF), 25 encoding CPases with disrupted porins, and two controls encoding intact porins and no CPases. Results We observed that the two mechanisms result in distinct profiles; first the carbapenem MICs of CPase-encoding strains show a strong inoculum dependence (Fig 1.A), whereas the MICs of porin deficient strains remain largely constant at all inocula (Fig 1.B). The synergistic action of these two mechanisms leads to high-level resistance that we termed “hyper-CRE” (Fig 1.C). Together these factors explain the level of resistance in nearly all our CRE isolates. To validate the hyper-CRE phenotype, we successfully employed CRISPR-based gene editing to show that knocking out the major porin in CPase-producing strains elevates their carbapenem resistance to hyper-CRE levels. We also determined 18% of our isolates changed susceptibility classification within the Clinical Laboratory and Standards Institute (CLSI) recommended inoculum range. This is worrisome for the treatment of infections with strains that are deemed susceptible via in vitro AST assays but are truly resistant in vivo. Conclusion Overall, our approach has demonstrated that measuring MICs at different inoculum can yield crucial diagnostic information about mechanisms of resistance which has important implications for patient care, infection control, and surveillance of emerging CPases. Disclosures All Authors: No reported disclosures.
Microbiota-Centered Interventions: The Next Breakthrough in Immuno-Oncology? (2021)

The cancer-immune dialogue subject to immuno-oncological intervention is profoundly influenced by microenvironmental factors. Indeed, the mucosal microbiota-and more specifically, the intestinal ecosystem-influences the tone of anticancer immune responses and the clinical benefit of immunotherapy. Antibiotics blunt the efficacy of immune checkpoint inhibitors (ICI), and fecal microbial transplantation may restore responsiveness of ICI-resistant melanoma. Here, we review the yin and yang of intestinal bacteria at the crossroads between the intestinal barrier, metabolism, and local or systemic immune responses during anticancer therapies. We discuss diagnostic tools to identify gut dysbiosis and the future prospects of microbiota-based therapeutic interventions. SIGNIFICANCE: Given the recent proof of concept of the potential efficacy of fecal microbial transplantation in patients with melanoma primarily resistant to PD-1 blockade, it is timely to discuss how and why antibiotics compromise the efficacy of cancer immunotherapy, describe the balance between beneficial and harmful microbial species in play during therapies, and introduce the potential for microbiota-centered interventions for the future of immuno-oncology.
Surgical applications of femtosecond lasers (2009)

Femtosecond laser ablation permits non-invasive surgeries in the bulk of a sample with submicrometer resolution. We briefly review the history of optical surgery techniques and the experimental background of femtosecond laser ablation. Next, we present several clinical applications, including dental surgery and eye surgery. We then summarize research applications, encompassing cell and tissue studies, research on C. elegans, and studies in zebrafish. We conclude by discussing future trends of femtosecond laser systems and some possible application directions.
Stochastic-master-equation description of an optical bistability: A comparison with the microscopic theory (1979)

We consider a gas of homogeneously broadened two-level atoms in a Fabry-Perot cavity injected with a coherent resonant electric field. Adopting a macroscopic birth-death description, we construct a stochastic master equation for the output intensity distribution. From this starting point we find the steady-state distribution and show it to be bimodal in the region of the optical bistability. We compare our results for the mean and variance with the microscopic results of Bonifacio, Gronchi, and Lugiato as a test of the stochastic-master-equation approach.
Matrix Metalloproteinase Expression in Lung Cancer (2003)

The importance of matrix metalloproteinases (MMPs) in the growth and spread of solid tumors has been known for over a decade (1,2). However, the molecular mechanisms that regulate their expression and the elucidation of their role in angiogenesis are subjects of extensive, ongoing investigation. The MMPs are a family of extracellular, zinc-dependent proteinases that control tumor growth via tumor promotion (3) and angiogenesis (2,4). They are secreted as latent proenzymes and become activated after cleavage of their propeptide domain. MMPs are regulated on several levels including transcription, protein activation, and the interaction with endogenous inhibitors such as the tissue inhibitors of metalloproteinases (TIMPs) (5). Over 20 MMPs have been described to date (6; see Table 1). Although traditionally subclassified according to substrate specifi city (e.g., collagenases, gelatinases, stromelysins), collectively they are capable of breaking down all of the components of the extracellular matrix (ECM), including components of basement membranes (BMs) and submucosa (1,5,6). MMP-2 and MMP-9, gelatinase A and B, respectively, are of particular interest because they degrade type IV collagen, the major component of basement membranes. Recently, Fang et al. (7) demonstrated in an animal model of chondrosarcoma that MMP-2 shifts the “proteolytic balance” towards an angiogenic phenotype, and is required for new blood vessel formation.
Radiographic Predictors of Lead Conductor Fracture (2014)

Pocket, intravascular and intracardiac lead characteristics on x-ray correlate with risk of lead conductor fracture. These observations may be useful to direct implant technique to optimize lead durability. Validation in larger populations and other lead models may inform the application of these results.
Top-Down Simulation Methodology of a Mixed-Signal Read Channel Using Standard VHDL (2007)

This paper presents a mixed-signal system modeling and simulation methodology using an event-driven simulator that supports real-valued signals, such as standard VHDL. Success of this methodology has been demonstrated by a commercial 550 MHz Partial Response Maximum Likelihood (PRML) magnetic recording read channel. The read channel IC is of mixed-signal design type with 30% analog and 70% digital content. The digital portion has been synthesized from the RTL subset of VHDL (1987 standard). The analog part has been behaviorally modeled using the 1993 standard version of VHDL. Five abstraction levels of digital circuits modeling are also described.
Chemically modified potassium hydride. Significant improvement in yields in some oxy-Cope rearrangements (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChemically modified potassium hydride. Significant improvement in yields in some oxy-Cope rearrangementsTimothy L. Macdonald, Kenneth J. Natalie Jr., Girija Prasad, and J. Scott SawyerCite this: J. Org. Chem. 1986, 51, 7, 1124–1126Publication Date (Print):April 1, 1986Publication History Published online1 May 2002Published inissue 1 April 1986https://pubs.acs.org/doi/10.1021/jo00357a035https://doi.org/10.1021/jo00357a035research-articleACS PublicationsRequest reuse permissionsArticle Views550Altmetric-Citations38LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
PlyKp104, a Novel Phage Lysin for the Treatment of Klebsiella pneumoniae, Pseudomonas aeruginosa, and Other Gram-Negative ESKAPE Pathogens (2023)

Klebsiella pneumoniae and Pseudomonas aeruginosa are two leading causes of burn and wound infections, pneumonia, urinary tract infections, and more severe invasive diseases, which are often multidrug resistant (MDR) or extensively drug resistant. Due to this, it is critical to discover alternative antimicrobials, such as bacteriophage lysins, against these pathogens. Unfortunately, most lysins that target Gram-negative bacteria require additional modifications or outer membrane permeabilizing agents to be bactericidal. We identified four putative lysins through bioinformatic analysis of Pseudomonas and Klebsiella phage genomes in the NCBI database and then expressed and tested their intrinsic lytic activity <i>in vitro</i>. The most active lysin, PlyKp104, exhibited >5-log killing against K. pneumoniae, P. aeruginosa, and other Gram-negative representatives of the multidrug-resistant ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, K. pneumonia, Acinetobacter baumannii, P. aeruginosa, and Enterobacter species) without further modification. PlyKp104 displayed rapid killing and high activity over a wide pH range and in high concentrations of salt and urea. Additionally, pulmonary surfactants and low concentrations of human serum did not inhibit PlyKp104 activity <i>in vitro</i>. PlyKp104 also significantly reduced drug-resistant K. pneumoniae >2 logs in a murine skin infection model after one treatment of the wound, suggesting that this lysin could be used as a topical antimicrobial against K. pneumoniae and other MDR Gram-negative infections.
A Materials Screening Methodology for Scaled Non-Volatile Memory in the AI Era (2019)

We demonstrate a simulation workflow based on first-principles calculations to rapidly screen candidate materials for viability as ferromagnetic electrodes in magnetic tunnel junctions (MTJs) for the next generation of high-performance magnetic random access memory (MRAM) technology. For a series of Fe-based alloys with a fixed crystal structure, we calculate formation energies, bulk spin polarization, and essential magnetic properties including magnetic anisotropy energy (MAE) and tunneling magnetoresistance (TMR). This work demonstrates a materials optimization strategy that can guide on-wafer experiments.
Toward Controlled Generation of Text (2017)

Generic generation and manipulation of text is challenging and has limited success compared to recent deep generative modeling in visual domain. This paper aims at generating plausible natural language sentences, whose attributes are dynamically controlled by learning disentangled latent representations with designated semantics. We propose a new neural generative model which combines variational auto-encoders and holistic attribute discriminators for effective imposition of semantic structures. With differentiable approximation to discrete text samples, explicit constraints on independent attribute controls, and efficient collaborative learning of generator and discriminators, our model learns highly interpretable representations from even only word annotations, and produces realistic sentences with desired attributes. Quantitative evaluation validates the accuracy of sentence and attribute generation.
Novel Integrated Class F Power Amplifier Design for RF Power Infrastructure Applications (2018)

This paper presents a comprehensive study of the impact of resistive harmonic loading on the design of integrated Class-F power amplifiers (PAs). The proposed time-domain waveform-based analysis allows for an evaluation of the performance of Class-F PAs while controlling both second and third harmonics simultaneously. The voltage mapping is presented to include the impact of the resistive second harmonic impedance in the design of Class-F PAs. Besides, drain current formulations as a function of conduction angle are used to evaluate the harmonic coefficients under the impact of resistive third harmonic impedance. As such, the combination of resistive second and third harmonics is modeled to study its impact on efficiency and optimum impedance in the Class-F PAs. For practical validation, the derived knowledge is applied to propose a novel integrated Class-F PA that absorbs the output capacitance into the match while maintaining a purely resistive load at the fundamental frequency. The output match is fabricated on a highly integrated NXP Laterally Diffused MOSFET (LDMOS) process. At 1.8 GHz, using NXP 5-mm LDMOS die, the integrated Class-F achieves a drain efficiency ranging from 52% to 61% at 5-W output power based on two different design topologies. Both prototypes demonstrate excellent isolation at the second and third harmonics. Measurement results confirm the theoretical framework reported in this paper.
Thermodynamic equipartition for increased second law efficiency (2014)

In this work, a clear distinction is drawn between irreversibility associated with a finite mean driving force in a transport process and irreversibility associated with variance in the spatial and/or temporal distribution of this driving force. The portion of irreversibility associated with driving force variance is quantified via a newly defined dimensionless quantity, the equipartition factor. This equipartition factor, related to the variance in dimensionless driving force throughout the system, is employed to formulate an expression for second law efficiency. Consequently, the equipartition factor may be employed to identify the improvement in efficiency achievable via system redesign for a reduction in driving force variance, while holding fixed the system output for fixed system dimensions in time and space. It is shown that systems with low second law efficiency and low equipartition factor will have the greatest benefit from a redesign to obtain equipartition. The utility of the equipartition factor in identifying situations where efficiency can be increased without requiring a spatial or temporal increase in system size is illustrated through its application to several simple systems.
Uncooled CWDM 25-Gbps EA/DFB Lasers for Cost-Effective 100-Gbps Ethernet Transceiver over 10-km SMF Transmission (2008)

Uncooled 1300-nm range 4-channel 25-Gbps EA/DFB lasers that support CWDM scheme for 100-Gbps Ethernet has been realized. A wide temperature ranged 12-km transmission with over 9.6-dB dynamic extinction ratio was demonstrated for the first time.
Polyamine metabolism and polyamine excretion in normal and tumor bearing rodents. (1985)

Aminoguanidine sulfate (AG) inhibits in vivo oxidative deaminations of the polyamines and their derivatives. This compound was used to study urinary polyamine excretion by normal, and tumor bearing rodents. Of the total expendable polyamines, 64 percent were catabolized by AG-sensitive oxidases and escaped observation. Tumor bearing animals did not excrete enhanced amounts of polyamines at any stage of tumoral growth. However, treatment with adriamycin caused an increased polyamine excretion. Prolonged administration of a 2% solution of a-difluoromethylornithine (DFMO), reduced urinary polyamine excretion to the same level of about 27%, irrespective whether the animals carried a large tumor or not. Cadaverine excretion was not affected by treatment with DFMO. Based on these animal data, it appears that urinary polyamines are of restricted value in the diagnosis of tumors.
The Epilepsy Genetic Association Database (epiGAD): Analysis of 165 genetic association studies, 1996–2008 (2010)

We have created the Epilepsy Genetic Association Database (epiGAD, http://www.epigad.org, an online database of epilepsy genetic association studies. A systematic search using several search engines identified 165 studies. Herein we analyze the types of studies available, the sample sizes used, and the strength of the findings. Common questions examined were susceptibility to idiopathic generalized epilepsy, focal epilepsy, or febrile seizures, and pharmacogenomic approaches to drug-resistant epilepsy. Sample sizes were generally small; 80% of studies had 200 or fewer cases, although more recent studies published from 2005-2008 incorporated slightly larger sample sizes. No association was judged as "strong" using current criteria for assessing genetic associations--this is probably due to inadequate sample sizes. Sample sizes need to increase, either by research collaboration or via systematic reviews and meta-analyses. We believe epiGAD will facilitate future meta-analyses.
Hyperspectral Imaging Microscopy of Acetaminophen Adsorbed on Multiwalled Carbon Nanotubes (2018)

In this study, enhanced dark-field hyperspectral imaging (ED-HSI) was employed to directly observe acetaminophen (AAP), a model pharmaceutical and personal care product (PPCP), adsorbed on multiwalled carbon nanotubes with large diameters (L-MWCNT) and small diameters (S-MWCNT) under equilibrium conditions. The ED-HSI results revealed that (1) AAP molecules primarily adsorbed onto the external surfaces, rather than the internal surfaces of L- and S-MWCNT aggregates, (2) or on sidewall of the dispersed tubes, but not at their end caps. Besides, ED-HSI images showed that the surface coverage ratio of AAP/S-MWCNT is smaller than that of AAP/L-MWCNT (1.1 vs 3.4), indicating that there are more available adsorption sites on S-MWCNT than L-MWCNT when the adsorption reached equilibrium. This finding was consistent with the adsorption capacities of S-MWCNT and L-MWCNT (252.7 vs 54.6 mg g<sup>-1</sup>). Direct visualization of sorption sites for PPCP molecules provides new insights into the heterogeneous structures and surface properties of MWCNT and helps elucidate the adsorption mechanisms that are fundamental to the design of functional adsorbents for PPCP contaminants.
Effect of Arteriovenous Anastomosis on Blood Pressure Reduction in Patients With Isolated Systolic Hypertension Compared With Combined Hypertension (2016)

URL: http://www.clinicaltrials.gov. Unique identifier: NCT01642498.
A blind channel identification-based two-stage approach to separation and dereverberation of speech signals in a reverberant environment (2005)

Blind separation of independent speech sources from their convolutive mixtures in a reverberant acoustic environment is a difficult problem and the state-of-the-art blind source separation techniques are still unsatisfactory. The challenge lies in the coexistence of spatial interference from competing sources and temporal echoes due to room reverberation in the observed mixtures. Focusing only on optimizing the signal-to-interference ratio is inadequate for most if not all speech processing systems. In this paper, we deduce that spatial interference and temporal echoes can be separated and an M/spl times/N MIMO system will be converted into M SIMO systems that are free of spatial interference. Furthermore we show that the channel matrices of these SIMO systems are irreducible if the channels from the same source in the MIMO system do not share common zeros. Thereafter we can apply the Bezout theorem to remove reverberation in those SIMO systems. Such a two-stage procedure leads to a novel sequential source separation and speech dereverberation algorithm based on blind multichannel identification. Simulations with measurements obtained in the varechoic chamber at Bell Labs demonstrate the success and robustness of the proposed algorithm in highly reverberant acoustic environments.